Genome editing compositions and methods for treatment of retinitis pigmentosa

Abstract

Provided herein are compositions and methods of using prime editing systems comprising prime editors and prime editing guide RNAs for treatment of genetic disorders.

Description

WSGR Docket No. 59761-791.601 GENOME EDITING COMPOSITIONS AND METHODS FOR TREATMENT OF RETINITIS PIGMENTOSA CROSS-REFERENCE

[0001] This application claims the benefit of U.S. Provisional Application No.63 / 592,461, filed October 23, 2023, which is incorporated herein by reference in its entirety. BACKGROUND

[0002] Retinal degeneration diseases, such as retinitis pigmentosa, may be caused in humans by disruption to the RHO gene (OMIM# 180380), which is mainly expressed in photoreceptor cells of the retina and related tissues and encodes the rhodopsin protein (wild-type sequence given in NCBI ref. NP_000530, SEQ ID NO: 943. RHO is located in the human genome at 3q22.1 and contains 5 exons and spans about 5.0 kb. RHO mRNA is approximately 2.7 kb (NCBI ref. NM_000539, SEQ ID NO: 944. There is a hotspot of 18 pathogenic mutations at the C-terminus of exon 5 of the RHO gene. These mutations can cause the mis-localization of rhodopsin protein and are associated with fast progression with symptoms of retinitis pigmentosa appearing in the 1stdecade of life. The most prominent disease causing mutations within this hotspot include a G-to-C transversion at position 1033 of the coding sequence in exon 5 which causes a missense mutation from valine to leucine (c.1033G>C (p.Val345Leu)) and a C-to-T transversion at position 1040 of the coding sequence in exon 5 which causes a missense mutation from proline to leucine c.1040C>T (p.Pro347Leu). Other pathogenic mutations in the hotspot include c.1033G>A (p.Val345Met), c.1030C>T (p.Gln344Ter), c.1040C>A (p.Pro347Gln), c.1040C>G (p.Pro347Arg), c.1039C>G (p.Pro347Ala), c.1039C>T (p.Pro347Ser), c.1045T>G (p.Ter349Glu), c.1034T>G (p.Val345Gly), c.1045T>C (p.Ter349Gln), c.1028G>A (p.Ser343Asn), c.1033G>T (p.Val345Leu), c.1031A>C (p.Gln344Pro), c.1039C>A (p.Pro347Thr), c.1034T>C (p.Val345Ala), c.1034T>A (p.Val345Glu), and c.1040del (p.Pro347fs). Retinitis pigmentosa is characterized by progressive destruction of photoreceptors, especially of rods, resulting in night blindness, loss of peripheral vision, and in some cases cone destruction may cause loss of color discrimination and general visual acuity. SUMMARY

[0003] In some aspects, disclosed herein is a prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 678; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 678, wherein the first strand and secondWSGR Docket No. 59761-791.601 strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

[0004] In some aspects, disclosed herein is a prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 678; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end any one of SEQ ID NOs: 698-701, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 678.

[0005] In some embodiments, the spacer is from 17-22 nucleotides in length.

[0006] In some embodiments, the spacer comprises at its 3’ end any one of SEQ ID NOs: 679-682, or 147.

[0007] In some embodiments, the spacer comprises at its 3’ end SEQ ID NO: 147.

[0008] In some embodiments, the spacer comprises at its 3’ end SEQ ID NO: 681.

[0009] In some embodiments, the editing template comprises SEQ ID NO: 698 at its 3’ end and encodes a AGG-to-GGT PAM silencing edit.

[0010] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 702, 706, 710, 714, 718, 722, 726, 730, 734, 738, 742, 746, 750, 754, 758, 762, 766, 770, 774, 778, 782, 786, 790, 794, or 798.

[0011] In some embodiments, the editing template comprises SEQ ID NO: 699 at its 3’ end.

[0012] In some embodiments, the editing template comprises at its 3’ end any one of SEQ ID NOs: 703, 707, 711, 715, 719, 723, 727, 731, 735, 739, 743, 747, 751, 755, 759 ,763, 767, 771, 775, 779, 783, 787, 791, 795, or 799.

[0013] In some embodiments, the editing template comprises at its 3’ end SEQ ID NO: 711.

[0014] In some embodiments, the editing template comprises SEQ ID NO: 700 at its 3’ end and encodes a AGG-to-GGC PAM silencing edit.

[0015] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 704, 708, 712, 716, 720, 724, 728, 732, 736, 740, 744, 748, 752, 756, 760, 764, 768, 772, 776, 780, 784, 788, 792, 796, or 800.

[0016] In some embodiments, the editing template comprises at its 3’ end SEQ ID NO: 712.

[0017] In some embodiments, the editing template comprises SEQ ID NO: 701 at its 3’ end and encodes a AGG-to-GGA PAM silencing edit.

[0018] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 705, 709, 713, 717, 721, 725, 729, 733, 737, 741, 745, 749, 753, 757, 761, 765, 769, 773, 777, 781, 785, 789, 793, 797, or 801.WSGR Docket No. 59761-791.601

[0019] In some embodiments, the editing template comprises at its 3’ end SEQ ID NO: 713.

[0020] In some embodiments, the editing template has a length of 40 nucleotides or less.

[0021] In some embodiments, the editing template is 15 to 40 nucleotides in length.

[0022] In some embodiments, the PBS comprises at its 5’end a sequence corresponding to sequence number 683.

[0023] In some embodiments, the PBS comprises any one of sequence numbers 684, 685, 686, 687, 688, 689, 690, 691, 692, 693, 694, 695, 696, or 697.

[0024] In some embodiments, the PBS comprises a sequence of sequence number or SEQ ID NO: 690.

[0025] In some embodiments, the PBS comprises a sequence of sequence number or SEQ ID NO: 692.

[0026] In some embodiments, the PBS is 5 to 19 nucleotides in length.

[0027] In some embodiments, the PEgRNA comprises a PEgRNA sequence selected from any one of SEQ ID NOs: 802-845, 1064-1132, 1151-1219, 1238-1306, 1325-1393, 1417, 1418, 1422, 1423, 1427, 1428, 1432, 1433, 1460-1469, 1482, 1483, 1491-1511, 1535, 1536, 1538-1544, 1570, 1596, or 1597.

[0028] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 815.

[0029] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 813.

[0030] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 826.

[0031] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 1100.

[0032] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 1596.

[0033] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 1363.

[0034] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 1597.

[0035] In some embodiments, the spacer comprises a sequence of SEQ ID NO: 147, the editing template comprises a sequence of SEQ ID NO: 713, and the PBS comprises a sequence of SEQ ID NO: 690.

[0036] In some embodiments, the spacer comprises a sequence of SEQ ID NO: 147, the editing template comprises a sequence of SEQ ID NO: 711, and the PBS comprises a sequence of SEQ ID NO: 690.

[0037] In some embodiments, the spacer comprises a sequence of SEQ ID NO: 147, the editing template comprises a sequence of SEQ ID NO: 712, and the PBS comprises a sequence of SEQ ID NO: 692.

[0038] In some embodiments, the gRNA core comprises a sequence of SEQ ID NO: 854.

[0039] In some embodiments, the gRNA core comprises a sequence of SEQ ID NO: 858.

[0040] In some embodiments, the gRNA core comprises a sequence of SEQ ID NO: 859.

[0041] In some embodiments, the PEgRNA comprises a 3’ motif.

[0042] In some embodiments, the PEgRNA comprises a linker between the PBS and a 3’ motif.

[0043] In some embodiments, the linker comprises a sequence of sequence number 1000.

[0044] In some embodiments, the 3' motif comprises a sequence of SEQ ID NO: 948.

[0045] In some embodiments, the PEgRNA further comprises a COMP-tag.

[0046] In some embodiments, the PEgRNA comprises a linker between the PBS and the COMP-tag.

[0047] In some embodiments, the linker comprises a sequence of sequence number 1018.WSGR Docket No. 59761-791.601

[0048] In some embodiments, the COMP-tag comprises a sequence of sequence number 1052.

[0049] In some embodiments, the spacer comprises a sequence of SEQ ID NO: 147, the editing template comprises a sequence of SEQ ID NO: 712, the PBS comprises a sequence of SEQ ID NO: 692, the gRNA core comprises a sequence of SEQ ID NO: 858, the 3’ motif comprises a sequence of SEQ ID NO: 948, and the linker between the PBS and the 3’ motif comprises a sequence of sequence number 1000.

[0050] In some embodiments, the spacer comprises a sequence of SEQ ID NO: 147, the editing template comprises a sequence of SEQ ID NO: 712, the PBS comprises a sequence of SEQ ID NO: 692, the gRNA core comprises a sequence of SEQ ID NO: 859, the COMP -tag comprises a sequence of sequence number 1052, and the linker between the PBS and the 3’ motif comprises a sequence of sequence number 1018.

[0051] In some aspects, provided herein is a prime editing system comprising: (a) the PEgRNA or the nucleic acid of the disclosure or any of the aspects herein, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NO: 307, 308, 309, 191, 311, 312, 507, 313, 508, 509, or 314; and (ii) an ngRNA core capable of binding a Cas9 protein.

[0052] In some embodiments, the spacer of the ngRNA comprises at its 3’ end any one of SEQ ID NOs: 307, 308, 309, 191, 311, 312, 507, 313, 508, 509, or 314.

[0053] In some embodiments, the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO: 307.

[0054] In some embodiments, the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO: 308.

[0055] In some embodiments, the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO: 314.

[0056] In some embodiments, the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO: 509.

[0057] In some embodiments, the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO: 313.

[0058] In some embodiments, the ngRNA comprises a sequence selected from any one of SEQ ID NOs: 333-339, or 846-849.

[0059] In some embodiments, the ngRNA comprises a sequence of SEQ ID NO: 849.

[0060] In some embodiments, the ngRNA comprises a sequence of SEQ ID NO: 334.

[0061] In some embodiments, the ngRNA comprises a sequence of SEQ ID NO: 336.

[0062] In some embodiments, the ngRNA comprises a sequence of SEQ ID NO: 846.

[0063] In some embodiments, the ngRNA comprises a sequence of SEQ ID NO: 337.WSGR Docket No. 59761-791.601

[0064] In some embodiments, the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 713, and the PBS of SEQ ID NO: 690; and the ngRNA comprises the spacer of SEQ ID NO: 307.

[0065] In some embodiments, the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 713, and the PBS of SEQ ID NO: 690; and the ngRNA comprises the spacer of SEQ ID NO: 308.

[0066] In some embodiments, the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 713, and the PBS of SEQ ID NO: 690; and the ngRNA comprises the spacer of SEQ ID NO: 314.

[0067] In some embodiments, the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 713, and the PBS of SEQ ID NO: 690; and the ngRNA comprises the spacer of SEQ ID NO: 509.

[0068] In some embodiments, the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 711, and the PBS of SEQ ID NO: 690; and the ngRNA comprises the spacer of SEQ ID NO: 313.

[0069] In some embodiments, the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 712, and the PBS of SEQ ID NO: 692; and the ngRNA comprises the spacer of SEQ ID NO: 314.

[0070] In some embodiments, the ngRNA core or the gRNA core comprises a sequence of SEQ ID NO: 854.

[0071] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 815 and the ngRNA comprises a sequence of SEQ ID NO: 849.

[0072] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 815 and the ngRNA comprises a sequence of SEQ ID NO: 334.

[0073] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 815 and the ngRNA comprises a sequence of SEQ ID NO: 336.

[0074] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 815 and the ngRNA comprises a sequence of SEQ ID NO: 846.

[0075] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 813 and the ngRNA comprises a sequence of SEQ ID NO: 337.

[0076] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 826 and the ngRNA comprises a sequence of SEQ ID NO: 336.

[0077] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 1100 and the ngRNA comprises a sequence of SEQ ID NO: 336.

[0078] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 1363 and the ngRNA comprises a sequence of SEQ ID NO: 336.WSGR Docket No. 59761-791.601

[0079] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 1596 and the ngRNA comprises a sequence of SEQ ID NO: 336.

[0080] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 1597 and the ngRNA comprises a sequence of SEQ ID NO: 336.

[0081] In some aspects, provided herein is a prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 542; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 542, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

[0082] In some aspects, provided herein is a prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 542; b. a gRNA core capable of binding to a Cas9 protein, and c. an extension arm comprising: i. an editing template comprising at its 3’ end any one of SEQ ID NOs: 562-565, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 542.

[0083] In some embodiments, the spacer is from 17-22 nucleotides in length.

[0084] In some embodiments, the spacer comprises at its 3’ end any one of SEQ ID NOs: 543, 544, 132, 545, or 546.

[0085] In some embodiments, the spacer comprises at its 3’ end SEQ ID NO: 132.

[0086] In some embodiments, the editing template comprises SEQ ID NO: 562 at its 3’ end and encodes a AGG-to-ATG PAM silencing edit.

[0087] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 566, 570, 574, 578, 582, 586, 590, 594, 598, 602, 606, 610, 614, 618, 622, 626, 630, 634, 638, or 642.

[0088] In some embodiments, the editing template comprises at its 3’ end SEQ ID NO: 566.

[0089] In some embodiments, the editing template comprises SEQ ID NO: 563 at its 3’ end.

[0090] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 567, 571, 575, 579, 583, 587, 591, 595, 599, 603, 607, 611, 615, 619, 623, 627, 631, 635, 639, or 643.

[0091] In some embodiments, the editing template comprises SEQ ID NO: 564 at its 3’ end and encodes a AGG-to-ACG PAM silencing edit.WSGR Docket No. 59761-791.601

[0092] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 568, 572, 576, 580, 584, 588, 592, 596, 600, 604, 608, 612, 616, 620, 624, 628, 632, 636, 640, or 644.

[0093] In some embodiments, the editing template comprises SEQ ID NO: 565 at its 3’ end and encodes a AGG-to-AAG PAM silencing edit.

[0094] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 569, 573, 577, 581, 585, 589, 593, 597, 601, 605, 609, 613, 617, 621, 625, 629, 633, 637, 641, or 645.

[0095] In some embodiments, the editing template has a length of 40 nucleotides or less.

[0096] In some embodiments, the editing template is 20 to 40 nucleotides in length.

[0097] In some embodiments, the PBS comprises at its 5’end a sequence corresponding to sequence number 547.

[0098] In some embodiments, the PBS comprises any one of sequence numbers 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, or 561.

[0099] In some embodiments, the PBS comprises a sequence of sequence number 550.

[0100] In some embodiments, the PBS is 5 to 19 nucleotides in length.

[0101] In some embodiments, the PEgRNA comprises a PEgRNA sequence selected from any one of SEQ ID NOs: 646-677, 1133-1150, 1220-1237, 1307-1324, 1394-1411, 1437, 1438, 1470-1473, 1476, 1477, 1513, 1514, 1545, 1546, or 1584-1595.

[0102] In some embodiments, the PEgRNA sequence comprises a sequence of SEQ ID NO: 1584.

[0103] In some embodiments, the spacer comprises a sequence of SEQ ID NO: 132, the editing template comprises a sequence of SEQ ID NO: 566, and the PBS comprises a sequence of SEQ ID NO: 550.

[0104] In some embodiments, the gRNA core comprises a sequence of SEQ ID NO: 859.

[0105] In some embodiments, the PEgRNA comprises a 3’ motif.

[0106] In some embodiments, the PEgRNA comprises a linker between the PBS and the 3’ motif.

[0107] In some embodiments, the linker comprises a sequence of sequence number 999.

[0108] In some embodiments, the 3’ motif comprises a sequence of SEQ ID NO: 948.

[0109] In some embodiments, the spacer comprises a sequence of SEQ ID NO: 132, the editing template comprises a sequence of SEQ ID NO: 712, the PBS comprises a sequence of sequence number 550, the gRNA core comprises a sequence of SEQ ID NO: 859, the 3’motif comprises a sequence of SEQ ID NO: 948, and the linker between the PBS and the 3’ motif comprises a sequence of sequence number 999.

[0110] In some aspects, disclosed herein is a prime editing system comprising: (a) the PEgRNA or the nucleic acid of the disclosure or any of the aspects herein, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 307, 308, 309, 191, 311, 312, 313, or 314; and (ii) an ngRNA core capable of binding a Cas9 protein.

[0111] In some embodiments, the spacer of the ngRNA comprises at its 3’ end any one of SEQ ID NOs: 307, 308, 309, 191, 311, 312, 313, or 314.WSGR Docket No. 59761-791.601

[0112] In some embodiments, the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO: 314.

[0113] In some embodiments, the ngRNA comprises a sequence selected from any one of SEQ ID NOs: 333-339.

[0114] In some embodiments, the ngRNA comprises a sequence of SEQ ID NO: 336.

[0115] In some embodiments, the PEgRNA comprises: the spacer of SEQ ID NO: 132, the editing template of SEQ ID NO: 566, and the PBS of SEQ ID NO: 550; and the ngRNA comprises the spacer of SEQ ID NO: 314.

[0116] In some embodiments, the PEgRNA comprises a sequence of SEQ ID NO: 1584 and the ngRNA comprises a sequence of SEQ ID NO: 336.

[0117] In some embodiments, the ngRNA core or the gRNA core comprises a sequence of SEQ ID NO: 854.

[0118] In some aspects, disclosed herein is a prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 1; and b. a gRNA core capable of binding to a Cas9 protein; c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 1, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

[0119] In some aspects, disclosed herein is a prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 1; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end any one of SEQ ID NOs: 22-25, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 1.

[0120] In some embodiments, the spacer is from 17-22 nucleotides in length.

[0121] In some embodiments, the spacer comprises at its 3’ end any one of SEQ ID NOs: 2-6.

[0122] In some embodiments, the spacer comprises at its 3’ end SEQ ID NO: 4.

[0123] In some embodiments, the editing template comprises SEQ ID NO: 22 at its 3’ end and encodes a TGG-to-TTG PAM silencing edit.

[0124] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 26, 30, 34, 38, 42, 46, 50, 54, 58, 62, 66, 70, 74, 78, 82, 86, 90, 94, 98, 102, 106, 110, 114, 118, 122, or 126.WSGR Docket No. 59761-791.601

[0125] In some embodiments, the editing template comprises SEQ ID NO: 23 at its 3’ end.

[0126] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 27, 31, 35, 39, 43, 47, 51, 55, 59, 63, 67, 71, 75, 79, 83, 87, 91, 95, 99, 103, 107, 111, 115, 119, 123, or 127.

[0127] In some embodiments, the editing template comprises SEQ ID NO: 24 at its 3’ end and encodes a TGG-to-TCG PAM silencing edit.

[0128] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 28, 32, 36, 40, 44, 48, 52, 56, 60, 64, 68, 72, 76, 80, 84, 88, 92, 96, 100, 104, 108, 112, 116, 120, 124, or 128.

[0129] In some embodiments, the editing template comprises SEQ ID NO: 25 at its 3’ end and encodes a TGG-to-TAG PAM silencing edit.

[0130] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 29, 33, 37, 41, 45, 49, 53, 57, 61, 65, 69, 73, 77, 81, 85, 89, 93, 97, 101, 105, 109, 113, 117, 121, or 125 .

[0131] In some embodiments, the editing template has a length of 40 nucleotides or less.

[0132] In some embodiments, the editing template is 14 to 40 nucleotides in length.

[0133] In some embodiments, the PBS comprises at its 5’end a sequence corresponding to sequence number 7.

[0134] In some embodiments, the PBS comprises any one of sequence numbers 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22.

[0135] In some embodiments, the PBS is 5 to 19 nucleotides in length.

[0136] In some embodiments, the PEgRNA comprises a PEgRNA sequence selected from any one of SEQ ID NOs: 156-187.

[0137] In some aspects, provided herein is a prime editing system comprising: (a) the PEgRNA or the nucleic acid of the disclosure or any of the aspects herein, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 130-155; and (ii) an ngRNA core capable of binding a Cas9 protein.

[0138] In some embodiments, the spacer of the ngRNA comprises at its 3’ end any one of SEQ ID NOs: 130-155.

[0139] In some aspects, provided herein is a prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 188; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 188, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045,WSGR Docket No. 59761-791.601 and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

[0140] In some aspects, provided herein is a prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 188; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end any one of SEQ ID NOs: 209, 210, 211, or 212, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 188.

[0141] In some embodiments, the spacer is from 17-22 nucleotides in length.

[0142] In some embodiments, the spacer comprises at its 3’ end any one of SEQ ID NOs: 189, 190, 191, 192, or 193.

[0143] In some embodiments, the spacer comprises at its 3’ end SEQ ID NO: 191.

[0144] In some embodiments, the editing template comprises SEQ ID NO: 209 at its 3’ end and encodes a CGG-to-CTG PAM silencing edit.

[0145] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 213, 217, 221, 225, 229, 233, 237, 241, 245, 249, or 253.

[0146] In some embodiments, the editing template comprises SEQ ID NO: 210 at its 3’ end.

[0147] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 214, 218, 222, 226, 230, 234, 238, 242, 246, 250, or 254.

[0148] In some embodiments, the editing template comprises SEQ ID NO: 211 at its 3’ end and encodes a CGG-to-CCG PAM silencing edit.

[0149] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 215, 219, 223, 227, 231, 235, 239, 243, 247, 251, or 255.

[0150] In some embodiments, the editing template comprises SEQ ID NO: 212 at its 3’ end and encodes a CGG-to-CAG PAM silencing edit.

[0151] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 216, 220, 224, 228, 232, 236, 240, 244, 248, 252, or 256.

[0152] In some embodiments, the editing template has a length of 40 nucleotides or less.

[0153] In some embodiments, the editing template is 29 to 40 nucleotides in length.

[0154] In some embodiments, the PBS comprises at its 5’end a sequence corresponding to sequence number 194.

[0155] In some embodiments, the PBS comprises any one of sequence numbers 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, or 208.

[0156] In some embodiments, the PBS is 5 to 19 nucleotides in length.

[0157] In some embodiments, the PEgRNA comprises a PEgRNA sequence selected from any one of SEQ ID NOs: 261-272.WSGR Docket No. 59761-791.601

[0158] In some aspects, provided herein is a prime editing system comprising: (a) the PEgRNA or the nucleic acid of the disclosure or any of the aspects herein, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 130, 131, 257, 258, 259, 260, 132, 133, 134, 135, 136, 137, 138, 139, 140, 142, 145, 146, 147, 148, 150, 151, 152, 153, 154, or 155; and (ii) an ngRNA core capable of binding a Cas9 protein.

[0159] In some embodiments, the spacer of the ngRNA comprises at its 3’ end any one of SEQ ID NOs: 130, 131, 257, 258, 259, 260, 132, 133, 134, 135, 136, 137, 138, 139, 140, 142, 145, 146, 147, 148, 150, 151, 152, 153, 154, or 155.

[0160] In some aspects, provided herein is a prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 273; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 273, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

[0161] In some aspects, provided herein is a prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 273; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end SEQ ID NO: 293, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 273.

[0162] In some embodiments, the spacer is from 17-22 nucleotides in length.

[0163] In some embodiments, the spacer comprises at its 3’ end any one of SEQ ID NOs: 274, 275, 148, 276, or 277.

[0164] In some embodiments, the spacer comprises at its 3’ end SEQ ID NO: 148.

[0165] In some embodiments, the editing template comprises SEQ ID NO: 293 at its 3’ end.

[0166] In some embodiments, the editing template comprises at its 3’ end any one of SEQ ID NOs: 294- 306.

[0167] In some embodiments, the editing template has a length of 40 nucleotides or less.

[0168] In some embodiments, the editing template is 27 to 40 nucleotides in length.

[0169] In some embodiments, the PBS comprises at its 5’end a sequence corresponding to sequence number 278.WSGR Docket No. 59761-791.601

[0170] In some embodiments, the PBS comprises any one of sequence numbers 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, or 292.

[0171] In some embodiments, the PBS is 5 to 19 nucleotides in length.

[0172] In some embodiments, the PEgRNA comprises a PEgRNA sequence selected from any one of SEQ ID NOs: 315-332.

[0173] In some aspects, disclosed herein is a prime editing system comprising: (a) the PEgRNA or the nucleic acid of the disclosure or any of the aspects herein, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises:(i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 307, 308, 309, 310, 191, 311, 312, 313, or 314; and (ii) an ngRNA core capable of binding a Cas9 protein.

[0174] In some embodiments, the spacer of the ngRNA comprises at its 3’ end SEQ ID NOs: 307, 308, 309, 310, 191, 311, 312, 313, or 314.

[0175] In some embodiments, the ngRNA comprises a sequence selected from any one of SEQ ID NOs: 333-339.

[0176] In some aspects, disclosed herein is a prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 340; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 340, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

[0177] In some aspects, disclosed herein is a prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 340; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end SEQ ID NO: 360, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 340.

[0178] In some embodiments, the spacer is from 17-22 nucleotides in length.

[0179] In some embodiments, the spacer comprises at its 3’ end any one of SEQ ID NOs: 341, 342, 131, 343, or 344.

[0180] In some embodiments, the spacer comprises at its 3’ end SEQ ID NO: 131.

[0181] In some embodiments, the editing template comprises SEQ ID NO: 360 at its 3’ end.

[0182] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 361-369.WSGR Docket No. 59761-791.601

[0183] In some embodiments, the editing template has a length of 40 nucleotides or less.

[0184] In some embodiments, the editing template is 31 to 40 nucleotides in length.

[0185] In some embodiments, the PBS comprises at its 5’end a sequence corresponding to sequence number 345.

[0186] In some embodiments, the PBS comprises any one of sequence numbers 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, or 359.

[0187] In some embodiments, the PBS is 9 to 19 nucleotides in length.

[0188] In some embodiments, the PEgRNA comprises a PEgRNA sequence selected from any one of SEQ ID NOs: 370-377.

[0189] In some aspects, provided herein is a prime editing system comprising: (a) the PEgRNA or the nucleic acid of the disclosure or any of the aspects herein, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises:(i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 308, 309, 310, 191, 311, 312, 313, or 314; and (ii) an ngRNA core capable of binding a Cas9 protein.

[0190] In some embodiments, the spacer of the ngRNA comprises at its 3’ end any one of SEQ ID NOs: 308, 309, 310, 191, 311, 312, 313, or 314.

[0191] In some embodiments, the ngRNA comprises a sequence selected from any one of SEQ ID NOs: 333-339.

[0192] In some aspects, provided herein is a prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 378; and b. a gRNA core capable of binding to a Cas9 protein; c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 378, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

[0193] In some aspects, provided herein is a prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 378; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end any one of SEQ ID NOs: 399-402, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 378.

[0194] In some embodiments, the spacer is from 17-22 nucleotides in length.WSGR Docket No. 59761-791.601

[0195] In some embodiments, the spacer comprises at its 3’ end any one of SEQ ID NOs: 379, 380, 381, 382, or 383.

[0196] In some embodiments, the spacer comprises at its 3’ end SEQ ID NO: 381.

[0197] In some embodiments, the editing template comprises SEQ ID NO: 399 at its 3’ end and encodes a GGG-to-GTG PAM silencing edit.

[0198] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 403, 407, 411, 415, 419, 423, 427, 431, 435, 439, 443, 447, 451, 455, 459, 463, 467, 471, 475, 479, 483, 487, 491, 495, 499, or 503.

[0199] In some embodiments, the editing template comprises SEQ ID NO: 400 at its 3’ end.

[0200] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 404, 408, 412, 416, 420, 424, 428, 432, 436, 440, 444, 448, 452, 456, 460, 464, 468, 472, 476, 480, 484, 488, 492, 496, 500, or 504.

[0201] In some embodiments, the editing template comprises SEQ ID NO: 401 at its 3’ end and encodes a GGG-to-GCG PAM silencing edit.

[0202] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 405, 409, 413, 417, 421, 425, 429, 433, 437, 441, 445, 449, 453, 457, 461, 465, 469, 473, 477, 481, 485, 489, 493, 497, 501, or 505.

[0203] In some embodiments, the editing template comprises SEQ ID NO: 402 at its 3’ end and encodes a GGG-to-GAG PAM silencing edit.

[0204] In some embodiments, the editing template comprises at its 3’ end SEQ ID NOs: 406, 410, 414, 418, 422, 426, 430, 434, 438, 442, 446, 450, 454, 458, 462, 466, 470, 474, 478, 482, 486, 490, 494, 498, 502, or 506.

[0205] In some embodiments, the editing template has a length of 40 nucleotides or less.

[0206] In some embodiments, the editing template is 14 to 40 nucleotides in length.

[0207] In some embodiments, the PBS comprises at its 5’end a sequence corresponding to sequence number 384.

[0208] In some embodiments, the PBS comprises any one of sequence numbers 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, or 398.

[0209] In some embodiments, the PBS is 5 to 19 nucleotides in length.

[0210] In some embodiments, the PEgRNA comprises a PEgRNA sequence selected from any one of SEQ ID NOs: 510-541.

[0211] In some aspects, provided herein is a prime editing system comprising: (a) the PEgRNA or the nucleic acid of the disclosure and any of the aspects herein, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 307, 308, 309, 191, 311, 312, 507, 313, 508, 509, or 314; and (ii) an ngRNA core capable of binding a Cas9 protein.WSGR Docket No. 59761-791.601

[0212] In some embodiments, the spacer of the ngRNA comprises at its 3’ end SEQ ID NOs: 307, 308, 309, 191, 311, 312, 507, 313, 508, 509, or 314.

[0213] In some embodiments, the ngRNA comprises a sequence selected from any one of SEQ ID NOs: 333-339.

[0214] In some embodiments, the PEgRNA comprises from 5’ to 3’, the spacer, the gRNA core, the editing template, and the PBS.

[0215] In some embodiments, the spacer, the gRNA core, the editing template, and the PBS form a contiguous sequence in a single molecule.

[0216] In some embodiments, the gRNA core comprises a sequence of any one of SEQ ID NOs: 854- 859.

[0217] In some embodiments, the PEgRNA further comprises 3’ mN*mN*mN*N and 5’mN*mN*mN* modifications, where m indicates that the nucleotide contains a 2’-O-Me modification and a * indicates the presence of a phosphorothioate bond.

[0218] In some embodiments, the PEgRNA further comprises 3’ mT*mT*mT*T and 5’mN*mN*mN* modifications, where m indicates that the nucleotide contains a 2’-O-Me modification, a * indicates the presence of a phosphorothioate bond, and a T indicates the presence of an additional uridine nucleotide.

[0219] In some embodiments, the spacer selected from any one of Tables 14-20 further comprises a G at the 5’ end.

[0220] In some embodiments, the PEgRNA selected from any one of Tables 14-20, further comprises a G at the 5’ end.

[0221] In some embodiments, the spacer comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from any one of Tables 14-20.

[0222] In some embodiments, the editing template comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from any one of Tables 14-20.

[0223] In some embodiments, the editing template encodes one or more synonymous mutations relative to a wild type Rhodopsin gene.

[0224] In som embodiments, the editing template encodes a wild type amino acid sequence of a Rhodopsin protein.

[0225] In some embodiments, the PBS comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from any one of Tables 14-20.

[0226] In some embodiments, the gRNA core comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from Table 10.WSGR Docket No. 59761-791.601

[0227] In some embodiments, the PEgRNA comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from any one of Tables 14-20.

[0228] In some embodiments, the editing template encodes one or more synonymous mutations relative to a wild type Rhodopsin gene.

[0229] In some embodiments, the editing template encodes a wild type amino acid sequence of a Rhodopsin protein.

[0230] In some embodiments, the spacer comprises no more than 1, 2, 3, 4, or 5 mutations, deletions, substitutions, or insertions compared to a sequence selected from any one of Tables 14-20.

[0231] In some embodiments, the editing template comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 mutations, deletions, substitutions, or insertions compared to a sequence selected from any one of Tables 14-20.

[0232] In some embodiments, the editing template encodes one or more synonymous mutations relative to a wild type Rhodopsin gene.

[0233] In some embodiments, the editing template encodes a wild type amino acid sequence of a Rhodopsin protein.

[0234] In some embodiments, the PBS comprises no more than 1, 2, 3, 4, or 5 mutations, deletions, substitutions, or insertions compared to a sequence selected from any one of Tables 14-20.

[0235] In some embodiments, the gRNA core comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 mutations, deletions, substitutions, or insertions compared to a sequence selected from Table 10.

[0236] In some embodiments, the PEgRNA comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 mutations, deletions, substitutions, or insertions compared to a sequence selected from any one of Tables 14-20.

[0237] In some embodiments, the editing template encodes one or more synonymous mutations relative to a wild type Rhodopsin gene.

[0238] In some embodiments, the editing template encodes a wild type amino acid sequence of a Rhodopsin protein.

[0239] In some embodiments, the ngRNA comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from any one of Tables 14-20.

[0240] In some embodiments, the ngRNA comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 mutations, deletions, substitutions, or insertions compared to a sequence selected from any one of Tables 14-20.WSGR Docket No. 59761-791.601

[0241] In some embodiments, the PEgRNA further comprises: (c) a prime editor comprising a Cas9 nickase having a nuclease inactivating mutation in the HNH domain, or a nucleic acid encoding the Cas9 nickase, and a reverse transcriptase, or a nucleic acid encoding the reverse transcriptase.

[0242] In some embodiments, the prime editor is a fusion protein.

[0243] In some embodiments, the PEgRNA further comprises: (c) an N-terminal extein comprising an N-terminal fragment of a prime editor fusion protein and an N-intein or a polynucleotide encoding the N- terminal extein; and (d) a C-terminal extein comprising a C-terminal fragment of the prime editor fusion protein and a C-intein, or a polynucleotide encoding the C-terminal extein; wherein the N-intein and the C-intein of the N-terminal and C-terminal exteins are capable of self-excision to join the N-terminal fragment and the C-terminal fragment to form the prime editor fusion protein, and wherein the prime editor fusion protein comprises a Cas9 nickase and a reverse transcriptase (RT) domain.

[0244] In some aspects, disclosed herein is a prime editing system comprising: (a) the PEgRNA of the disclosure or any of the aspects herein, or the nucleotide encoding the PEgRNA; and (b) a prime editor comprising a Cas9 nickase having a nuclease inactivating mutation in the HNH domain, or a nucleic acid encoding the Cas9 nickase, and a reverse transcriptase, or a nucleic acid encoding the reverse transcriptase.

[0245] In some aspects, disclosed herein is a prime editing system comprising: (a) the PEgRNA of the disclosure or any of the aspects herein, or the nucleotide encoding the PEgRNA; (b) an N-terminal extein comprising an N-terminal fragment of a prime editor fusion protein and an N-intein or a polynucleotide encoding the N-terminal extein; and (c) a C-terminal extein comprising a C-terminal fragment of the prime editor fusion protein and a C-intein, or a polynucleotide encoding the C-terminal extein; wherein the N-intein and the C-intein of the N-terminal and C-terminal exteins are capable of self-excision to join the N-terminal fragment and the C-terminal fragment to form the prime editor fusion protein, and wherein the prime editor fusion protein comprises a Cas9 nickase and a reverse transcriptase (RT) domain.

[0246] In some embodiments, the Cas9 nickase comprises an amino acid sequence having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 875 or SEQ ID NO: 876.

[0247] In some embodiments, the reverse transcriptase comprises an amino acid sequence having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 872.

[0248] In some embodiments, the sequence identities are determined by Needleman-Wunsch alignment of two protein sequences with Gap Costs set to Existence: 11 Extension: 1 where percent identity is calculated by dividing the number of identities by the length of the global alignment.

[0249] In some aspects, provided herein is a population of viral particles collectively comprising the one or more nucleic acids encoding the prime editing system of the disclosure of any of the aspects herein.

[0250] In some embodiments, the viral particles are AAV particles.WSGR Docket No. 59761-791.601

[0251] In some aspects, provided herein is an LNP comprising the prime editing system of the disclosure or any of the aspects herein.

[0252] In some embodiments, the LNP comprises the PEgRNA, the nucleic acid encoding the Cas9 nickase, and the nucleic acid encoding the reverse transcriptase.

[0253] In some embodiments, the nucleic acid encoding the Cas9 nickase and the nucleic acid encoding the reverse transcriptase are mRNA.

[0254] In some embodiments, the nucleic acid encoding the Cas9 nickase and the nucleic acid encoding the reverse transcriptase are the same molecule.

[0255] In some aspects, provided herein is a method of correcting or editing a RHO gene, the method comprising contacting the RHO gene with: (a) the PEgRNA of the disclosure or any of the aspects herein and a prime editor comprising a Cas9 nickase having a nuclease inactivating mutation in the HNH domain and a reverse transcriptase or (b) the prime editing system of the disclosure or any of the aspects herein.

[0256] In some embodiments, the RHO gene comprises a mutation selected from the group consisting of: c.1033G>C (p.Val345Leu), c.1040C>T (p.Pro347Leu), c.1033G>A (p.Val345Met), c.1030C>T (p.Gln344Ter), c.1040C>A (p.Pro347Gln), c.1040C>G (p.Pro347Arg), c.1039C>G (p.Pro347Ala), c.1039C>T (p.Pro347Ser), c.1045T>G (p.Ter349Glu), c.1034T>G (p.Val345Gly), c.1045T>C (p.Ter349Gln), c.1028G>A (p.Ser343Asn), c.1033G>T (p.Val345Leu), c.1031A>C (p.Gln344Pro), c.1039C>A (p.Pro347Thr), c.1034T>C (p.Val345Ala), c.1034T>A (p.Val345Glu), and c.1040del (p.Pro347fs).

[0257] In some embodiments, the RHO gene is in a cell.

[0258] In some embodiments, the cell is a mammalian cell.

[0259] In some embodiments, the cell is a human cell.

[0260] In some embodiments, the cell is a primary cell.

[0261] In some embodiments, the cell is in a subject.

[0262] In some embodiments, the subject is a human.

[0263] In some embodiments, the cell is from a subject having Retinitis pigmentosa.

[0264] In some embodiments, the method of contacting the RHO gene comprises contacting the cell with (i) the population of viral particles of the disclosure or any of the aspects herein or (ii) the LNP of the disclosure or any of the aspects herein.

[0265] In some aspects, provided herein is a method for treating Retinitis pigmentosa in a subject in need thereof, the method comprising administering to the subject: (A) the PEgRNA of the disclosure or any of the aspects herein and a prime editor comprising a Cas9 nickase having a nuclease inactivating mutation in the HNH domain and a reverse transcriptase, (B) the prime editing system of the disclosure or any of the aspects herein, (C) the population of viral particles of the disclosure or any of the aspects herein or (D) the LNP of the disclosure or any of the aspects herein.WSGR Docket No. 59761-791.601

[0266] In some embodiments, the subject comprises a mutation in a RHO gene, wherein the mutation is selected form the group consisting of: c.1033G>C (p.Val345Leu), c.1040C>T (p.Pro347Leu), c.1033G>A (p.Val345Met), c.1030C>T (p.Gln344Ter), c.1040C>A (p.Pro347Gln), c.1040C>G (p.Pro347Arg), c.1039C>G (p.Pro347Ala), c.1039C>T (p.Pro347Ser), c.1045T>G (p.Ter349Glu), c.1034T>G (p.Val345Gly), c.1045T>C (p.Ter349Gln), c.1028G>A (p.Ser343Asn), c.1033G>T (p.Val345Leu), c.1031A>C (p.Gln344Pro), c.1039C>A (p.Pro347Thr), c.1034T>C (p.Val345Ala), c.1034T>A (p.Val345Glu), and c.1040del (p.Pro347fs).

[0267] In some embodiments, the method is performed ex vivo.

[0268] In some embodiments, the method is performed in vivo.

[0269] In some embodiments, the method is performed in vitro.

[0270] In some embodiments, the method is performed ex vitro.

[0271] In some embodiments, the correcting or editing the RHO gene results in a restoration of a wild type Rhodopsin protein sequence.

[0272] In some aspects, provided herein is a cell generated by the method of the disclosure or any of the aspects herein.

[0273] In some aspects, provided herein is a population of cells generated by the method of the disclosure or any of the aspects herein.

[0274] In some aspects, provided herein is a pharmaceutical composition comprising the cell of the disclosure or any of the aspects herein or the population of cells of the disclosure or any of the aspects herein. INCORPORATION BY REFERENCE

[0275] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. BRIEF DESCRIPTION OF THE DRAWINGS

[0276] The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which:

[0277] FIG. 1 depicts a schematic of a prime editing guide RNA (PEgRNA) binding to a double stranded target DNA sequence.

[0278] FIG. 2 depicts a PEgRNA architectural overview in an exemplary schematic of PEgRNA designed for a prime editor.

[0279] FIG. 3 is a schematic showing the spacer and gRNA core part of an exemplary guide RNA, in two separate molecules. The rest of the PEgRNA structure is not shown.WSGR Docket No. 59761-791.601 DETAILED DESCRIPTION

[0280] Provided herein, in some embodiments, are compositions and methods to edit the target gene RHO with prime editing. In certain embodiments, provided herein are compositions and methods for correction of mutations in the RHO gene associated with retinitis pigmentosa. Compositions provided herein can comprise prime editors (PEs) that may use engineered guide polynucleotides, e.g., prime editing guide RNAs (PEgRNAs), that can direct PEs to specific DNA targets and can encode DNA edits on the target gene RHO that serve a variety of functions, including direct correction of disease-causing mutations.

[0281] The following description and examples illustrate embodiments of the present disclosure in detail. It is to be understood that this disclosure is not limited to the particular embodiments described herein and as such can vary. Those of skill in the art will recognize that there are numerous variations and modifications of this disclosure, which are encompassed within its scope. Although various features of the present disclosure can be described in the context of a single embodiment, the features can also be provided separately or in any suitable combination. Conversely, although the present disclosure can be described herein in the context of separate embodiments for clarity, the present disclosure can also be implemented in a single embodiment. Definitions

[0282] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art.

[0283] The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting. As used herein, the singular forms “a”, “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. Furthermore, to the extent that the terms “including”, “includes”, “having”, “has”, “with”, or variants thereof as used herein mean “comprising”.

[0284] Unless otherwise specified, the words “comprising”, “comprise”, “comprises”, “having”, “have”, “has”, “including”, “includes”, “include”, “containing”, “contains” and “contain” are inclusive or open- ended and do not exclude additional, unrecited elements or method steps.

[0285] Reference to “some embodiments”, “an embodiment”, “one embodiment”, or “other embodiments” means that a particular feature or characteristic described in connection with the embodiments is included in at least one or more embodiments, but not necessarily all embodiments, of the present disclosure.

[0286] The term “about” or “approximately” in relation to a numerical means, a range of values that fall within 10% greater than or less than the value. For example, about x means x±(10% * x).

[0287] In some embodiments, the cell is a human cell. A cell may be of or derived from different tissues, organs, and / or cell types. In some embodiments, the cell is a primary cell. As used herein, theWSGR Docket No. 59761-791.601 term “primary cell” means a cell isolated from an organism, e.g., a mammal, which is grown in tissue culture (i.e., in vitro) for the first time before subdivision and transfer to a subculture. In some non- limiting examples, mammalian cells, including primary cells and stem cells can be modified through introduction of one or more polynucleotides, polypeptide, and / or prime editing compositions (e.g., through transfection, transduction, electroporation and the like) and further passaged. Such modified cells include retinal cells (e.g., photoreceptors, retinal pigment epithelium cells), epithelial cells (e.g., mammary epithelial cells, intestinal epithelial cells, hepatocytes), endothelial cells, glial cells, neural cells, formed elements of the blood (e.g., lymphocytes, bone marrow cells), precursors of any of these somatic cell types, and stem cells. In some embodiments, the cell is a fibroblast. In some embodiments, the cell is a stem cell. In some embodiments, the cell is a pluripotent cell (e.g., a pluripotent stem cell). In some embodiments, the cell (e.g., a stem cell) is an embryonic stem cell, tissue-specific stem cell, mesenchymal stem cell, or an induced pluripotent stem cell. In some embodiments, the cell is an induced pluripotent stem cell (iPSC). In some embodiments, the cell is a retinal progenitor cell. In some embodiments, the cell is a retinal precursor cell. In some embodiments, the cell is an embryonic stem cell (ESC). In some embodiments, the cell is a human stem cell. In some embodiments, the cell is a human pluripotent stem cell. In some embodiments, the cell is a human fibroblast. In some embodiments, the cell is an induced human pluripotent stem cell. In some embodiments, the cell is a human stem cell. In some embodiments, the cell is a human embryonic stem cell. In some embodiments, the cell is a human retinal progenitor cell. In some embodiments, the cell is a human retinal precursor cell.

[0288] In some embodiments, a cell is not isolated from an organism but forms part of a tissue or organ of an organism, e.g., a mammal. In some non-limiting examples, mammalian cells include muscle cells (e.g., cardiac muscle cells, smooth muscle cells, myosatellite cells), epithelial cells (e.g., mammary epithelial cells, intestinal epithelial cells, hepatocytes), endothelial cells, glial cells, neural cells, formed elements of the blood (e.g., lymphocytes, bone marrow cells), precursors of any of these somatic cell types, and stem cells. In some embodiments, the cell is a pigmented epithelial cell. In some embodiments, the cell is a retinal cell. In some embodiments, the cell is a photoreceptor cell. In some embodiments, the cell is a rod cell.. In some embodiments, the cell is a cone cell. In some embodiments, the cell is a human stem cell.

[0289] In some embodiments, the cell is a differentiated cell. In some embodiments, cell is a fibroblast. In some embodiments, the cell is differentiated from an induced pluripotent stem cell. In some embodiments, the cell is a retinal cell, a pigmented epithelial cell, a rod cell, a cone cell, or a retinal ganglion differentiated from an iPSC, ESC or a retinal progenitor cell.

[0290] In some embodiments, the cell is a differentiated human cell. In some embodiments, cell is a human fibroblast. In some embodiments, the cell is differentiated from an induced human pluripotent stem cell. In some embodiments, the cell is a retinal cell, a pigmented epithelial cell, a rod cell, a cone cell, or a retinal ganglion differentiated from a human iPSC, a human ESC or a human retinal progenitorWSGR Docket No. 59761-791.601 cell. In some embodiments, the cell edited by prime editing can be differentiated into, or give rise to recovery of a population of cells, e.g., a retinal cell, a pigmented epithelial cell, a rod cell, a cone cell, or a retinal ganglion. In some embodiments, the cell is in a subject, e.g., a human subject. In some embodiments, the cell is obtained from a subject prior to editing. For example, in some embodiments, the cell is obtained from a retinitis pigmentosa patient having a mutation in the RHO gene.

[0291] In some embodiments, the cell comprises a prime editor, a PEgRNA, or a prime editing composition disclosed herein. In some embodiments, the cell further comprises an ngRNA. In some embodiments, the cell is from a human subject. In some embodiments, the human subject has a disease or a condition, or is at a risk of developing a disease or a condition associated with a mutation to be corrected by prime editing, for example, retinitis pigmentosa. In some embodiments, the cell is from a human subject, and comprises a prime editor, a PEgRNA, or a prime editing composition for correction of the mutation. In some embodiments, the cell is from the human subject and the mutation has been edited or corrected by prime editing. In some embodiments, the cell is in a human subject, and comprises a prime editor or a prime editing composition for correction of the mutation. In some embodiments, the cell is from the human subject and the mutation has been edited or corrected by prime editing.

[0292] The term “substantially” as used herein may refer to a value approaching 100% of a given value. In some embodiments, the term may refer to an amount that may be at least about 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 99.99% of a total amount. In some embodiments, the term may refer to an amount that may be about 100% of a total amount.

[0293] The terms “protein” and “polypeptide” can be used interchangeably to refer to a polymer of two or more amino acids joined by covalent bonds (e.g., an amide bond) that can adopt a three-dimensional conformation. In some embodiments, a protein or polypeptide comprises at least 10 amino acids, 15 amino acids, 20 amino acids, 30 amino acids or 50 amino acids joined by covalent bonds (e.g., amide bonds). In some embodiments, a protein comprises at least two amide bonds. In some embodiments, a protein comprises multiple amide bonds. In some embodiments, a protein comprises an enzyme, enzyme precursor proteins, regulatory protein, structural protein, receptor, nucleic acid binding protein, a biomarker, a member of a specific binding pair (e.g., a ligand or aptamer), or an antibody. In some embodiments, a protein may be a full-length protein (e.g., a fully processed protein having certain biological function). In some embodiments, a protein may be a variant or a fragment of a full-length protein. For example, in some embodiments, a Cas9 protein domain comprises an H840A amino acid substitution compared to a naturally occurring S. pyogenes Cas9 protein. A variant of a protein or enzyme, for example a variant reverse transcriptase, comprises a polypeptide having an amino acid sequence that is about 60% identical, about 70% identical, about 80% identical, about 90% identical, about 95% identical, about 96% identical, about 97% identical, about 98% identical, about 99% identical, about 99.5% identical, or about 99.9% identical to the amino acid sequence of a reference protein.WSGR Docket No. 59761-791.601

[0294] In some embodiments, a protein comprises one or more protein domains or subdomains. As used herein, the term “polypeptide domain”, “protein domain”, or “domain” when used in the context of a protein or polypeptide, refers to a polypeptide chain that has one or more biological functions, e.g., a catalytic function, a protein-protein binding function, or a protein-DNA function. In some embodiments, a protein comprises multiple protein domains. In some embodiments, a protein comprises multiple protein domains that are naturally occurring. In some embodiments, a protein comprises multiple protein domains from different naturally occurring proteins. For example, in some embodiments, a prime editor may be a fusion protein comprising a Cas9 protein domain of S. pyogenes and a reverse transcriptase protein domain of a retrovirus (e.g., a Moloney murine leukemia virus) or a variant of the retrovirus. A protein that comprises amino acid sequences from different origins or naturally occurring proteins may be referred to as a fusion, or chimeric protein.

[0295] In some embodiments, a protein comprises a functional variant or functional fragment of a full- length wild type protein. A “functional fragment” or “functional portion”, as used herein, refers to any portion of a reference protein (e.g., a wild type protein) that encompasses less than the entire amino acid sequence of the reference protein while retaining one or more of the functions, e.g., catalytic or binding functions. For example, a functional fragment of a reverse transcriptase may encompass less than the entire amino acid sequence of a wild type reverse transcriptase, but retains the ability under at least one set of conditions to catalyze the polymerization of a polynucleotide. When the reference protein is a fusion of multiple functional domains, a functional fragment thereof may retain one or more of the functions of at least one of the functional domains. For example, a functional fragment of a Cas9 may encompass less than the entire amino acid sequence of a wild type Cas9, but retains its DNA binding ability and lacks its nuclease activity partially or completely.

[0296] A “functional variant” or “functional mutant”, as used herein, refers to any variant or mutant of a reference protein (e.g., a wild type protein) that encompasses one or more alterations to the amino acid sequence of the reference protein while retaining one or more of the functions, e.g., catalytic or binding functions. In some embodiments, the one or more alterations to the amino acid sequence comprises amino acid substitutions, insertions or deletions, or any combination thereof. In some embodiments, the one or more alterations to the amino acid sequence comprises amino acid substitutions. For example, a functional variant of a reverse transcriptase may comprise one or more amino acid substitutions compared to the amino acid sequence of a wild type reverse transcriptase, but retains the ability under at least one set of conditions to catalyze the polymerization of a polynucleotide. When the reference protein is a fusion of multiple functional domains, a functional variant thereof may retain one or more of the functions of at least one of the functional domains. For example, in some embodiments, a functional fragment of a Cas9 may comprise one or more amino acid substitutions in a nuclease domain, e.g., an H840A amino acid substitution, compared to the amino acid sequence of a wild type Cas9, but retains the DNA binding ability and lacks the nuclease activity partially or completely.WSGR Docket No. 59761-791.601

[0297] The term “function” and its grammatical equivalents as used herein may refer to a capability of operating, having, or serving an intended purpose. Functional may comprise any percent from baseline to 100% of an intended purpose. For example, functional may comprise or comprise about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or up to about 100% of an intended purpose. In some embodiments, the term functional may mean over or over about 100% of normal function, for example, 125%, 150%, 175%, 200%, 250%, 300%, 400%, 500%, 600%, 700% or up to about 1000% of an intended purpose.

[0298] In some embodiments, a protein or polypeptides includes naturally occurring amino acids (e.g., one of the twenty amino acids commonly found in peptides synthesized in nature, and known by the one letter abbreviations A, R, N, C, D, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y and V). In some embodiments, a protein or polypeptides includes non-naturally occurring amino acids (e.g., amino acids which is not one of the twenty amino acids commonly found in peptides synthesized in nature, including synthetic amino acids, amino acid analogs, and amino acid mimetics). In some embodiments, a protein or polypeptide is modified.

[0299] In some embodiments, a protein comprises an isolated polypeptide. The term “isolated” means free or removed to varying degrees from components which normally accompany it as found in the natural state or environment. For example, a polypeptide naturally present in a living animal is not isolated, and the same polypeptide partially or completely separated from the coexisting materials of its natural state is isolated.

[0300] In some embodiments, a protein is present within a cell, a tissue, an organ, or a virus particle. In some embodiments, a protein is present within a cell or a part of a cell (e.g., a bacteria cell, a plant cell, or an animal cell). In some embodiments, the cell is in a tissue, in a subject, or in a cell culture. In some embodiments, the cell is a microorganism (e.g., a bacterium, fungus, protozoan, or virus). In some embodiments, a protein is present in a mixture of analytes (e.g., a lysate). In some embodiments, the protein is present in a lysate from a plurality of cells or from a lysate of a single cell.

[0301] The terms “homologous,” “homology,” or “percent homology” as used herein refer to the degree of sequence identity between an amino acid and a corresponding reference amino acid sequence or a polynucleotide sequence and a corresponding reference polynucleotide sequence. “Homology” can refer to polymeric sequences, e.g., polypeptide or DNA sequences that are similar. Homology can mean, for example, nucleic acid sequences with at least about: 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity. In other embodiments, a “homologous sequence” of nucleic acid sequences may exhibit 93%, 95% or 98% sequence identity to the reference nucleic acid sequence. For example, a “region of homology to a genomic region” can be a region of DNA that has a similar sequence to a given genomic region in the genome. A region of homology can be of any length that is sufficient to promote binding of a spacer, a primer binding site or protospacer sequence to the genomic region. For example, the region ofWSGR Docket No. 59761-791.601 homology can comprise at least 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100 or more bases in length such that the region of homology has sufficient homology to undergo binding with the corresponding genomic region.

[0302] When a percentage of sequence homology or identity is specified, in the context of two nucleic acid sequences or two polypeptide sequences, the percentage of homology or identity generally refers to the alignment of two or more sequences across a portion of their length when compared and aligned for maximum correspondence. When a position in the compared sequence can be occupied by the same base or amino acid, then the molecules can be homologous at that position. Unless stated otherwise, sequence homology or identity is assessed over the specified length of the nucleic acid, polypeptide or portion thereof. In some embodiments, the homology or identity is assessed over a functional portion or specified portion of the length.

[0303] Alignment of sequences for assessment of sequence homology can be conducted by algorithms known in the art, such as the Basic Local Alignment Search Tool (BLAST) algorithm, which is described in Altschul et al, J. Mol. Biol.215:403- 410, 1990. A publicly available, internet interface, for performing BLAST analyses is accessible through the National Center for Biotechnology Information. Additional known algorithms include those published in: Smith & Waterman, “Comparison of Biosequences”, Adv. Appl. Math. 2:482, 1981; Needleman & Wunsch, “A general method applicable to the search for similarities in the amino acid sequence of two proteins” J. Mol. Biol. 48:443, 1970; Pearson & Lipman “Improved tools for biological sequence comparison”, Proc. Natl. Acad. Sci. USA 85:2444, 1988; or by automated implementation of these or similar algorithms. Global alignment programs may also be used to align similar sequences of roughly equal size. Examples of global alignment programs include NEEDLE (available at www.ebi.ac.uk / Tools / psa / emboss_needle / ) which is part of the EMBOSS package (Rice P et al., Trends Genet., 2000; 16: 276-277), and the GGSEARCH program https: / / fasta.bioch.virginia.edu / fasta_www2 / , which is part of the FASTA package (Pearson W and Lipman D, 1988, Proc. Natl. Acad. Sci. USA, 85: 2444-2448). Both of these programs are based on the Needleman-Wunsch algorithm which is used to find the optimum alignment (including gaps) of two sequences along their entire length. A detailed discussion of sequence analysis can also be found in Unit 19.3 of Ausubel et al (“Current Protocols in Molecular Biology” John Wiley & Sons Inc, 1994-1998, Chapter 15, 1998). In some embodiments, alignment between a query sequence and a reference sequence is performed with Needleman-Wunsch alignment with Gap Costs set to Existence: 11 Extension: 1 where percent identity is calculated by dividing the number of identities by the length of the global alignment, as further described in Altschul et al.("Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402, 1997) and Altschul et al, ("Protein database searches using compositionally adjusted substitution matrices", FEBS J.272:5101-5109, 2005).WSGR Docket No. 59761-791.601

[0304] A skilled person understands that amino acid (or nucleotide) positions may be determined in homologous sequences based on alignment, for example, “H840” in a reference Cas9 sequence may correspond to H839, or another position in a Cas9 homolog.

[0305] The term “polynucleotide” or “nucleic acid molecule” can be any polymeric form of nucleotides, including DNA, RNA, a hybridization thereof, or RNA-DNA chimeric molecules. In some embodiments, a polynucleotide comprises cDNA, genomic DNA, mRNA, tRNA, rRNA, or microRNA. In some embodiments, a polynucleotide is double stranded, e.g., a double-stranded DNA in a gene. In some embodiments, a polynucleotide is single-stranded or substantially single-stranded, e.g., single-stranded DNA or an mRNA. In some embodiments, a polynucleotide is a cell-free nucleic acid molecule. In some embodiments, a polynucleotide circulates in blood. In some embodiments, a polynucleotide is a cellular nucleic acid molecule. In some embodiments, a polynucleotide is a cellular nucleic acid molecule in a cell circulating in blood.

[0306] Polynucleotides can have any three-dimensional structure. The following are nonlimiting examples of polynucleotides: a gene or gene fragment (for example, a probe, primer, EST or SAGE tag), an exon, an intron, intergenic DNA (including, without limitation, heterochromatic DNA), messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), a ribozyme, cDNA, a recombinant polynucleotide, a branched polynucleotide, a plasmid, a vector, isolated DNA, isolated RNA, sgRNA, guide RNA, a nucleic acid probe, a primer, an snRNA, a long non-coding RNA, a snoRNA, a siRNA, a miRNA, a tRNA-derived small RNA (tsRNA), an antisense RNA, an shRNA, or a small rDNA-derived RNA (srRNA).

[0307] In some embodiments, a polynucleotide comprises deoxyribonucleotides, ribonucleotides or analogs thereof. In some embodiments, a polynucleotide comprises modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure can be imparted before or after assembly of the polynucleotide. The sequence of nucleotides can be interrupted by non-nucleotide components. A polynucleotide can be further modified after polymerization, such as by conjugation with a labeling component.

[0308] In some embodiments, a polynucleotide is composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); thymine (T); and uracil (U) for thymine when the polynucleotide is RNA. In some embodiments, the polynucleotide may comprise one or more other nucleotide bases, such as inosine (I), which is read by the translation machinery as guanine (G).

[0309] In some embodiments, a polynucleotide may be modified. As used herein, the terms “modified” or “modification” refers to chemical modification with respect to the A, C, G, T and U nucleotides, and is indicated as mA, mC, mG, mT, and mT. In some embodiments, modifications may be on the nucleoside base and / or sugar portion of the nucleosides that comprise the polynucleotide. In some embodiments, the modification may be on the internucleoside linkage (e.g., phosphate backbone). In some embodiments,WSGR Docket No. 59761-791.601 multiple modifications are included in the modified nucleic acid molecule. In some embodiments, a single modification is included in the modified nucleic acid molecule.

[0310] The term “complement,” “complementary,” or “complementarity” as used herein, refers to the ability of two polynucleotide molecules to base pair with each other. Complementary polynucleotides may base pair via hydrogen bonding, which may be Watson Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding. For example, an adenine on one polynucleotide molecule will base pair to a thymine or an uracil on a second polynucleotide molecule and a cytosine on one polynucleotide molecule will base pair to guanine on a second polynucleotide molecule. Two polynucleotide molecules are complementary to each other when a first polynucleotide molecule comprising a first nucleotide sequence can base pair with a second polynucleotide molecule comprising a second nucleotide sequence. -ATGC- -GCAT- -ATGC- -GCAT- indicates the percentage of nucleotides in a polynucleotide molecule which can base pair with a second polynucleotide molecule (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary, respectively). “Perfectly complementary” means that all the contiguous nucleotides of a polynucleotide molecule will base pair with the same number of contiguous nucleotides in a second polynucleotide molecule. “Substantially complementary” as used herein refers to a degree of complementarity that can be 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% over all or a portion of two polynucleotide molecules. In some embodiments, the portion of complementarity may be a region of 10, 15, 20, 25, 30, 35, 40, 45, 50, or more nucleotides. “Substantial complementary” can also refer to a 100% complementarity over a portion or a region of two polynucleotide molecules. In some embodiments, the portion or the region of complementarity between the two polynucleotide molecules is at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% of the length of at least one of the two polynucleotide molecules or a functional or defined portion thereof.

[0311] As used herein, “expression” refers to the process by which polynucleotides are transcribed into mRNA and / or the process by which polynucleotides, e.g., the transcribed mRNA, translated into peptides, polypeptides, or proteins. If the polynucleotide is derived from genomic DNA, expression may include splicing of the mRNA in a eukaryotic cell. In some embodiments, expression of a polynucleotide, e.g., a gene or a DNA encoding a protein, is determined by the amount of the protein encoded by the gene after transcription and translation of the gene. In some embodiments, expression of a polynucleotide, e.g., a gene or a DNA encoding a protein, is determined by the amount of a functional form of the protein encoded by the gene after transcription and translation of the gene. In some embodiments, expression of a gene is determined by the amount of the mRNA, or transcript, that is encoded by the gene after transcription the gene. In some embodiments, expression of a polynucleotide, e.g., an mRNA, is determined by the amount of the protein encoded by the mRNA after translation of the mRNA. In some embodiments, expression of a polynucleotide, e.g., a mRNA or coding RNA, isWSGR Docket No. 59761-791.601 determined by the amount of a functional form of the protein encoded by the polypeptide after translation of the polynucleotide.

[0312] The term “sequencing” as used herein, may comprise capillary sequencing, bisulfite-free sequencing, bisulfite sequencing, TET-assisted bisulfite (TAB) sequencing, ACE-sequencing, high- throughput sequencing, Maxam-Gilbert sequencing, massively parallel signature sequencing, Polony sequencing, 454 pyrosequencing, Sanger sequencing, Illumina sequencing, SOLiD sequencing, Ion Torrent semiconductor sequencing, DNA nanoball sequencing, Heliscope single molecule sequencing, single molecule real time (SMRT) sequencing, nanopore sequencing, shot gun sequencing, RNA sequencing, or any combination thereof.

[0313] The terms “equivalent” or “biological equivalent” are used interchangeably when referring to a particular molecule, or biological or cellular material, and means a molecule having minimal homology to another molecule while still maintaining a desired structure or functionality.

[0314] The term “encode” as it is applied to polynucleotides refers to a polynucleotide which is said to “encode” another polynucleotide, a polypeptide, or an amino acid if, in its native state or when manipulated by methods well known to those skilled in the art, it can be used as polynucleotide synthesis template, e.g., transcribed into an RNA, reverse transcribed into a DNA or cDNA, and / or translated to produce an amino acid, or a polypeptide or fragment thereof. In some embodiments, a polynucleotide comprising three contiguous nucleotides form a codon that encodes a specific amino acid. In some embodiments, a polynucleotide comprises one or more codons that encode a polypeptide. In some embodiments, a polynucleotide comprising one or more codons comprises a mutation in a codon compared to a wild-type reference polynucleotide. In some embodiments, the mutation in the codon encodes an amino acid substitution in a polypeptide encoded by the polynucleotide as compared to a wild-type reference polypeptide.

[0315] The term “mutation” as used herein refers to a change and / or alteration in an amino acid sequence of a protein or nucleic acid sequence of a polynucleotide. Such changes and / or alterations may comprise the substitution, insertion, deletion and / or truncation of one or more amino acids, in the case of an amino acid sequence, and / or nucleotides, in the case of nucleic acid sequence, compared to a reference amino acid or a reference nucleic acid sequence. In some embodiments, the reference sequence is a wild- type sequence. In some embodiments, a mutation in a nucleic acid sequence of a polynucleotide encodes a mutation in the amino acid sequence of a polypeptide. In some embodiments, the mutation in the amino acid sequence of the polypeptide or the mutation in the nucleic acid sequence of the polynucleotide is a mutation associated with a disease state.

[0316] The term “subject” and its grammatical equivalents as used herein may refer to a human or a non-human. A subject may be a mammal. A human subject may be male or female. A human subject may be of any age. A subject may be a human embryo. A human subject may be a newborn, an infant, aWSGR Docket No. 59761-791.601 child, an adolescent, or an adult. A human subject may be in need of treatment for a genetic disease or disorder.

[0317] The terms “treatment” or “treating” and their grammatical equivalents may refer to the medical management of a subject with an intent to cure, ameliorate, or ameliorate a symptom of, a disease, condition, or disorder. Treatment may include active treatment, that is, treatment directed specifically toward the improvement of a disease, condition, or disorder. Treatment may include causal treatment, that is, treatment directed toward removal of the cause of the associated disease, condition, or disorder. In addition, this treatment may include palliative treatment, that is, treatment designed for the relief of symptoms rather than the curing of the disease, condition, or disorder. Treatment may include supportive treatment, that is, treatment employed to supplement another specific therapy directed toward the improvement of the disease, condition, or disorder. In some embodiments, a condition may be pathological. In some embodiments, a treatment may not completely cure or prevent a disease, condition, or disorder. In some embodiments, a treatment ameliorates, but does not completely cure or prevent a disease, condition, or disorder. In some embodiments, a subject may be treated for 12 hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 2 months, 3 months, 4 months, 5 months, 6 months, 1 year, 2 years, 3 years, 4 years, 5 years, 6 years, indefinitely, or life of the subject.

[0318] The term “ameliorate” and its grammatical equivalents means to decrease, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease.

[0319] The terms “prevent” or “preventing” means delaying, forestalling, or avoiding the onset or development of a disease, condition, or disorder for a period of time. Prevent also means reducing risk of developing a disease, disorder, or condition. Prevention includes minimizing or partially or completely inhibiting the development of a disease, condition, or disorder. In some embodiments, a composition, e.g., a pharmaceutical composition, prevents a disorder by delaying the onset of the disorder for 12 hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 2 months, 3 months, 4 months, 5 months, 6 months, 1 year, 2 years, 3 years, 4 years, 5 years, 6 years, indefinitely, or life of a subject.

[0320] The term “effective amount” or “therapeutically effective amount” refers to a quantity of a composition, for example a prime editing composition comprising a construct, that can be sufficient to result in a desired activity upon introduction into a subject as disclosed herein. An effective amount of the prime editing compositions can be provided to the target gene or cell, whether the cell is ex vivo or in vivo.

[0321] An effective amount can be the amount to induce, for example, at least about a 2-fold change (increase or decrease) or more in the amount of target nucleic acid modulation (e.g., expression of RHO gene to produce functional rhodopsin (RHO) protein) observed relative to a negative control. An effective amount or dose can induce, for example, about 2-fold increase, about 3-fold increase, about 4- fold increase, about 5-fold increase, about 6-fold increase, about 7-fold increase, about 8-fold increase,WSGR Docket No. 59761-791.601 about 9-fold increase, about 10-fold increase, about 25-fold increase, about 50-fold increase, about 100- fold increase, about 200-fold increase, about 500-fold increase, about 700-fold increase, about 1000-fold increase, about 5000-fold increase, or about 10,000-fold increase in target gene modulation (e.g., expression of a target RHO gene to produce functional rhodopsin).

[0322] The amount of target gene modulation may be measured by any suitable method known in the art. In some embodiments, the “effective amount” or “therapeutically effective amount” is the amount of a composition that is required to ameliorate the symptoms of a disease relative to an untreated patient. In some embodiments, an effective amount is the amount of a composition sufficient to introduce an alteration in a gene of interest in a cell (e.g., a cell in vitro or in vivo).

[0323] In some embodiments, an effective amount can be an amount to induce, when administered to a population of cells, a certain percentage of the population of cells to have a correction of the V345L mutation. For example, in some embodiments, an effective amount can be the amount to induce, when administered to or introduced to a population of cells, installation of one or more intended nucleotide edits that correct a c.1033 G->C (encoding V345L amino acid substitution) mutation in the RHO gene, in at least about 1%, 2%, 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 99% of the population of cells.

[0324] In some embodiments, an effective amount can be an amount to induce, when administered to a population of cells, a certain percentage of the population of cells to have a correction of the P347L mutation. For example, in some embodiments, an effective amount can be the amount to induce, when administered to or introduced to a population of cells, installation of one or more intended nucleotide edits that correct a c.1040 C->T (encoding P347L amino acid substitution) mutation in the RHO gene, in at least about 1%, 2%, 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 99% of the population of cells.

[0325] In some embodiments, an effective amount can be an amount to induce, when administered to a population of cells, a certain percentage of the population of cells to have a correction of a c.1033G>C (p.Val345Leu), c.1040C>T (p.Pro347Leu), c.1033G>A (p.Val345Met), c.1030C>T (p.Gln344Ter), c.1040C>A (p.Pro347Gln), c.1040C>G (p.Pro347Arg), c.1039C>G (p.Pro347Ala), c.1039C>T (p.Pro347Ser), c.1045T>G (p.Ter349Glu), c.1034T>G (p.Val345Gly), c.1045T>C (p.Ter349Gln), c.1028G>A (p.Ser343Asn), c.1033G>T (p.Val345Leu), c.1031A>C (p.Gln344Pro), c.1039C>A (p.Pro347Thr), c.1034T>C (p.Val345Ala), c.1034T>A (p.Val345Glu), or c.1040del (p.Pro347fs) mutation. For example, in some embodiments, an effective amount can be the amount to induce, when administered to or introduced to a population of cells, installation of one or more intended nucleotide edits that correct a c.1033G>C (p.Val345Leu), c.1040C>T (p.Pro347Leu), c.1033G>A (p.Val345Met), c.1030C>T (p.Gln344Ter), c.1040C>A (p.Pro347Gln), c.1040C>G (p.Pro347Arg), c.1039C>GWSGR Docket No. 59761-791.601 (p.Pro347Ala), c.1039C>T (p.Pro347Ser), c.1045T>G (p.Ter349Glu), c.1034T>G (p.Val345Gly), c.1045T>C (p.Ter349Gln), c.1028G>A (p.Ser343Asn), c.1033G>T (p.Val345Leu), c.1031A>C (p.Gln344Pro), c.1039C>A (p.Pro347Thr), c.1034T>C (p.Val345Ala), c.1034T>A (p.Val345Glu), or c.1040del (p.Pro347fs) mutation in the RHO gene, in at least about 1%, 2%, 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 99% of the population of cells. Prime Editing

[0326] The term “prime editing” refers to programmable editing of a target DNA using a prime editor complexed with a PEgRNA to incorporate an intended nucleotide edit (also referred to herein as a nucleotide change) into the target DNA through target-primed DNA synthesis. A target gene of prime editing may comprise a double stranded DNA molecule having two complementary strands: a first strand that may be referred to as a “target strand” or a “non-edit strand,” and a second strand that may be referred to as a “non-target strand,” or an “edit strand.” In some embodiments, in a prime editing guide RNA (PEgRNA), a spacer sequence is complementary or substantially complementary to a specific sequence on the target strand, which may be referred to as a “search target sequence.” In some embodiments, the spacer sequence anneals with the target strand at the search target sequence. The target strand may also be referred to as the “non-Protospacer Adjacent Motif (non-PAM strand).” In some embodiments, the non-target strand may also be referred to as the “PAM strand.” In some embodiments, the PAM strand comprises a protospacer sequence and optionally a protospacer adjacent motif (PAM) sequence. In prime editing using a Cas-protein-based prime editor, a PAM sequence refers to a short DNA sequence immediately adjacent to the protospacer sequence on the PAM strand of the target gene. A PAM sequence may be specifically recognized by a programmable DNA binding protein, e.g., a Cas nickase or a Cas nuclease. In some embodiments, a specific PAM is characteristic of a specific programmable DNA binding protein, e.g., a Cas nickase or a Cas nuclease A protospacer sequence refers to a specific sequence in the PAM strand of the target gene that is complementary to the search target sequence. In a PEgRNA, a spacer sequence may have a substantially identical sequence as the protospacer sequence on the edit strand of a target gene, except that the spacer sequence may comprise Uracil (U) and the protospacer sequence may comprise Thymine (T).

[0327] In some embodiments, the double stranded target DNA comprises a nick site on the PAM strand (or non-target strand). As used herein, a “nick site” refers to a specific position in between two nucleotides or two base pairs of the double stranded target DNA. In some embodiments, the position of a nick site is determined relative to the position of a specific PAM sequence. In some embodiments, the nick site is the particular position where a nick will occur when the double stranded target DNA is contacted with a nickase, for example, a Cas nickase, that recognizes a specific PAM sequence. In someWSGR Docket No. 59761-791.601 embodiments, the nick site is upstream of a specific PAM sequence on the PAM strand of the double stranded target DNA. In some embodiments, the nick site is downstream of a specific PAM sequence on the PAM strand of the double stranded target DNA. In some embodiments, the nick site is upstream of a PAM sequence recognized by a Cas9 nickase, wherein the Cas9 nickase comprises a nuclease active RuvC domain and a nuclease inactive HNH domain. In some embodiments, the nick site is 3 nucleotides upstream of the PAM sequence, and the PAM sequence is recognized by a Streptococcus pyogenes Cas9 nickase, a P. lavamentivorans Cas9 nickase, a C. diphtheriae Cas9 nickase, a N. cinerea Cas9, a S. aureus Cas9, or a N. lari Cas9 nickase. In some embodiments, the nick site is 3 base pairs upstream of the PAM sequence, and the PAM sequence is recognized by a Cas9 nickase, wherein the Cas9 nickase that comprises a nuclease active RuvC domain and a nuclease inactive HNH domain. In some embodiments, the nick site is 2 nucleotides upstream of the PAM sequence, and the PAM sequence is recognized by a S. thermophilus Cas9 nickase that comprises a nuclease active RuvC domain and a nuclease inactive HNH domain.

[0328] A “primer binding site” (also referred to as PBS or primer binding site sequence) is a single- stranded portion of the PEgRNA that comprises a region of complementarity to the PAM strand (i.e. the non-target strand or the edit strand). The PBS is complementary or substantially complementary to a sequence on the PAM strand of the double stranded target DNA that is immediately upstream of the nick site. In some embodiments, in the process of prime editing, the PEgRNA complexes with and directs a prime editor to bind the search target sequence on the target strand of the double stranded target DNA, and generates a nick at the nick site on the non-target strand of the double stranded target DNA. In some embodiments, the PBS is complementary to or substantially complementary to, and can anneal to, a free -target strand of the double stranded target DNA at the nick site. In some embodiments, -target strand can initiate target-primed DNA synthesis.

[0329] An “editing template” of a PEgRNA is a single- PBS and which encodes a single strand of DNA. The editing template may comprise a region of complementarity to the PAM strand (i.e., the non-target strand or the edit strand), and comprises one or more intended nucleotide edits compared to the endogenous sequence of the double stranded target DNA. In some embodiments, the editing template and the PBS are immediately adjacent to each other. Accordingly, in some embodiments, a PEgRNA in prime editing comprises a single-stranded portion that comprises the PBS and the editing template immediately adjacent to each other. In some embodiments, the single stranded portion of the PEgRNA comprising both the PBS and the editing template is complementary or substantially complementary to an endogenous sequence on the PAM strand (i.e., the non-target strand or the edit strand) of the double stranded target DNA except for one or more non- complementary nucleotides at the intended nucleotide edit position(s). As used herein, regardless of - template, and the relative positions as among elements of a PEgRNA, are determined byWSGR Docket No. 59761-791.601 of the PEgRNA as a single molecule regardless of the position of sequences in the double stranded target DNA that may have complementarity or identity to elements of the PEgRNA. In some embodiments, the editing template is complementary or substantially complementary to a sequence on the PAM strand that is immediately downstream of the nick site, except for one or more non-complementary nucleotides at the intended nucleotide edit positions. The endogenous, e.g., genomic, sequence that is complementary or substantially complementary to the editing template, except for the one or more non-complementary nucleotides at the position corresponding to the intended nucleotide edit, may be referred to as an “editing target sequence”. In some embodiments, the editing template has identity or substantial identity to a sequence on the target strand that is complementary to, or having the same position in the genome as, the editing target sequence, except for one or more insertions, deletions, or substitutions at the intended nucleotide edit positions. In some embodiments, the editing template encodes a single stranded DNA, wherein the single stranded DNA has identity or substantial identity to the editing target sequence except for one or more insertions, deletions, or substitutions at the positions of the one or more intended nucleotide edits. In some embodiments, the editing template may encode the wild-type or non-disease associated gene sequence (or its complement if the edit strand is the antisense strand of a gene). In some embodiments, the editing template may encode the wild-type or non-disease associated protein, but contain one or more synonymous mutations relative to the wild-type or non-disease associated protein coding region. Such synonymous mutations may include, for example, mutations that decrease the ability of a PEgRNA to rebind to the same target sequence once the desired edit is installed in the genome (e.g., synonymous mutations that silence the endogenous PAM sequence or that edit the endogenous protospacer). “Synonymous mutation,” “silent edit,” or “silent mutation” can refer to a nucleotide change or substitution in a protein coding sequence that results in no alteration in the encoded amino acid sequence. A synonymous mutation results in encoding the same amino acid as the one encoded by the coding sequence lacking the synonymous mutation.

[0330] In some embodiments, a PEgRNA complexes with and directs a prime editor to bind to the search target sequence of the target gene. In some embodiments, the bound prime editor generates a nick on the edit strand (PAM strand) of the target gene at the nick site. In some embodiments, a primer - stranded DNA encoded by the editing template of the PEgRNA is synthesized. In some embodiments, the newly synthesized single-stranded DNA comprises one or more intended nucleotide edits compared to the endogenous target gene sequence. Accordingly, in some embodiments, the editing template of a PEgRNA is complementary to a sequence in the edit strand except for one or more mismatches at the intended nucleotide edit positions in the editing template. The endogenous, e.g., genomic, sequence that is partially complementary to the editing template may be referred to as an “editing target sequence”. Accordingly, in some embodiments, the newly synthesized single stranded DNA has identity orWSGR Docket No. 59761-791.601 substantial identity to a sequence in the editing target sequence, except for one or more insertions, deletions, or substitutions at the intended nucleotide edit positions. In some embodiments, the editing template comprises at least 4 contiguous nucleotides of complementarity with the edit strand wherein the at least 4 nucleotides contiguous are located upstream of the 5’ most edit in the editing template.

[0331] In some embodiments, the newly synthesized single-stranded DNA equilibrates with the editing target on the edit strand of the target gene for pairing with the target strand of the target gene. In some embodiments, the editing target sequence of the target gene is excised by a flap endonuclease (FEN), for example, FEN1. In some embodiments, the FEN is an endogenous FEN, for example, in a cell comprising the target gene. In some embodiments, the FEN is provided as part of the prime editor, either linked to other components of the prime editor or provided in trans. In some embodiments, the newly synthesized single stranded DNA, which comprises the intended nucleotide edit, replaces the endogenous single stranded editing target sequence on the edit strand of the target gene. In some embodiments, the newly synthesized single stranded DNA and the endogenous DNA on the target strand form a heteroduplex DNA structure at the region corresponding to the editing target sequence of the target gene. In some embodiments, the newly synthesized single-stranded DNA comprising the nucleotide edit is paired in the heteroduplex with the target strand of the target DNA that does not comprise the nucleotide edit, thereby creating a mismatch between the two otherwise complementary strands. In some embodiments, the mismatch is recognized by DNA repair machinery, e.g., an endogenous DNA repair machinery. In some embodiments, through DNA repair, the intended nucleotide edit is incorporated into the target gene. Prime Editor

[0332] The term “prime editor (PE)” refers to the polypeptide or polypeptide components involved in prime editing, or any polynucleotide(s) encoding the polypeptide or polypeptide components. In various embodiments, a prime editor includes a polypeptide domain having DNA binding activity and a polypeptide domain having DNA polymerase activity. In some embodiments, the prime editor further comprises a polypeptide domain having nuclease activity. In some embodiments, the polypeptide domain having DNA binding activity comprises a nuclease domain or nuclease activity. In some embodiments, the polypeptide domain having nuclease activity comprises a nickase, or a fully active nuclease. As used herein, the term “nickase” refers to a nuclease capable of cleaving only one strand of a double-stranded DNA target. In some embodiments, the prime editor comprises a polypeptide domain that is an inactive nuclease. In some embodiments, the polypeptide domain having programmable DNA binding activity comprises a nucleic acid guided DNA binding domain, for example, a CRISPR-Cas protein, for example, a Cas9 nickase, a Cpf1 nickase, or another CRISPR-Cas nuclease. In some embodiments, the polypeptide domain having DNA polymerase activity comprises a template-dependent DNA polymerase, for example, a DNA-dependent DNA polymerase or an RNA-dependent DNA polymerase. In someWSGR Docket No. 59761-791.601 embodiments, the DNA polymerase is a reverse transcriptase. In some embodiments, the prime editor comprises additional polypeptides involved in prime editing, for example, a polypeptide domain having e.g. e.g., FEN1), for helping to drive the prime editing process towards the edited product formation. In some embodiments, the prime editor further comprises an RNA-protein recruitment polypeptide, for example, a MS2 coat protein.

[0333] A prime editor may be engineered. In some embodiments, the polypeptide components of a prime editor do not naturally occur in the same organism or cellular environment. In some embodiments, the polypeptide components of a prime editor may be of different origins or from different organisms. In some embodiments, a prime editor comprises a DNA binding domain and a DNA polymerase domain that are derived from different species. In some embodiments, a prime editor comprises a Cas polypeptide (DNA binding domain) and a reverse transcriptase polypeptide (DNA polymerase) that are derived from different species. For example, a prime editor may comprise a S. pyogenes Cas9 polypeptide and a Moloney murine leukemia virus (M-MLV) reverse transcriptase polypeptide.

[0334] In some embodiments, polypeptide domains of a prime editor may be fused or linked by a peptide linker to form a fusion protein. In other embodiments, a prime editor comprises one or more polypeptide domains provided in trans as separate proteins, which are capable of being associated to each other through non-peptide linkages or through aptamers or recruitment sequences. For example, a prime editor may comprise a DNA binding domain and a reverse transcriptase domain associated with each other by an RNA-protein recruitment aptamer, e.g., a MS2 aptamer, which may be linked to a PEgRNA. Prime editor polypeptide components may be encoded by one or more polynucleotides in whole or in part. In some embodiments, a single polynucleotide, construct, or vector encodes the prime editor fusion protein. In some embodiments, multiple polynucleotides, constructs, or vectors each encode a polypeptide domain or portion of a domain of a prime editor, or a portion of a prime editor fusion protein. For example, a prime editor fusion protein may comprise an N-terminal portion fused to an intein-N and a C-terminal portion fused to an intein-C, each of which is individually encoded by an AAV vector. Prime Editor Nucleotide Polymerase Domain

[0335] In some embodiments, a prime editor comprises a nucleotide polymerase domain, e.g., a DNA polymerase domain. The DNA polymerase domain may be a wild-type DNA polymerase domain, a full- length DNA polymerase protein domain, or may be a functional mutant, a functional variant, or a functional fragment thereof. In some embodiments, the polymerase domain is a template dependent polymerase domain. For example, the DNA polymerase may rely on a template polynucleotide strand, e.g., the editing template sequence, for new strand DNA synthesis. In some embodiments, the prime editor comprises a DNA-dependent DNA polymerase. For example, a prime editor having a DNA- dependent DNA polymerase can synthesize a new single stranded DNA using a PEgRNA editingWSGR Docket No. 59761-791.601 template that comprises a DNA sequence as a template. In such cases, the PEgRNA is a chimeric or hybrid PEgRNA, and comprising an extension arm comprising a DNA strand. The chimeric or hybrid PEgRNA may comprise an RNA portion (including the spacer and the gRNA core) and a DNA portion (the extension arm comprising the editing template that includes a strand of DNA).

[0336] In some embodiments, the DNA polymerases can be wild type polymerases from eukaryotic, prokaryotic, archaeal, or viral organisms, and / or the polymerases may be modified by genetic engineering, mutagenesis, or directed evolution-based processes. The polymerases can be a T7 DNA polymerase, T5 DNA polymerase, T4 DNA polymerase, Klenow fragment DNA polymerase, DNA polymerase III and the like. The polymerases can be thermostable, and can include Taq, Tne, Tma, Pfu, Tfl, Tth, Stoffel fragment, VENT® and DEEPVENT® DNA polymerases, KOD, Tgo, JDF3, and mutants, variants and derivatives thereof.

[0337] In some embodiments, the DNA polymerase is a bacteriophage polymerase, for example, a T4, T7, or phi29 DNA polymerase. In some embodiments, the DNA polymerase is an archaeal polymerase, for example, pol I type archaeal polymerase or a pol II type archaeal polymerase. In some embodiments, the DNA polymerase comprises a thermostable archaeal DNA polymerase. In some embodiments, the DNA polymerase comprises a eubacterial DNA polymerase, for example, Pol I, Pol II, or Pol III polymerase. In some embodiments, the DNA polymerase is a Pol I family DNA polymerase. In some embodiments, the DNA polymerase is a E.coli Pol I DNA polymerase. In some embodiments, the DNA polymerase is a Pol II family DNA polymerase. In some embodiments, the DNA polymerase is a Pyrococcus furiosus (Pfu) Pol II DNA polymerase. In some embodiments, the DNA Polymerase is a Pol IV family DNA polymerase. In some embodiments, the DNA polymerase is a E.coli Pol IV DNA polymerase.

[0338] In some embodiments, the DNA polymerase comprises a eukaryotic DNA polymerase. In some embodiments, the DNA polymerase is a Pol-beta DNA polymerase, a Pol-lambda DNA polymerase, a Pol-sigma DNA polymerase, or a Pol-mu DNA polymerase. In some embodiments, the DNA polymerase is a Pol-alpha DNA polymerase. In some embodiments, the DNA polymerase is a POLA1 DNA polymerase. In some embodiments, the DNA polymerase is a POLA2 DNA polymerase. In some embodiments, the DNA polymerase is a Pol-delta DNA polymerase. In some embodiments, the DNA polymerase is a POLD1 DNA polymerase. In some embodiments, the DNA polymerase is a POLD2 DNA polymerase. In some embodiments, the DNA polymerase is a human POLD1 DNA polymerase. In some embodiments, the DNA polymerase is a human POLD2 DNA polymerase. In some embodiments, the DNA polymerase is a POLD3 DNA polymerase. In some embodiments, the DNA polymerase is a POLD4 DNA polymerase. In some embodiments, the DNA polymerase is a Pol-epsilon DNA polymerase. In some embodiments, the DNA polymerase is a POLE1 DNA polymerase. In some embodiments, the DNA polymerase is a POLE2 DNA polymerase. In some embodiments, the DNA polymerase is a POLE3 DNA polymerase. In some embodiments, the DNA polymerase is a Pol-etaWSGR Docket No. 59761-791.601 (POLH) DNA polymerase. In some embodiments, the DNA polymerase is a Pol-iota (POLI) DNA polymerase. In some embodiments, the DNA polymerase is a Pol-kappa (POLK) DNA polymerase. In some embodiments, the DNA polymerase is a Rev1 DNA polymerase. In some embodiments, the DNA polymerase is a human Rev1 DNA polymerase. In some embodiments, the DNA polymerase is a viral DNA-dependent DNA polymerase. In some embodiments, the DNA polymerase is a B family DNA polymerases. In some embodiments, the DNA polymerase is a herpes simplex virus (HSV) UL30 DNA polymerase. In some embodiments, the DNA polymerase is a cytomegalovirus (CMV) UL54 DNA polymerase.

[0339] In some embodiments, the DNA polymerase is an archaeal polymerase. In some embodiments, the DNA polymerase is a Family B / pol I type DNA polymerase. For example, in some embodiments, the DNA polymerase is a homolog of Pfu from Pyrococcus furiosus. In some embodiments, the DNA polymerase is a pol II type DNA polymerase. For example, in some embodiments, the DNA polymerase is a homolog of P. furiosus DP1 / DP22-subunit nuclease activity. Suitable DNA polymerases (pol I or pol II) can be derived from archaea with optimal growth temperatures that are similar to the desired assay temperatures.

[0340] In some embodiments, the DNA polymerase comprises a thermostable archaeal DNA polymerase. In some embodiments, the thermostable DNA polymerase is isolated or derived from Pyrococcus species (furiosus, species GB-D, woesii, abysii, horikoshii), Thermococcus species (kodakaraensis KOD1, litoralis, species 9 degrees North-7, species JDF-3, gorgonarius), Pyrodictium occultum, and Archaeoglobus fulgidus.

[0341] Polymerases may also be from eubacterial species. In some embodiments, the DNA polymerase is a Pol I family DNA polymerase. In some embodiments, the DNA polymerase is an E.coli Pol I DNA polymerase. In some embodiments, the DNA polymerase is a Pol II family DNA polymerase. In some embodiments, the DNA polymerase is a Pyrococcus furiosus (Pfu) Pol II DNA polymerase. In some embodiments, the DNA Polymerase is a Pol III family DNA polymerase. In some embodiments, the DNA Polymerase is a Pol IV family DNA polymerase. In some embodiments, the DNA polymerase is an E.coli Pol IV DNA polymerase. In some embodiments, the Pol I DNA polymerase is a DNA polymerase

[0342] Suitable thermostable pol I DNA polymerases can be isolated from a variety of thermophilic eubacteria, including Thermus species and Thermotoga maritima such as Thermus aquaticus (Taq), Thermus thermophilus (Tth) and Thermotoga maritima (Tma UlTma).

[0343] In some embodiments, a prime editor comprises an RNA-dependent DNA polymerase domain, for example, a reverse transcriptase (RT). A RT or an RT domain may be a wild type RT domain, a full- length RT domain, or may be a functional mutant, a functional variant, or a functional fragment thereof. An RT or an RT domain of a prime editor may comprise a wild-type RT, or may be engineered or evolved to contain specific amino acid substitutions, truncations, or variants. An engineered RT mayWSGR Docket No. 59761-791.601 comprise sequences or amino acid changes different from a naturally occurring RT. In some embodiments, the engineered RT may have improved reverse transcription activity over a naturally occurring RT or RT domain. In some embodiments, the engineered RT may have improved features over a naturally occurring RT, for example, improved thermostability, reverse transcription efficiency, or target fidelity. In some embodiments, a prime editor comprising the engineered RT has improved prime editing efficiency over a prime editor having a reference naturally occurring RT.

[0344] In some embodiments, a prime editor comprises a virus RT, for example, a retrovirus RT. Non- limiting examples of virus RT include Moloney murine leukemia virus (M-MLV, MMLVRT or M-MLV RT); human T-cell leukemia virus type 1 (HTLV-1) RT; bovine leukemia virus (BLV) RT; Rous Sarcoma Virus (RSV) RT; human immunodeficiency virus (HIV) RT, M-MFV RT, Avian Sarcoma- Leukosis Virus (ASLV) RT, Rous Sarcoma Virus (RSV) RT, Avian Myeloblastosis Virus (AMV) RT, Avian Erythroblastosis Virus (AEV) Helper Virus MCAV RT, Avian Myelocytomatosis Virus MC29 Helper Virus MCAV RT, Avian Reticuloendotheliosis Virus (REV-T) Helper Virus REV-A RT, Avian Sarcoma Virus UR2 Helper Virus (UR2AV) RT, Avian Sarcoma Virus Y73 Helper Virus YAV RT, Rous Associated Virus (RAV) RT, and Myeloblastosis Associated Virus (MAV) RT, all of which may be suitably used in the methods and composition described herein.

[0345] In some embodiments, the prime editor comprises a wild type M-MLV RT, a functional mutant, a functional variant, or a functional fragment thereof. Table 1 provides sequences of illustrative M-MLV RTs suitable for use with compositions and methods of the disclosure.

[0346] In some embodiments, a prime editor comprises a wild-type M-MLV RT as set forth in SEQ ID NO: 870. In some embodiments, a prime editor comprises a variant M-MLV RT as set forth in SEQ ID NO: 871. In some embodiments, a prime editor comprises a variant M-MLV RT as set forth in SEQ ID NO: 872.

[0347] Table 1. Illustrative M-MLV RT SequencesWSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601

[0348] In some embodiments, the prime editor comprises a M-MLV RT comprising one or more of amino acid substitutions: P51X, S67X, E69X, L139X, T197X, D200X, H204X, F209X, E302X, T306X, F309X, W313X, T330X, L345X, L435X, N454X, D524X, E562X, D583X, H594X, L603X, E607X, or D653X as compared to a reference M-MLV RT where X is any amino acid other than the original amino acid in the reference M-MLV RT. In some embodiments, the prime editor comprises a M-MLV RT comprising one or more of amino acid substitutions: P51L, S67K, E69K, L139P, T197A, D200N, H204R, F209N, E302K, E302R, T306K, F309N, W313F, T330P, L345G, L435G, N454K, D524G, E562Q, D583N, H594Q, L603W, E607K, or D653N as compared to a reference M-MLV RT. In some embodiments, the reference M-MLV RT is a variant M-MLV RT as set forth in SEQ ID NO: 871. In some embodiments, the reference M-MLV RT is a WT M-MLV RT as set forth in SEQ ID NO: 870.

[0349] In some embodiments, a prime editor comprises a M-MLV RT comprising one or more of amino acid substitutions D200N, T330P, L603W, T306K, or W313F as compared to a reference M-MLV RT . In some embodiments, a prime editor comprises a M-MLV RT comprising amino acid substitutions D200N, T330P, L603W, T306K, and W313F as compared to a reference M-MMLV RT . In some embodiments, the reference M-MLV RT is a variant M-MLV RT as set forth in SEQ ID NO: 871. In some embodiments, the reference M-MLV RT is a WT M-MLV RT as set forth in SEQ ID NO: 870.

[0350] In some embodiments, a prime editor comprises a M-MLV RT that comprises an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or at least 99.9% identical to an amino acid sequence set forth in in Table 1. In some embodiments, the prime editor comprises a M-MLV RT that comprises an amino acid sequence that is selected from the group consisting of: amino acid sequences provided in Table 1 or a variant or fragment thereof. In some embodiments, the prime editor comprises a variant M-MLV RT that comprises an amino acid sequence set forth in SEQ ID NO: 872.

[0351] In some embodiments, an RT variant may be a functional fragment of a reference RT that has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, up to 100, up to 200, up to 300, up to 400, or up to 500 or more amino acid changes compared to a reference RT. In some embodiments, the RT variant comprises a fragment of a reference RT, such that the fragment is about 70% identical, about 80% identical, about 90% identical, about 95% identical, about 96% identical, about 97% identical, about 98% identical, about 99% identical, about 99.5% identical, or about 99.9% identical to the corresponding fragment of the reference RT. In some embodiments, the fragment is 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% identical, 96%, 97%, 98%, 99%, orWSGR Docket No. 59761-791.601 99.5% of the amino acid length of a corresponding reference RT (M-MLV reverse transcriptase). A reference RT can be any one of the RTs shown in Table 1.

[0352] In some embodiments, the RT functional fragment is at least 100 amino acids in length. In some embodiments, the fragment is at least 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, or up to 600 or more amino acids in length.

[0353] In still other embodiments, the functional RT variant is truncated at the N-terminus or the C- terminus, or both, by a certain number of amino acids which results in a truncated variant which still retains sufficient DNA polymerase function. In some embodiments, the functional RT variant, e.g., a functional MMLV RT variant, is truncated at the C-terminus to abolish or reduce RNAase H activity and still retain DNA polymerase activity.

[0354] In some embodiments, a prime editing composition or a prime editing system disclosed herein comprises a polynucleotide (e.g., a DNA, a RNA, e.g., a mRNA) that encodes a M-MLV RT. In some embodiments, the polynucleotide encodes a M-MLV RT that comprises an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or at least 99.9% identical to an amino acid sequence set forth in Table 1. In some embodiments, the polynucleotide encodes a M-MLV RT that comprises an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or at least 99.9% identical to an amino acid sequence set forth in SEQ ID NO: 870, 871, or 872. In some embodiments, the polynucleotide encodes a M-MLV RT that comprises an amino acid sequence that is selected from the group consisting of: the amino acid sequences provided in Table 1. In some embodiments, the polynucleotide encodes a variant M-MLV RT that comprises an amino acid sequence that is set forth in SEQ ID NO: 872.

[0355] In some embodiments, a prime editor comprises a eukaryotic RT, for example, a yeast, drosophila, rodent, or primate RT. In some embodiments, the prime editor comprises a Group II intron RT, for example, a. Geobacillus stearothermophilus Group II Intron (GsI-IIC) RT or a Eubacterium rectale group II intron (Eu.re.I2) RT. In some embodiments, the prime editor comprises a retron RT. In some embodiments, a prime editor comprises a eukaryotic RT, for example, a yeast, drosophila, rodent, or primate RT. In some embodiments, the prime editor comprises a Group II intron RT, for example, a. Geobacillus stearothermophilus Group II Intron (GsI-IIC) RT or a Eubacterium rectale group II intron (Eu.re.I2) RT. In some embodiments, the prime editor comprises a retron RT. Programmable DNA Binding Domain

[0356] In some embodiments, the DNA-binding domain of a prime editor is a programmable DNA binding domain.

[0357] A programmable DNA binding domain refers to a protein domain that is designed to bind a specific nucleic acid sequence, e.g., a target DNA or a target RNA. In some embodiments, the DNA-WSGR Docket No. 59761-791.601 binding domain is a polynucleotide programmable DNA-binding domain that can associate with a guide polynucleotide (e.g., a PEgRNA) that guides the DNA-binding domain to a specific DNA sequence, e.g., a search target sequence in a target gene. In some embodiments, the DNA-binding domain comprises a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Associated (Cas) protein. A Cas protein may comprise any Cas protein described herein or a functional fragment or functional variant thereof. In some embodiments, a DNA-binding domain may also comprise a zinc-finger protein domain. In other cases, a DNA-binding domain comprises a transcription activator-like effector domain (TALE). In some embodiments, the DNA-binding domain comprises a DNA nuclease. For example, the DNA- binding domain of a prime editor may comprise an RNA-guided DNA endonuclease, e.g., a Cas protein. In some embodiments, the DNA-binding domain comprises a zinc finger nuclease (ZFN) or a transcription activator like effector domain nuclease (TALEN), where one or more zinc finger motifs or TALE motifs are associated with one or more nucleases, e.g., a Fok I nuclease domain.

[0358] In some embodiments, the DNA-binding domain comprises a nuclease activity. In some embodiments, the DNA-binding domain of a prime editor comprises an endonuclease domain having single strand DNA cleavage activity. For example, the endonuclease domain may comprise a FokI nuclease domain. In some embodiments, the DNA-binding domain of a prime editor comprises a nuclease having full nuclease activity. In some embodiments, the DNA-binding domain of a prime editor comprises a nuclease having modified or reduced nuclease activity as compared to a wild type endonuclease domain. For example, the endonuclease domain may comprise one or more amino acid substitutions as compared to a wild type endonuclease domain. In some embodiments, the DNA-binding domain of a prime editor has a nickase activity. In some embodiments, the DNA-binding domain of a prime editor comprises a Cas protein domain that is a nickase. In some embodiments, compared to a wild type Cas protein, the Cas nickase comprises one or more amino acid substitutions in a nuclease domain that reduces or abolishes its double strand nuclease activity but retains DNA binding activity. In some embodiments, the Cas nickase comprises an amino acid substitution in a HNH domain. In some embodiments, the Cas nickase comprises an amino acid substitution in a RuvC domain.

[0359] In some embodiments, the DNA-binding domain comprises a CRISPR associated protein (Cas protein) domain. A Cas protein may be a Class 1 or a Class 2 Cas protein. A Cas protein can be a type I, type II, type III, type IV, type V Cas protein, or a type VI Cas protein. Non-limiting examples of Cas proteins include Casl, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas5d, Cas5t, Cas5h, Cas5a, Cas6, Cas7, Cas8, Cas8a, Cas8b, Cas8c, Cas9 (e.g., Csnl or Csx12), Cas10, CaslOd, Cas12a / Cpfl, Cas12b / C2c1, Cas12c / C2c3, Cas12d / CasY, Cas12e / CasX, Cas12g, Cas12h, Cas12i, Csyl , Csy2, Csy3, Csy4, Csel, Cse2, Cse3, Cse4, Cse5e, Cscl, Csc2, Csa5, Csnl, Csn2, Csml, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csxl, Csx1S, Csx11, Csfl, Csf2, CsO, Csf4, Csdl, Csd2, Cstl, Cst2, Cshl, Csh2, Csal, Csa2, Csa3, Csa4, Csa5, Type II Cas effector proteins, Type V Cas effector proteins, Type VI Cas effector proteins, CARF, DinG, Cpfl,WSGR Docket No. 59761-791.601 Cas12b / C2c1, Cas12c / C2c3, Cas12b / C2c1, Cas12c / C2c3, SpCas9(K855A), eSpCas9(1.1), SpCas9-HF1, mutants, and / or functional fragments thereof. A Cas protein can be a chimeric Cas protein that is fused to other proteins or polypeptides. A Cas protein can be a chimera of various Cas proteins, for example, comprising domains of Cas proteins from different organisms.

[0360] A Cas protein, e.g., Cas9, can be from any suitable organism. In some aspects, the organism is Streptococcus pyogenes (S. pyogenes). In some aspects, the organism is Staphylococcus aureus (S. aureus). In some aspects, the organism is Streptococcus thermophilus (S. thermophilus). In some embodiments, the organism is Staphylococcus lugdunensis.

[0361] Non-limiting examples of suitable organism include Streptococcus pyogenes, Streptococcus thermophilus, Streptococcus sp., Staphylococcus aureus, Nocardiopsis dassonvillei, Streptomyces pristinae spiralis, Streptomyces viridochromo genes, Streptomyces viridochromogenes, Streptosporangium roseum, Streptosporangium roseum, AlicyclobacHlus acidocaldarius, Bacillus pseudomycoides, Bacillus selenitireducens, Exiguobacterium sibiricum, Lactobacillus delbrueckii, Lactobacillus salivarius, Microscilla marina, Burkholderiales bacterium, Polaromonas naphthalenivorans, Polaromonas sp., Crocosphaera watsonii, Cyanothece sp., Microcystis aeruginosa, Pseudomonas aeruginosa, Synechococcus sp., Acetohalobium arabaticum, Ammonifex degensii, Caldicelulosiruptor becscii, Candidatus Desulforudis, Clostridium botulinum, Clostridium difficile, Finegoldia magna, Natranaerobius thermophilus, Pelotomaculum thermopropionicum, Acidithiobacillus caldus, Acidithiobacillus ferrooxidans, Allochromatium vinosum, Marinobacter sp., Nitrosococcus halophilus, Nitrosococcus watsoni, Pseudoalteromonas haloplanktis, Ktedonobacter racemifer, Methanohalobium evestigatum, Anabaena variabilis, Nodularia spumigena, Nostoc sp., Arthrospira maxima, Arthrospira platensis, Arthrospira sp., Lyngbya sp., Microcoleus chthonoplastes, Oscillatoria sp., Petrotoga mobilis, Thermosipho africanus, Acaryochloris marina, Leptotrichia shahii, and Francisella novicida. In some embodiments, the organism is Streptococcus pyogenes (S. pyogenes). In some embodiments, the organism is Staphylococcus aureus (S. aureus). In some embodiments, the organism is Streptococcus thermophilus (S. thermophilus). In some embodiments, the organism is Staphylococcus lugdunensis (S. lugdunensis).

[0362] In some embodiments, a Cas protein can be derived from a variety of bacterial species including, but not limited to, Veillonella atypical, Fusobacterium nucleatum, Filifactor alocis, Solobacterium moorei, Coprococcus catus, Treponema denticola, Peptoniphilus duerdenii, Catenibacterium mitsuokai, Streptococcus mutans, Listeria innocua, Staphylococcus pseudintermedius, Acidaminococcus intestine, Olsenella uli, Oenococcus kitaharae, Bifidobacterium bifidum, Lactobacillus rhamnosus, Lactobacillus gasseri, Finegoldia magna, Mycoplasma mobile, Mycoplasma gallisepticum, Mycoplasma ovipneumoniae, Mycoplasma canis, Mycoplasma synoviae, Eubacterium rectale, Streptococcus thermophilus, Eubacterium dolichum, Lactobacillus coryniformis subsp. Torquens, IlyobacterWSGR Docket No. 59761-791.601 polytropus, Ruminococcus albus, Akkermansia muciniphila, Acidothermus cellulolyticus, Bifidobacterium longum, Bifidobacterium dentium, Corynebacterium diphtheria, Elusimicrobium minutum, Nitratifractor salsuginis, Sphaerochaeta globus, Fibrobacter succinogenes subsp. Succinogenes, Bacteroides fragilis, Capnocytophaga ochracea, Rhodopseudomonas palustris, Prevotella micans, Prevotella ruminicola, Flavobacterium columnare, Aminomonas paucivorans, Rhodospirillum rubrum, Candidatus Puniceispirillum marinum, Verminephrobacter eiseniae, Ralstonia syzygii, Dinoroseobacter shibae, Azospirillum, Nitrobacter hamburgensis, Bradyrhizobium, Wolinella succinogenes, Campylobacter jejuni subsp. Jejuni, Helicobacter mustelae, Bacillus cereus, Acidovorax ebreus, Clostridium perfringens, Parvibaculum lavamentivorans, Roseburia intestinalis, Neisseria meningitidis, Pasteurella multocida subsp. Multocida, Sutterella wadsworthensis, proteobacterium, Legionella pneumophila, Parasutterella excrementihominis, Wolinella succinogenes, and Francisella novicida.

[0363] In some embodiments, a Cas protein, e.g., Cas9, can be a wild type or a modified form of a Cas protein. In some embodiments, a Cas protein, e.g., Cas9, can be a nuclease active variant, nuclease inactive variant, a nickase, or a functional variant or functional fragment of a wild type Cas protein. In some embodiments, a Cas protein, e.g., Cas9, can be a wild type or a modified form of a Cas protein. A Cas protein, e.g., Cas9, can be a nuclease active variant, nuclease inactive variant, a nickase, or a functional variant or functional fragment of a wild type Cas protein. In some embodiments, a Cas protein, e.g., Cas9, can comprise an amino acid change such as a deletion, insertion, substitution, fusion, chimera, or any combination thereof relative to a corresponding wild-type version of the Cas protein. In some embodiments, a Cas protein can be a polypeptide with at least about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity or sequence similarity to a wild type exemplary Cas protein.

[0364] A Cas protein, e.g., Cas9, may comprise one or more domains. Non-limiting examples of Cas domains include, guide nucleic acid recognition and / or binding domain, nuclease domains (e.g., DNase or RNase domains, RuvC, HNH), DNA binding domain, RNA binding domain, helicase domains, protein-protein interaction domains, and dimerization domains. In various embodiments, a Cas protein comprises a guide nucleic acid recognition and / or binding domain can interact with a guide nucleic acid, and one or more nuclease domains that comprise catalytic activity for nucleic acid cleavage.

[0365] In some embodiments, a Cas protein, e.g., Cas9, comprises one or more nuclease domains. A Cas protein can comprise an amino acid sequence having at least about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a nuclease domain (e.g., RuvC domain, HNH domain) of a wild-type Cas protein. In some embodiments, a Cas protein comprises a single nuclease domain. For example, a Cpf1 may comprise a RuvC domain but lacks HNH domain. In some embodiments, a Cas protein comprises two nuclease domains, e.g., a Cas9 protein can comprise an HNH nuclease domain and a RuvC nuclease domain.WSGR Docket No. 59761-791.601

[0366] In some embodiments, a prime editor comprises a Cas protein, e.g., Cas9, wherein all nuclease domains of the Cas protein are active. In some embodiments, a prime editor comprises a Cas protein having one or more inactive nuclease domains. One or a plurality of the nuclease domains (e.g., RuvC, HNH) of a Cas protein can be deleted or mutated so that they are no longer functional or comprise reduced nuclease activity. In some embodiments, a Cas protein, e.g., Cas9, comprising mutations in a nuclease domain has reduced (e.g., nickase) or abolished nuclease activity while maintaining its ability to target a nucleic acid locus at a search target sequence when complexed with a guide nucleic acid, e.g., a PEgRNA.

[0367] In some embodiments, a prime editor comprises a Cas nickase that can bind to the target gene in a sequence-specific manner and generate a single-strand break at a protospacer within double-stranded DNA in the target gene, but not a double-strand break. For example, the Cas nickase can cleave the edit strand or the non-edit strand of the target gene, but may not cleave both. In some embodiments, a prime editor comprises a Cas nickase comprising two nuclease domains (e.g., Cas9), with one of the two nuclease domains modified to lack catalytic activity or deleted. In some embodiments, the Cas nickase of a prime editor comprises a nuclease inactive RuvC domain and a nuclease active HNH domain. In some embodiments, the Cas nickase of a prime editor comprises a nuclease inactive HNH domain and a nuclease active RuvC domain. In some embodiments, a prime editor comprises a Cas9 nickase having an amino acid substitution in the RuvC domain e.g., an amino acid substitution that reduces or abolishes nuclease activity of the RuvC domain. In some embodiments, the Cas9 nickase comprises a D10X amino acid substitution compared to a wild type S. pyogenes Cas9, wherein X is any amino acid other than D. In some embodiments, a prime editor comprises a Cas9 nickase having an amino acid substitution in the HNH domain e.g., an amino acid substitution that reduces or abolishes nuclease activity of the HNH domain. In some embodiments, the Cas9 nickase comprises a H840X amino acid substitution compared to a wild type S. pyogenes Cas9, wherein X is any amino acid other than H.

[0368] In some embodiments, a prime editor comprises a Cas protein that can bind to the target gene in a sequence-specific manner but lacks or has abolished nuclease activity and may not cleave either strand of a double stranded DNA in a target gene. Abolished activity or lacking activity can refer to an enzymatic activity less than 1%, less than 2%, less than 3%, less than 4%, less than 5%, less than 6%, less than 7%, less than 8%, less than 9%, or less than 10% activity compared to a wild-type exemplary activity (e.g., wild-type Cas9 nuclease activity). In some embodiments, a Cas protein of a prime editor completely lacks nuclease activity. A nuclease, e.g., Cas9, that lacks nuclease activity may be referred to as nuclease inactive or “nuclease dead” (abbreviated by “d”). A nuclease dead Cas protein (e.g., dCas, dCas9) can bind to a target polynucleotide but may not cleave the target polynucleotide. In some embodiments, a dead Cas protein is a dead Cas9 protein. In some embodiments, a prime editor comprises a nuclease dead Cas protein wherein all of the nuclease domains (e.g., both RuvC and HNH nucleaseWSGR Docket No. 59761-791.601 domains in a Cas9 protein; RuvC nuclease domain in a Cpf1 protein) are mutated to lack catalytic activity, or are deleted.

[0369] A Cas protein can be modified. A Cas protein, e.g., Cas9, can be modified to increase or decrease nucleic acid binding affinity, nucleic acid binding specificity, and / or enzymatic activity. Cas proteins can also be modified to change any other activity or property of the protein, such as stability. For example, one or more nuclease domains of the Cas protein can be modified, deleted, or inactivated, or a Cas protein can be truncated to remove domains that are not essential for the function of the protein or to optimize (e.g., enhance or reduce) the activity of the Cas protein.

[0370] A Cas protein can be a fusion protein. For example, a Cas protein can be fused to a cleavage domain, an epigenetic modification domain, a transcriptional regulation domain, or a polymerase domain. A Cas protein can also be fused to a heterologous polypeptide providing increased or decreased stability. The fused domain or heterologous polypeptide can be located at the N-terminus, the C-terminus, or internally within the Cas protein.

[0371] In some embodiments, the Cas protein of a prime editor is a Class 2 Cas protein. In some embodiments, the Cas protein is a type II Cas protein. In some embodiments, the Cas protein is a Cas9 protein, a modified version of a Cas9 protein, a Cas9 protein homolog, mutant, variant, or a functional fragment thereof. As used herein, a Cas9, Cas9 protein, Cas9 polypeptide or a Cas9 nuclease refers to an RNA guided nuclease comprising one or more Cas9 nuclease domains and a Cas9 gRNA binding domain having the ability to bind a guide polynucleotide, e.g., a PEgRNA. A Cas9 protein may refer to a wild type Cas9 protein from any organism or a homolog, ortholog, or paralog from any organisms; any functional mutants or functional variants thereof; or any functional fragments or domains thereof. In some embodiments, a prime editor comprises a full-length Cas9 protein. In some embodiments, the Cas9 protein can generally comprises at least about 50%, 60%, 70%, 80%, 90%, 100% sequence identity to a wild type reference Cas9 protein (e.g., Cas9 from S. pyogenes). In some embodiments, the Cas9 comprises an amino acid change such as a deletion, insertion, substitution, fusion, chimera, or any combination thereof as compared to a wild type reference Cas9 protein.

[0372] In some embodiments, a Cas9 protein may comprise a Cas9 protein from Streptococcus pyogenes (Sp), Staphylococcus aureus (Sa), Streptococcus canis (Sc), Streptococcus thermophilus (St), Staphylococcus lugdunensis (Slu), Neisseria meningitidis (Nm), Campylobacter jejuni (Cj), Francisella novicida (Fn), or Treponema denticola (Td), or any Cas9 homolog or ortholog from an organism known in the art. In some embodiments, a Cas9 polypeptide is a SpCas9 polypeptide, e.g., comprising an amino acid sequence as set forth in NCBI Accession No. WP_038431314 or a fragment or variant thereof. In some embodiments, a Cas9 polypeptide is a SaCas9 polypeptide, e.g., comprising an amino acid sequence as set forth in Uniprot Accession No. J7RUA5 or a fragment or variant thereof. In some embodiments, a Cas9 polypeptide is a ScCas9 polypeptide, e.g., comprising an amino acid sequence as set forth in Uniprot Accession No. A0A3P5YA78 or a fragment or variant thereof. In someWSGR Docket No. 59761-791.601 embodiments, a Cas9 polypeptide is a StCas9 polypeptide, e.g., comprising an amino acid sequence as set forth in NCBI Accession No. WP_007896501.1 or a fragment or variant thereof. In some embodiments, a Cas9 polypeptide is a SluCas9 polypeptide, e.g., comprising an amino acid sequence as set forth in any of NCBI Accession No. WP_230580236.1 or WP_250638315.1 or WP_242234150.1, WP_241435384.1, WP_002460848.1, KAK58371.1, or a fragment or variant thereof. In some embodiments, a Cas9 polypeptide is a NmCas9 polypeptide, e.g., comprising an amino acid sequence as set forth in any of NCBI Accession No. WP_002238326.1 or WP_061704949.1 or a fragment or variant thereof. In some embodiments, a Cas9 polypeptide is a CjCas9 polypeptide, e.g., comprising an amino acid sequence as set forth in any of NCBI Accession No. WP_100612036.1, WP_116882154.1, WP_116560509.1, WP_116484194.1, WP_116479303.1, WP_115794652.1, WP_100624872.1, or a fragment or variant thereof. In some embodiments, a Cas9 polypeptide is a FnCas9 polypeptide, e.g., comprising the amino acid sequence as set forth in Uniprot Accession No. A0Q5Y3 or a fragment or variant thereof. In some embodiments, a Cas9 polypeptide is a TdCas9 polypeptide, e.g., comprising the amino acid sequence as set forth in NCBI Accession No. WP_147625065.1 or a fragment or variant thereof. In some embodiments, a Cas9 polypeptide is a chimera comprising domains from two or more of the organisms described herein or those known in the art. In some embodiments, a Cas9 polypeptide is a Cas9 polypeptide from Streptococcus macacae, e.g., comprising the amino acid sequence as set forth in NCBI Accession No. WP_003079701.1 or a fragment or variant thereof. In some embodiments, a Cas9 polypeptide is a Cas9 polypeptide generated by replacing a PAM interaction domain of a SpCas9 with that of a Streptococcus macacae Cas9 (Spy-mac Cas9). Exemplary Cas9 and Cas9 nickase variants are provided in Table 2.

[0373] In some embodiments, a prime editor comprises a DNA binding domain that comprises an amino acid sequence that is at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to any one of the sequences set forth in Table 2. In some embodiments, the DNA binding domain comprises an amino acid sequence that has no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 differences e.g., mutations e.g., deletions, substitutions and / or insertions compared to any one of the amino acid sequences set forth in Table 2.

[0374] In some embodiments, a prime editor comprises a Cas9 protein that comprises an amino acid sequence that is at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to any one of the sequences set forth in Table 2. In some embodiments, a prime editor comprises a Cas9 protein is a Cas9 nickase that comprises an amino acid sequence that is at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%,WSGR Docket No. 59761-791.601 at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to any one of the nickase sequences set forth in Table 2. In some embodiments, a Cas9 protein comprises an amino acid sequence that is selected from the group consisting of the sequences set forth in Table 2. In some embodiments, a prime editor comprises a Cas9 protein that comprises an amino acid sequence that lacks a N-terminus methionine relative to an amino acid sequence set forth Table 2. In some embodiments, the prime editing compositions or prime editing systems disclosed herein comprises a polynucleotide (e.g., a DNA, or an RNA, e.g., an mRNA) that encodes a Cas9 protein that comprises an amino acid sequence that is at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to any one of the sequences set forth in Table 2.

[0375] In some embodiments, a Cas9 protein comprises a Cas9 protein from Streptococcus pyogenes (Sp), e.g., as according to NC_002737.2:854751-858857 or the protein encoded by UniProt Q99ZW2, e.g., as according to SEQ ID NO: 1865. In some embodiments, a prime editor comprises a Cas9 protein (e.g., a SpCas9) as according to any one of the sequences set forth in SEQ ID NOs: 1865-1868 or a variant thereof. In some embodiments, the Cas9 protein is a SpCas9. In some embodiments, a SpCas9 can be a wild type SpCas9, a SpCas9 variant, or a nickase SpCas9. In some embodiments, the SpCas9 lacks the N-terminus methionine relative to a corresponding SpCas9 (e.g., a wild type SpCas9, a SpCas9 variant or a nickase SpCas9). In some embodiments, a prime editor comprises a Cas9 protein, having an amino acid sequence as according to SEQ ID NO: 873, not including the N-terminus methionine. In some embodiments, a wild type SpCas9 comprises an amino acid sequence set forth in SEQ ID NO: 873. In some embodiments, a prime editor comprises a Cas9 protein comprising one or more mutations (e.g., amino acid substitutions, insertions and / or deletions) relative to a corresponding wild type Cas9 protein (e.g., a wild type SpCas9). In some embodiments, the Cas9 protein comprising one or more mutations relative to a wild type Cas9 (e.g., a wild type SpCas9) protein comprises an amino acid sequence set forth in SEQ ID NO: 874, 875, or 876. Exemplary Streptococcus pyogenes Cas9 (SpCas9) amino acid sequence useful in the prime editors disclosed herein are provided in Table 2.

[0376] In some embodiments, a prime editor comprises a Cas9 protein (e.g., a SluCas9) as according to any one of the SEQ ID NOS: 1869-1871 or a variant thereof. In some embodiments, a prime editor comprises a Cas9 protein from Staphylococcus lugdunensis (SluCas9) e.g., as according to any one of the SEQ ID NOs: 877-879 or a variant thereof. In some embodiments, the Cas9 protein is a SluCas9. In some embodiments, a SluCas9 can be a wild type SluCas9, a SluCas9 variant, or a nickase SluCas9. In some embodiments, the SluCas9 lacks the N-terminus methionine relative to a corresponding SluCas9 (e.g., a wild type SluCas9, a SluCas9 variant or a nickase SluCas9). In some embodiments, a prime editor comprises a Cas9 protein, having an amino acid sequence as according to SEQ ID NO: 877, not including the N-terminus methionine. In some embodiments, a wild type SluCas9 comprises an aminoWSGR Docket No. 59761-791.601 acid sequence set forth in SEQ ID NO: 877. In some embodiments, a prime editor comprises a Cas9 protein comprising one or more mutations (e.g., amino acid substitutions, insertions and / or deletions) relative to a corresponding wild type Cas9 protein (e.g., a wild type SluCas9). In some embodiments, the Cas9 protein comprising one or mutations relative to a wild type Cas9 protein comprises an amino acid sequence set forth in SEQ ID NO: 878 or SEQ ID NO: 879. Exemplary Staphylococcus lugdunensis Cas9 (SluCas9) amino acid sequence useful in the prime editors disclosed herein are provided in Table 2.

[0377] In some embodiments, a prime editor comprises a Cas9 protein from Staphylococcus aureus (SaCas9) e.g., as according to any of the SEQ ID NOS: 880-882, or a variant thereof. In some embodiments, a prime editor comprises a Cas9 protein from Staphylococcus aureus (SaCas9) e.g., as according to any one of the SEQ ID NOS: 880-882, or a variant thereof. In some embodiments, the Cas9 protein is a SaCas9. In some embodiments, a SaCas9 can be a wild type SaCas9, a SaCas9 variant, or a nickase SaCas9. In some embodiments, the SaCas9 lacks the N-terminus methionine relative to a corresponding SaCas9 (e.g., a wild type SaCas9, a SaCas9 variant or a nickase SaCas9). In some embodiments, a prime editor comprises a Cas9 protein, having an amino acid sequence as according to SEQ ID NO: 880, not including the N-terminus methionine. In some embodiments, a wild type SaCas9 comprises an amino acid sequence set forth in SEQ ID NO: 880. In some embodiments, a prime editor comprises a Cas9 protein comprising one or more mutations (e.g., amino acid substitutions, insertions and / or deletions relative to a corresponding wild type Cas9 protein (e.g., a wild type SaCas9). In some embodiments, the Cas9 protein comprising one or more mutations relative to a wild type Cas9 protein comprises an amino acid sequence set forth in SEQ ID NO: 881 or SEQ ID NO: 882. Exemplary Staphylococcus aureus Cas9 (SaCas9) amino acid sequence useful in the prime editors disclosed herein are provided Table 2.

[0378] In some embodiments, a prime editor comprises a Cas9 protein as according to any one of the sequences set forth in SEQ ID NOs: 883-891, 898-900 or a variant thereof. In some embodiments, the Cas9 protein is a Cas9 variant, for example, a SpCas9 variant (e.g., SpCas9-NG, SpCas9-NGA, SpRY, or SpG). In some embodiments, the Cas9 protein lacks the N-terminus methionine relative to a corresponding Cas9 protein (e.g., a Cas9 variant set forth in any one of SEQ ID NOs: 883, 884, 886, 887, 889, 890, 898, or 899). In some embodiments, a prime editor comprises a Cas9 protein (e.g., a Cas9 variant), having an amino acid sequence as according to any one of SEQ ID NOs: 883, 886, 889, or 898 not including the N-terminus methionine. In some embodiments, a prime editor comprises a Cas9 protein comprising one or more mutations (e.g., amino acid substitutions, insertions and / or deletions) relative to a corresponding Cas9 protein (e.g., a Cas9 protein set forth in any one of SEQ ID NOs: 883, 886, 889, or 898). In some embodiments, the Cas9 protein comprising one or mutations relative to a corresponding Cas9 protein comprises an amino acid sequence set forth in any one of SEQ ID NOs: 884, 885, 887, 888, 890, 891, 899, or 900.WSGR Docket No. 59761-791.601

[0379] In some embodiments, a Cas9 protein is a chimeric Cas9, e.g., modified Cas9, e.g., synthetic RNA-guided nucleases (sRGNs), e.g., modified by DNA family shuffling, e.g., sRGN3.1, sRGN3.3. In some embodiments, the DNA family shuffling comprises, fragmentation and reassembly of parental Cas9 genes, e.g., one or more of Cas9s from Staphylococcus hyicus (Shy), Staphylococcus lugdunensis (Slu), Staphylococcus microti (Smi), and Staphylococcus pasteuri (Spa). In some embodiments, a modified sluCas9 shows increased editing efficiency and / or specificity relative to a sluCas9 that is not modified. In some embodiments, a modified Cas9, e.g., a sRGN shows at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 200%, at least 300%, at least 400%, at least 500%, at least 600%, at least 700%, at least 800%, at least 900%, or at least 1000% increase in editing efficiency compared to a Cas9 that is not modified. In some embodiments, a Cas9, e.g., a sRGN shows at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 200%, at least 300%, at least 400%, at least 500%, at least 600%, at least 700%, at least 800%, at least 900%, or at least 1000% increase in specificity compared to a Cas9 that is not modified. In some embodiments, a Cas9, e.g., a sRGN shows at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 200%, at least 300%, at least 400%, at least 500%, at least 600%, at least 700%, at least 800%, at least 900%, or at least 1000% increase in cleavage activity compared to a Cas9 that is not modified. In some -NNGG- -containing target. In some embodiments, a prime editor comprises a Cas9 protein (e.g., a chimeric Cas9), e.g., as according any one of the sequences set forth in SEQ ID NOs: 892-897, or a variant thereof. Exemplary amino acid sequences of Cas9 protein (e.g., sRGN) useful in the prime editors disclosed herein are provided below in SEQ ID NOs: 892-897. In some embodiments, a prime editor comprises a Cas9 protein, that lacks a N- terminus methionine relative to SEQ ID NO: 892 or SEQ ID NO: 895. In some embodiments, a prime editor comprises a Cas9 protein comprising one or more mutations (e.g., amino acid substitutions, insertions and / or deletions) relative to a corresponding Cas9 protein (e.g., a Cas9 protein set forth in SEQ ID NO: 892 or SEQ ID NO: 895). In some embodiments, the Cas9 protein comprising one or mutations relative to a corresponding Cas9 protein comprises an amino acid sequence set forth in any one of SEQ ID NOs: 893, 894, 896, or 897.

[0380] Table 2: Exemplary Cas protein sequencesWSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601

[0381] In some embodiments, a Cas9 protein comprises a variant Cas9 protein containing one or more amino acid substitutions. In some embodiments, a wildtype Cas9 protein comprises a RuvC domain andWSGR Docket No. 59761-791.601 an HNH domain. In some embodiments, a prime editor comprises a nuclease active Cas9 protein that may cleave both strands of a double stranded target DNA sequence. In some embodiments, the nuclease active Cas9 protein comprises a functional RuvC domain and a functional HNH domain. In some embodiments, a prime editor comprises a Cas9 nickase that can bind to a guide polynucleotide and recognize a target DNA, but can cleave only one strand of a double stranded target DNA. In some embodiments, the Cas9 nickase comprises only one functional RuvC domain or one functional HNH domain. In some embodiments, a prime editor comprises a Cas9 that has a non-functional HNH domain and a functional RuvC domain. In some embodiments, the prime editor can cleave the edit strand (i.e., the PAM strand), but not the non-edit strand of a double stranded target DNA sequence. In some embodiments, a prime editor comprises a Cas9 having a non-functional RuvC domain that can cleave the target strand (i.e., the non-PAM strand), but not the edit strand of a double stranded target DNA sequence. In some embodiments, a prime editor comprises a Cas9 that has neither a functional RuvC domain nor a functional HNH domain, which may not cleave any strand of a double stranded target DNA sequence.

[0382] In some embodiments, a prime editor comprises a Cas9 having a mutation in the RuvC domain that reduces or abolishes the nuclease activity of the RuvC domain. In some embodiments, the Cas9 comprises a mutation at amino acid D10 as compared to a wild type SpCas9 as set forth in SEQ ID NO: 873, or a corresponding mutation thereof. In some embodiments, the Cas9 comprises a D10A mutation as compared to a wild type SpCas9 as set forth in SEQ ID NO: 873, or a corresponding mutation thereof. In some embodiments, the Cas9 polypeptide comprises a mutation at amino acid D10, G12, and / or G17 as compared to a wild type SpCas9 as set forth in SEQ ID NO: 873, or a corresponding mutation thereof. In some embodiments, the Cas9 polypeptide comprises a D10A mutation, a G12A mutation, and / or a G17A mutation as compared to a wild type SpCas9 as set forth in SEQ ID NO: 873, or a corresponding mutation thereof.

[0383] In some embodiments, a prime editor comprises a Cas9 polypeptide having a mutation in the HNH domain that reduces or abolishes the nuclease activity of the HNH domain. In some embodiments, the Cas9 polypeptide comprises a mutation at amino acid H840 as compared to a wild type SpCas9 as set forth in SEQ ID NO: 873, or a corresponding mutation thereof. In some embodiments, the Cas9 polypeptide comprises a H840A mutation as compared to a wild type SpCas9 as set forth in SEQ ID NO: 873, or a corresponding mutation thereof. In some embodiments, the Cas9 polypeptide comprises a mutation at amino acid E762, D839, H840, N854, N856, N863, H982, H983, A984, D986, and / or a A987 as compared to a wild type SpCas9 as set forth in SEQ ID NO: 873, or a corresponding mutation thereof. In some embodiments, the Cas9 polypeptide comprises a E762A, D839A, H840A, N854A, N856A, N863A, H982A, H983A, A984A, and / or a D986A mutation as compared to a wild type SpCas9 as set forth in SEQ ID NO: 873, or a corresponding mutation thereof. In some embodiments, the Cas9 polypeptide comprises a mutation at amino acid residue R221, N394, and / or H840 as compared to a wildWSGR Docket No. 59761-791.601 type SpCas9 (e.g., SEQ ID NO: 873). In some embodiments, the Cas9 polypeptide comprises a R221K, N394L, and / or H840A mutation as compared to a wild type SpCas9 as set forth in SEQ ID NO: 873, or a corresponding mutation thereof. In some embodiments, the Cas9 polypeptide comprises a mutation at amino acid residue R220, N393, and / or H839 as compared to a wild type SpCas9 (e.g., SEQ ID NO: 873) lacking a N-terminal methionine, or a corresponding mutation thereof. In some embodiments, the Cas9 polypeptide comprises a R220K, N393K, and / or H839A mutation as compared to a wild type SpCas9 (as set forth in SEQ ID NO: 873) lacking a N-terminal methionine, or a corresponding mutation thereof.

[0384] In some embodiments, a prime editor comprises a Cas9 having one or more amino acid substitutions in both the HNH domain and the RuvC domain that reduce or abolish the nuclease activity of both the HNH domain and the RuvC domain. In some embodiments, the prime editor comprises a nuclease inactive Cas9, or a nuclease dead Cas9 (dCas9). In some embodiments, the dCas9 comprises a H840X substitution and a D10X mutation compared to a wild type SpCas9 as set forth in SEQ ID NO: 873or corresponding mutations thereof, wherein X is any amino acid other than H for the H840X substitution and any amino acid other than D for the D10X substitution. In some embodiments, the dead Cas9 comprises a H840A and a D10A mutation as compared to a wild type SpCas9 as set forth in SEQ ID NO: 873, or corresponding mutations thereof.

[0385] In some embodiments, the N-terminal methionine is removed from the amino acid sequence of a Cas9 nickase, or from any Cas9 variant, ortholog, or equivalent disclosed or contemplated herein. For example, methionine-minus (Met (-)) Cas9 nickases include any one of the sequences set forth in SEQ ID NOs: 875, 876, 879, 882, 885, 888, 891, 894, 897, 900, or a variant thereof having an amino acid sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto.

[0386] Besides dead Cas9 and Cas9 nickase variants, the Cas9 proteins used herein may also include other Cas9 variants having at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to any reference Cas9 protein, including any wild type Cas9, or mutant Cas9 (e.g., a dead Cas9 or Cas9 nickase), or fragment Cas9, or circular permutant Cas9, or other variant of Cas9 disclosed herein or known in the art. In some embodiments, a Cas9 variant may have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more amino acid changes compared to a reference Cas9, e.g., a wild type Cas9. In some embodiments, the Cas9 variant comprises a fragment of a reference Cas9 (e.g., a gRNA binding domain or a DNA-cleavage domain), such that the fragment is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to the corresponding fragment of a reference Cas9, e.g., a wild type Cas9. In some embodiments, theWSGR Docket No. 59761-791.601 fragment is at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% identical, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% of the amino acid length of a corresponding wild type Cas9.

[0387] In some embodiments, a Cas9 fragment is a functional fragment that retains one or more Cas9 activities. In some embodiments, the Cas9 fragment is at least 100 amino acids in length. In some embodiments, the fragment is at least 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, or at least 1300 amino acids in length.

[0388] In some embodiments, a prime editor comprises a Cas protein, e.g., a Cas9 variant, comprising modifications that allow altered PAM recognition. Exemplary Cas9 protein amino acid sequence (e.g., Cas9 variant with altered PAM recognition specificities) that are useful in the Prime editors of the disclosure are provided in Table 2. In some embodiments, a prime editor comprises a Cas protein, e.g., Cas9, containing modifications that allow altered PAM recognition. In prime editing using a Cas-protein- based prime editor, a “protospacer adjacent motif (PAM)”, PAM sequence, or PAM-like motif, may be used to refer to a short DNA sequence immediately following the protospacer sequence on the PAM strand of the target gene. In some embodiments, the PAM is recognized by the Cas nuclease in the prime editor during prime editing. In certain embodiments, the PAM is required for target binding of the Cas protein. The specific PAM sequence required for Cas protein recognition may depend on the specific type of the Cas protein. A PAM can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleotides in length. In some embodiments, a PAM is between 2- PAM (i.e. i.e., located -NGG- some embodiments, the Cas protein of a prime editor has altered or non-canonical PAM specificities. Exemplary PAM sequences and corresponding Cas variants are described in Table 3 below. It should be appreciated that for each of the variants provided, the Cas protein comprises one or more of the amino acid substitutions as indicated compared to a wild type Cas protein sequence, for example, the Cas9 as set forth in SEQ ID NO: 873. The PAM motifs as shown in Table 3 below are in the order of 5’ to 3’. In some embodiments, the Cas proteins of the disclosure can also be used to direct transcriptional control of target sequences, for example silencing transcription by sequence-specific binding to target sequences. In some embodiments, a Cas protein described herein may have one or mutations in a PAM recognition motif. In some embodiments, a Cas protein described herein may have altered PAM specificity.

[0389] As used in PAM sequences in Table 3, “N” refers to any one of nucleotides A, G, C, and T, “R” refers to nucleotide A or G, and “Y” refers to nucleotide C or T.

[0390] Table 3: Cas protein variants and corresponding PAM sequencesWSGR Docket No. 59761-791.601

[0391] In some embodiments, a prime editor comprises a Cas9 polypeptide comprising one or mutations selected from the group consisting of: A61R, L111R, D1135V, R221K, A262T, R324L, N394K, S409I, S409I, E427G, E480K, M495V, N497A, Y515N, K526E, F539S, E543D, R654L, R661A, R661L, R691A, N692A, M694A, M694I, Q695A, H698A, R753G, M763I, K848A, K890N, Q926A, K1003A, R1060A, L1111R, R1114G, D1135E, D1135L, D1135N, S1136W, V1139A, D1180G, G1218K,WSGR Docket No. 59761-791.601 G1218R, G1218S, E1219Q, E1219V, E1219V, Q1221H, P1249S, E1253K, N1317R, A1320V, P1321S, A1322R, I1322V, D1332G, R1332N, A1332R, R1333K, R1333P, R1335L, R1335Q, R1335V, T1337N, T1337R, S1338T, H1349R, and any combinations thereof as compared to a wildtype SpCas9 polypeptide as set forth in SEQ ID NO: 873.

[0392] In some embodiments, a prime editor comprises a SaCas9 polypeptide. In some embodiments, the SaCas9 polypeptide comprises one or more of mutations E782K, N968K, and R1015H as compared to a wild type SaCas9. In some embodiments, a prime editor comprises a FnCas9 polypeptide, for example, a wildtype FnCas9 polypeptide or a FnCas9 polypeptide comprising one or more of mutations E1369R, E1449H, or R1556A as compared to the wild type FnCas9. In some embodiments, a prime editor comprises a Sc Cas9, for example, a wild type ScCas9 or a ScCas9 polypeptide comprises one or more of mutations I367K, G368D, I369K, H371L, T375S, T376G, and T1227K as compared to the wild type ScCas9. In some embodiments, a prime editor comprises a St1 Cas9 polypeptide, a St3 Cas9 polypeptide, or a SluCas9 polypeptide.

[0393] In some embodiments, a prime editor comprises a Cas polypeptide that comprises a circular permutant Cas variant. For example, a Cas9 polypeptide of a prime editor may be engineered such that the N-terminus and the C-terminus of a Cas9 protein (e.g., a wild type Cas9 protein, or a Cas9 nickase) are topically rearranged to retain the ability to bind DNA when complexed with a guide RNA (gRNA). An exemplary circular permutant configuration may be N-terminus–[original C-terminus]–[original N- terminus]–C-terminus. Any of the Cas9 proteins described herein, including any variant, ortholog, or naturally occurring Cas9 or equivalent thereof, may be reconfigured as a circular permutant variant.

[0394] In various embodiments, the circular permutants of a Cas protein, e.g., a Cas9, may have the following structure: N-terminus–[original C-terminus]–[optional linker]–[original N-terminus]–C- terminus. In some embodiments, a circular permutant Cas9 comprises any one of the following structures (amino acid positions as set forth in SEQ ID NO: 873):

[0395] N-terminus–[1268-1368]–[optional linker]–[1-1267]–C-terminus;

[0396] N-terminus–[1168-1368]–[optional linker]–[1-1167]–C-terminus;

[0397] N-terminus–[1068-1368]–[optional linker]–[1-1067]–C-terminus;

[0398] N-terminus–[968-1368]–[optional linker]–[1-967]–C-terminus;

[0399] N-terminus–[868-1368]–[optional linker]–[1-867]–C-terminus;

[0400] N-terminus–[768-1368]–[optional linker]–[1-767]–C-terminus;

[0401] N-terminus–[668-1368]–[optional linker]–[1-667]–C-terminus;

[0402] N-terminus–[568-1368]–[optional linker]–[1-567]–C-terminus;

[0403] N-terminus–[468-1368]–[optional linker]–[1-467]–C-terminus;

[0404] N-terminus–[368-1368]–[optional linker]–[1-367]–C-terminus;

[0405] N-terminus–[268-1368]–[optional linker]–[1-267]–C-terminus;

[0406] N-terminus–[168-1368]–[optional linker]–[1-167]–C-terminus;WSGR Docket No. 59761-791.601

[0407] N-terminus–[68-1368]–[optional linker]–[1-67]–C-terminus;

[0408] N-terminus–[10-1368]–[optional linker]–[1-9]–C-terminus, or the corresponding circular permutants of other Cas9 proteins (including other Cas9 orthologs, variants, etc.).

[0409] In some embodiments, a circular permutant Cas9 comprises any one of the following structures (amino acid positions as set forth in SEQ ID NO: 873-876 amino acids of UniProtKB - Q99ZW2:

[0410] N-terminus–[102-1368]–[optional linker]–[1-101]–C-terminus;

[0411] N-terminus–[1028-1368]–[optional linker]–[1-1027]–C-terminus;

[0412] N-terminus–[1041-1368]–[optional linker]–[1-1043]–C-terminus;

[0413] N-terminus–[1249-1368]–[optional linker]–[1-1248]–C-terminus; or

[0414] N-terminus–[1300-1368]–[optional linker]–[1-1299]–C-terminus, or the corresponding circular permutants of other Cas9 proteins (including other Cas9 orthologs, variants, etc.).

[0415] In some embodiments, a circular permutant Cas9 comprises any one of the following structures (amino acid positions as set forth in SEQ ID NO: 873-876 amino acids of UniProtKB - Q99ZW2 N- terminus–[103-1368]–[optional linker]–[1-102]–C-terminus:

[0416] N-terminus–[1029-1368]–[optional linker]–[1-1028]–C-terminus;

[0417] N-terminus–[1042-1368]–[optional linker]–[1-1041]–C-terminus;

[0418] N-terminus–[1250-1368]–[optional linker]–[1-1249]–C-terminus; or

[0419] N-terminus–[1301-1368]–[optional linker]–[1-1300]–C-terminus, or the corresponding circular permutants of other Cas9 proteins (including other Cas9 orthologs, variants, etc.).

[0420] In some embodiments, the circular permutant can be formed by linking a C-terminal fragment of a Cas9 to an N-terminal fragment of a Cas9, either directly or by using a linker, such as an amino acid linker. In some embodiments, thee C-terminal fragment may correspond to the 95% or more of the C- terminal amino acids of a Cas9 (e.g., amino acids about 1300-1368 as set forth in SEQ ID No: 873 or corresponding amino acid positions thereof), or the 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, or 5% or more of the C-terminal amino acids of a Cas9 (e.g., SEQ ID NO 873 or a ortholog or a variant thereof). The N-terminal portion may correspond to 95% or more of the N-terminal amino acids of a Cas9 (e.g., amino acids about 1-1300 as set forth in SEQ ID NO: 873 or corresponding amino acid positions thereof), or 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, or 5% or more of the N terminal amino acids of a Cas9 (e.g., as set forth in SEQ ID NO: 873 or corresponding amino acid positions thereof).

[0421] In some embodiments, the circular permutant can be formed by linking a C-terminal fragment of a Cas9 to an N-terminal fragment of a Cas9, either directly or by using a linker, such as an amino acid linker. In some embodiments, the C-terminal fragment that is rearranged to the N-terminus includes or corresponds to the C-terminal 30% or less of the amino acids of a Cas9 (e.g., amino acids 1012-1368 as set forth in SEQ ID NO: 873 or corresponding amino acid positions thereof). In some embodiments, the C-terminal fragment that is rearranged to the N-terminus, includes or corresponds to the C-terminal 30%,WSGR Docket No. 59761-791.601 29%, 28%, 27%, 26%, 25%, 24%, 23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%,5%, 4%, 3%, 2%, or 1% of the amino acids of a Cas9 (e.g., as set forth in SEQ ID NO: 873 or corresponding amino acid positions thereof). In some embodiments, the C-terminal fragment that is rearranged to the N-terminus, includes or corresponds to the C-terminal 410 residues or less of a Cas9 (e.g., as set forth in SEQ ID No: 873 or corresponding amino acid positions thereof). In some embodiments, the C-terminal portion that is rearranged to the N-terminus, includes or corresponds to the C-terminal 410, 400, 390, 380, 370, 360, 350, 340, 330, 320, 310, 300, 290, 280, 270, 260, 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60, 50, 40, 30, 20, or 10 residues of a Cas9 ( e.g., as set forth in SEQ ID NO: 873 or corresponding amino acid positions thereof). In some embodiments, the C-terminal portion that is rearranged to the N-terminus includes or corresponds to the C-terminal 357, 341, 328, 120, or 69 residues of a Cas9 (e.g., as set forth in SEQ ID NO: 873 or corresponding amino acid positions thereof).

[0422] In other embodiments, circular permutant Cas9 variants may be a topological rearrangement of a Cas9 primary structure based on the following method, which is based on S. pyogenes Cas9 of SEQ ID NO: 873: (a) selecting a circular permutant (CP) site corresponding to an internal amino acid residue of the Cas9 primary structure, which dissects the original protein into two halves: an N-terminal region and a C-terminal region; (b) modifying the Cas9 protein sequence (e.g., by genetic engineering techniques) by moving the original C-terminal region (comprising the CP site amino acid) to precede the original N- terminal region, thereby forming a new N-terminus of the Cas9 protein that now begins with the CP site amino acid residue. The CP site can be located in any domain of the Cas9 protein, including, for example, the helical-II domain, the RuvCIII domain, or the CTD domain. For example, the CP site may be located (as set forth in SEQ ID NO: 873 or corresponding amino acid positions thereof) at original amino acid residue 181, 199, 230, 270, 310, 1010, 1016, 1023, 1029, 1041, 1247, 1249, or 1282. Thus, once relocated to the N-terminus, original amino acid 181, 199, 230, 270, 310, 1010, 1016, 1023, 1029, 1041, 1247, 1249, or 1282 would become the new N-terminal amino acid. Nomenclature of these CP-Cas9 proteins may be referred to as Cas9-CP181, Cas9-CP199, Cas9-CP230, Cas9-CP270, Cas9-CP310, Cas9-CP1010, Cas9- CP1016, Cas9-CP1023, Cas9-CP1029, Cas9-CP1041, Cas9-CP1247, Cas9-CP1249, and Cas9-CP1282, respectively. This description is not meant to be limited to making CP variants from SEQ ID NO: 873, but may be implemented to make CP variants in any Cas9 sequence, either at CP sites that correspond to these positions, or at other CP sites entirely. This description is not meant to limit the specific CP sites in any way. Virtually any CP site may be used to form a CP-Cas9 variant.

[0423] In some embodiments, a prime editor comprises a Cas9 functional variant that is of smaller molecular weight than a wild type SpCas9 protein. In some embodiments, a smaller-sized Cas9 functional variant may facilitate delivery to cells, e.g., by an expression vector, nanoparticle, or other means of delivery. In certain embodiments, a smaller-sized Cas9 functional variant is a Class 2 Type II Cas protein. In certain embodiments, a smaller-sized Cas9 functional variant is a Class 2 Type V CasWSGR Docket No. 59761-791.601 protein. In certain embodiments, a smaller-sized Cas9 functional variant is a Class 2 Type VI Cas protein.

[0424] In some embodiments, a prime editor comprises a SpCas9 that is 1368 amino acids in length and has a predicted molecular weight of 158 kilodaltons. In some embodiments, a prime editor comprises a Cas9 functional variant or functional fragment that is less than 1300 amino acids, less than 1290 amino acids, than less than 1280 amino acids, less than 1270 amino acids, less than 1260 amino acid, less than 1250 amino acids, less than 1240 amino acids, less than 1230 amino acids, less than 1220 amino acids, less than 1210 amino acids, less than 1200 amino acids, less than 1190 amino acids, less than 1180 amino acids, less than 1170 amino acids, less than 1160 amino acids, less than 1150 amino acids, less than 1140 amino acids, less than 1130 amino acids, less than 1120 amino acids, less than 1110 amino acids, less than 1100 amino acids, less than 1050 amino acids, less than 1000 amino acids, less than 950 amino acids, less than 900 amino acids, less than 850 amino acids, less than 800 amino acids, less than 750 amino acids, less than 700 amino acids, less than 650 amino acids, less than 600 amino acids, less than 550 amino acids, or less than 500 amino acids, but at least larger than about 400 amino acids and retaining the one or more functions, e.g., DNA binding function, of the Cas9 protein.

[0425] In some embodiments, the Cas protein may include any CRISPR associated protein, including but not limited to, Cas12a, Cas12b1, Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, homologs thereof, or modified versions thereof, and preferably comprising a nickase mutation (e.g., a mutation corresponding to the D10A mutation of the wild type Cas9 polypeptide of SEQ ID NO: 873). In various other embodiments, the napDNAbp can be any of the following proteins: a Cas9, a Cas12a (Cpf1), a Cas12e (CasX), a Cas12d (CasY), a Cas12b1 (C2c1), a Cas13a (C2c2), a Cas12c (C2c3), a GeoCas9, a CjCas9, a Cas12g, a Cas12h, a Cas12i, a Cas13b, a Cas13c, a Cas13d, a Cas14, a Csn2, an xCas9, an SpCas9-NG, a circularly permuted Cas9, or an Argonaute (Ago) domain, or a functional variant or fragment thereof.

[0426] Exemplary Cas proteins and nomenclature are shown in Table 4 below: Table 4: Exemplary Cas proteins and nomenclatureWSGR Docket No. 59761-791.601

[0427] In some embodiments, prime editors described herein may also comprise Cas proteins other than Cas9. For example, in some embodiments, a prime editor as described herein may comprise a Cas12a (Cpf1) polypeptide or functional variants thereof. In some embodiments, the Cas12a polypeptide comprises a mutation that reduces or abolishes the endonuclease domain of the Cas12a polypeptide. In some embodiments, the Cas12a polypeptide is a Cas12a nickase. In some embodiments, the Cas protein comprises an amino acid sequence that comprises at least about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a naturally occurring Cas12a polypeptide.

[0428] In some embodiments, a prime editor comprises a Cas protein that is a Cas12b (C2c1) or a Cas12c (C2c3) polypeptide. In some embodiments, the Cas protein comprises an amino acid sequence that comprises at least about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a naturally occurring Cas12b (C2c1) or Cas12c (C2c3) protein. In some embodiments, the Cas protein is a Cas12b nickase or a Cas12c nickase. In some embodiments, the Cas protein is a Cas12e, a Cas12d, a Cas13, Cas14a, Cas14b, Cas14c, Cas14d, Cas14e, Cas14f, Cas14g, Cas14h, Cas14u, sequence that comprises at least about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a naturally-occurring Cas12e, Cas12d, Cas13, Cas14a, Cas14b, Cas14c, Cas14d, Cas14e, Cas14f, Cas14g, Cas14h, Cas14u, Nuclear Localization Sequences

[0429] In some embodiments, a prime editor further comprises one or more nuclear localization sequence (NLS). In some embodiments, the NLS helps promote translocation of a protein into the cell nucleus. In some embodiments, a prime editor comprises a fusion protein, e.g., a fusion protein comprising a DNA binding domain and a DNA polymerase, that comprises one or more NLSs. In some embodiments, one or more polypeptides of the prime editor are fused to or linked to one or more NLSs. In some embodiments, the prime editor comprises a DNA binding domain and a DNA polymerase domain that are provided in trans, wherein the DNA binding domain and / or the DNA polymerase domain is fused or linked to one or more NLSs.WSGR Docket No. 59761-791.601

[0430] In certain embodiments, a prime editor or prime editing complex comprises at least one NLS. In some embodiments, a prime editor or prime editing complex comprises at least two NLSs. In some embodiments, a prime editor or prime editing complex comprises at least three NLSs. In some embodiments, a prime editor or prime editing complex comprises more than 4, 5, 6, 7, 8, 9 or 10 NLSs. In embodiments with at least two NLSs, the NLSs can be the same NLS, or they can be different NLSs. In some embodiments, the one or more NLSs of a prime editor comprise bipartite NLSs.

[0431] NLSs can be expressed as part of a prime editor complex. In some embodiments, a NLS can be positioned almost anywhere in a protein's amino acid sequence, and generally comprises a short sequence of three or more or four or more amino acids. The location of the NLS fusion can be at the N-terminus, the C-terminus, or positioned anywhere within a sequence of a prime editor or a component thereof (e.g., inserted between the DNA-binding domain and the DNA polymerase domain of a prime editor fusion protein, between the DNA binding domain and a linker sequence, between a DNA polymerase and a linker sequence, between two linker sequences of a prime editor fusion protein or a component thereof, in either N-terminus to C-terminus or C-terminus to N-terminus order). In some embodiments, a prime editor is fusion protein that comprises an NLS at the N terminus. In some embodiments, a prime editor is fusion protein that comprises an NLS at the C terminus. In some embodiments, a prime editor is fusion protein that comprises at least one NLS at both the N terminus and the C terminus. In some embodiments, the prime editor is a fusion protein that comprises two NLSs at the N terminus and / or the C terminus.

[0432] Any NLSs that are known in the art are also contemplated herein. The NLSs may be any naturally occurring NLS, or any non-naturally occurring NLS (e.g., an NLS with one or more mutations relative to a wild-type NLS). In some embodiments, a nuclear localization signal (NLS) is predominantly basic. In some embodiments, the one or more NLSs of a prime editor are rich in lysine and arginine residues. In some embodiments, the one or more NLSs of a prime editor comprise proline residues.

[0433] Non-limiting examples of NLS sequences suitable for use with methods and compositions of the disclosure are provided in Table 5.

[0434] In some embodiments, a NLS is a monopartite NLS. For example, in some embodiments, a NLS is a SV40 large T antigen NLS comprising the sequence SEQ ID NO: 901. In some embodiments, a NLS is a bipartite NLS. In some embodiments, a bipartite NLS comprises two basic domains separated by a spacer sequence comprising a variable number of amino acids. In some embodiments, a NLS is a bipartite NLS. In some embodiments, a bipartite NLS consists of two basic domains separated by a spacer sequence comprising a variable number of amino acids. In some embodiments, the spacer amino acid sequence comprises a Xenopus nucleoplasmin NLS SEQ ID NO: 919, wherein X is any amino acid. In some embodiments, the NLS comprises a nucleoplasmin NLS sequence SEQ ID NO: 918. In some embodiments, a NLS is a noncanonical sequences such as M9 of the hnRNP Al protein, the influenza virus nucleoprotein NLS, and the yeast Gal4 protein NLS.WSGR Docket No. 59761-791.601

[0435] In some embodiments, a NLS comprises an amino acid sequence that is at least about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence provided in Table 5.. In some embodiments, a NLS comprises an amino acid sequence selected from the group consisting of the amino acid sequences provided in Table 5. In some embodiments, a prime editing composition comprises a polynucleotide that encodes a NLS that comprises an amino acid sequence that is at least about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence provided in Table 5. In some embodiments, a prime editing composition comprises a polynucleotide that encodes a NLS that comprises an amino acid sequence provided in Table 5.

[0436] Table 5: Exemplary nuclear localization sequences

[0437] Components of a prime editor may be connected to each other in any order. In some embodiments, the DNA binding domain and the DNA polymerase domain of a prime editor may be fused to form a fusion protein, or may be joined by a peptide or protein linker, in any order from the N terminus to the C terminus. In some embodiments, a prime editor comprises a DNA binding domain fused or linked to the C-terminal end of a DNA polymerase domain. In some embodiments, a prime editor comprises a DNA binding domain fused or linked to the N-terminal end of a DNA polymeraseWSGR Docket No. 59761-791.601 domain. In some embodiments, the prime editor comprises a fusion protein comprising the structure NH2–[DNA binding domain]–[polymerase]–COOH; or NH2–[polymerase]–[DNA binding domain]– COOH, wherein each instance ofindicates the presence of an optional linker sequence. In some embodiments, a prime editor comprises a fusion protein and a DNA polymerase domain provided in trans, wherein the fusion protein comprises the structure NH2–[DNA binding domain]–[RNA-protein recruitment polypeptide]–COOH. In some embodiments, a prime editor comprises a fusion protein and a DNA binding domain provided in trans, wherein the fusion protein comprises the structure NH2–[DNA polymerase domain]–[RNA-protein recruitment polypeptide]–COOH.

[0438] In some embodiments, a prime editor fusion protein, a polypeptide component of a prime editor, or a polynucleotide encoding the prime editor fusion protein or polypeptide component, may be split into an N-terminal half and a C-terminal half or polypeptides that encode the N-terminal half and the C terminal half, and provided to a target DNA in a cell separately. For example, in certain embodiments, a prime editor fusion protein may be split into a N-terminal and a C-terminal half for separate delivery in AAV vectors, and subsequently translated and colocalized in a target cell to reform the complete polypeptide or prime editor protein. In such cases, separate halves of a protein or a fusion protein may each comprise a split-intein to facilitate colocalization and reformation of the complete protein or fusion protein by the mechanism of intein facilitated trans splicing. In some embodiments, a prime editor comprises a N-terminal half fused to an intein-N, and a C-terminal half fused to an intein-C, or polynucleotides or vectors (e.g., AAV vectors) encoding each thereof. When delivered and / or expressed in a target cell, the intein-N and the intein-C can be excised via protein trans-splicing, resulting in a complete prime editor fusion protein in the target cell. In some embodiments, an exemplary protein described herein may lack a methionine residue at the N-terminus.

[0439] In some embodiments, a prime editor fusion protein comprises a Cas9(H840A) nickase and a wild type M-MLV RT. In some embodiments, a prime editor fusion protein comprises a Cas9(H840A) nickase and a M-MLV RT that comprises amino acid substitutions D200N, T330P, T306K, W313F, and L603W compared to a wild type M-MLV RT. In some embodiments, a prime editor fusion protein comprises a Cas9(H840A) nickase and a M-MLV RT that comprises amino acid substitutions D200N, T330P, T306K, W313F, and L603W compared to a wild type M-MLV RT or a variant M-MLV RT of SEQ ID NO: 871. The amino acid sequence of an exemplary prime editor fusion protein and its individual components is shown in Table 6.

[0440] In some embodiments, a prime editor fusion protein comprises a Cas9 (R221K N394K H840A) nickase and a M-MLV RT that comprises amino acid substitutions D200N, T330P, T306K, W313F, and L603W compared to a wild type M-MLV RT or a variant M-MLV RT of SEQ ID NO: 871. The amino acid sequence of an exemplary Prime editor fusion protein and its individual components in shown in Table 7.WSGR Docket No. 59761-791.601

[0441] In some embodiments an exemplary prime editor protein may comprise an amino acid sequence as set forth in any of the SEQ ID NO: 920 or SEQ ID NO: 922.

[0442] In various embodiments, a prime editor fusion protein comprises an amino acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to PE1, PE2, or any of the prime editor fusion sequences described herein or known in the art.

[0443] In some embodiments, a prime editing complex comprises a fusion protein comprising a DNA binding domain (e.g., Cas9(H840A)) and a reverse transcriptase (e.g., a variant MMLV RT) having the following structure: [NLS]–[Cas9(H840A)]–[linker]– [MMLV_RT(D200N)(T330P)(L603W)(T306K)(W313F)], and a desired PEgRNA. In some embodiments, the prime editing complex comprises a prime editor fusion protein that has the amino acid sequence of SEQ ID NO: 920. Sequence of an exemplary prime editor fusion protein comprising a DNA binding domain (e.g., Cas9(H840A)) and a reverse transcriptase (e.g., a variant MMLV RT) having the following structure: [NLS]- [Cas9(H840A)]-[linker]- [MMLV_RT(D200N)(T330P)(L603W)(T306K)(W313F)] and its components are shown in Table 6.

[0444] In some embodiments, a prime editor or its components comprise an amino acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 91% identical, at least about 92% identical, at least about 93% identical, at least about 94% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, at least about 99.9% identical or 100% identical to a sequence in Table 6. In some embodiments, the prime editor or its components comprise an amino acid sequence that has no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 differences e.g., mutations e.g., deletions, substitutions and / or insertions compared to any one of the amino acid sequences set forth in Table 6.

[0445] Table 6: lists exemplary prime editor and its componentsWSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601

[0446] In some embodiments, a prime editing complex comprises a fusion protein comprising a DNA binding domain (e.g., Cas9((R221K N394K H840A)) and a reverse transcriptase (e.g., a variant MMLV RT) having the following structure: [NLS]- [Cas9((R221K N394K H840A)]-[linker]-WSGR Docket No. 59761-791.601 [MMLV_RT(D200N)(T330P)(L603W)(T306K)(W313F)], and a desired PEgRNA. In some embodiments, the prime editing complex comprises a prime editor fusion protein that has the amino acid sequence of SEQ ID NO: 922. Sequence of an exemplary prime editor fusion protein comprising a DNA binding domain (e.g., Cas9(H840A)) and a reverse transcriptase (e.g., a variant MMLV RT) having the following structure: [NLS]- [Cas9 (R221K N394K H840A)]-[linker]- [MMLV_RT(D200N)(T330P)(L603W)(T306K)(W313F)] and its components are shown in Table 7.

[0447] In some embodiments, a prime editor or its components comprises an amino acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 91% identical, at least about 92% identical, at least about 93% identical, at least about 94% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, at least about 99.9% identical or 100% identical to a sequence in Table 7. In some embodiments, the prime editor or its components comprise an amino acid sequence that has no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 differences e.g., mutations e.g., deletions, substitutions and / or insertions compared to any one of the amino acid sequences set forth in Table 7.

[0448] Table 7: lists exemplary prime editor and its componentsWSGR Docket No. 59761-791.601WSGR Docket No. 59761-791.601

[0449] Polypeptides comprising components of a prime editor may be fused via peptide linkers, or may be provided in trans relevant to each other. For example, a reverse transcriptase may be expressed, delivered, or otherwise provided as an individual component rather than as a part of a fusion protein with the DNA binding domain. In such cases, components of the prime editor may be associated through non- peptide linkages or co-localization functions. In some embodiments, a prime editor further comprises additional components capable of interacting with, associating with, or capable of recruiting other components of the prime editor or the prime editing system. For example, a prime editor may comprise an RNA-protein recruitment polypeptide that can associate with an RNA-protein recruitment RNA aptamer. In some embodiments, an RNA-protein recruitment polypeptide can recruit, or be recruited by, a specific RNA sequence. Non limiting examples of RNA-protein recruitment polypeptide and RNA aptamer pairs include a MS2 coat protein and a MS2 RNA hairpin, a PCP polypeptide and a PP7 RNA hairpin, a Com polypeptide and a Com RNA hairpin, a Ku protein and a telomerase Ku binding RNAWSGR Docket No. 59761-791.601 motif, and a Sm7 protein and a telomerase Sm7 binding RNA motif. In some embodiments, the prime editor comprises a DNA binding domain fused or linked to an RNA-protein recruitment polypeptide. In some embodiments, the prime editor comprises a DNA polymerase domain fused or linked to an RNA- protein recruitment polypeptide. In some embodiments, the DNA binding domain and the DNA polymerase domain fused to the RNA-protein recruitment polypeptide, or the DNA binding domain fused to the RNA-protein recruitment polypeptide and the DNA polymerase domain are co-localized by the corresponding RNA-protein recruitment RNA aptamer of the RNA-protein recruitment polypeptide. In some embodiments, the corresponding RNA-protein recruitment RNA aptamer fused or linked to a portion of the PEgRNA or ngRNA. For example, an MS2 coat protein fused or linked to the DNA polymerase and a MS2 hairpin installed on the PEgRNA for co-localization of the DNA polymerase and the RNA-guided DNA binding domain (e.g., a Cas9 nickase). In certain embodiments, components of a prime editor are directly fused to each other. In certain embodiments, components of a prime editor are associated to each other via a linker.

[0450] In some embodiments, a prime editor comprises a polypeptide domain, an MS2 coat protein (MCP), that recognizes an MS2 hairpin. In some embodiments, the nucleotide sequence of the MS2 hairpin (or equivalently referred to as the “MS2 aptamer”) is a sequence provided in Table 8.

[0451] Table 8: Exemplary MS2 hairpin and MCP sequences

[0452] As used herein, a linker can be any chemical group or a molecule linking two molecules or moieties, e.g., a DNA binding domain and a polymerase domain of a prime editor. In some embodiments, a linker is an organic molecule, group, polymer, or chemical moiety. In some embodiments, the linker comprises a non-peptide moiety. The linker may be as simple as a covalent bond, or it may be a polymeric linker many atoms in length, for example, a polynucleotide sequence. In certain embodiments, the linker is a covalent bond (e.g., a carbon-carbon bond, disulfide bond, carbon-heteroatom bond, etc.).

[0453] In certain embodiments, two or more components of a prime editor are linked to each other by a peptide linker. In some embodiments, a peptide linker is 5-100 amino acids in length, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35- 40, 40-45, 45-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length. In some embodiments, the peptide linker is 16 amino acids in length, 24 amino acids in length, 64 amino acids in length, or 96 amino acids in length. In some embodiments, a linker comprises 1-100 amino acids.

[0454] Non-limiting examples of linkers are provided in Table 9. In some embodiments, a linker comprises any one of the amino acid sequences set forth in Table 9, or any combination thereof.WSGR Docket No. 59761-791.601

[0455] Table 9. Illustrative Peptide Linker Sequences

[0456] In certain embodiments, two or more components of a prime editor are linked to each other by a non-peptide linker. In some embodiments, the linker is a carbon-nitrogen bond of an amide linkage. In certain embodiments, the linker is a cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic or heteroaliphatic linker. In certain embodiments, the linker is polymeric (e.g., polyethylene, polyethylene glycol, polyamide, polyester, etc.). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminoalkanoic acid. In certain embodiments, the linker comprises an aminoalkanoic acid (e.g., glycine, ethanoic acid, alanine, beta-alanine, 3- aminopropanoic acid, 4-aminobutanoic acid, 5-pentanoic acid, etc.). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminohexanoic acid (Ahx). In certain embodiments, the linker is based on a carbocyclic moiety (e.g., cyclopentane, cyclohexane). In other embodiments, the linker comprises a polyethylene glycol moiety (PEG). In certain embodiments, the linker comprises an aryl or heteroarylWSGR Docket No. 59761-791.601 moiety. In certain embodiments, the linker is based on a phenyl ring. The linker may include functionalized moieties to facilitate attachment of a nucleophile (e.g., thiol, amino) from the peptide to the linker. Any electrophile may be used as part of the linker. Exemplary electrophiles include, but are not limited to, activated esters, activated amides, Michael acceptors, alkyl halides, aryl halides, acyl halides, and isothiocyanates. PEgRNA for editing of RHO gene

[0457] The term “prime editing guide RNA”, or “PEgRNA”, refers to a guide polynucleotide that comprises one or more intended nucleotide edits for incorporation into the target DNA. In some embodiments, the PEgRNA associates with and directs a prime editor to incorporate the one or more intended nucleotide edits into the target gene via prime editing. “Nucleotide edit” or “intended nucleotide edit” refers to a specified deletion of one or more nucleotides at one specific position, insertion of one or more nucleotides at one specific position, substitution of a single nucleotide, or other alterations at one specific position to be incorporated into the sequence of the target gene. Intended nucleotide edit may refer to the edit on the editing template as compared to the sequence on the target strand of the target gene, or may refer to the edit encoded by the editing template on the newly synthesized single stranded DNA that replaces the editing target sequence, as compared to the editing target sequence. In some embodiments, a PEgRNA comprises a spacer sequence that is complementary or substantially complementary to a search target sequence on a target strand of the target gene. In some embodiments, the PEgRNA comprises a gRNA core that associates with a DNA binding domain, e.g., a CRISPR-Cas protein domain, of a prime editor. In some embodiments, the PEgRNA further comprises an extended nucleotide sequence comprising one or more intended nucleotide edits compared to the endogenous sequence of the target gene, wherein the extended nucleotide sequence may be referred to as an extension arm.

[0458] In certain embodiments, the extension arm comprises a primer binding site sequence (PBS) that can initiate target-primed DNA synthesis. In some embodiments, the PBS is complementary or by the prime editor. In some embodiments, the extension arm further comprises an editing template that comprises one or more intended nucleotide edits to be incorporated in the target gene by prime editing. In some embodiments, the editing template is a template for an RNA-dependent DNA polymerase domain or polypeptide of the prime editor, for example, a reverse transcriptase domain. The reverse transcriptase editing template may also be referred to herein as an RT template, or RTT. In some embodiments, the editing template comprises partial complementarity to an editing target sequence in the target gene, e.g., an RHO gene. In some embodiments, the editing template comprises substantial or partial complementarity to the editing target sequence except at the position of the intended nucleotideWSGR Docket No. 59761-791.601 edits to be incorporated into the target gene. An exemplary architecture of a PEgRNA including its components is as demonstrated in FIG. 2.

[0459] In some embodiments, a PEgRNA includes only RNA nucleotides and forms an RNA polynucleotide. In some embodiments, a PEgRNA is a chimeric polynucleotide that includes both RNA and DNA nucleotides. For example, a PEgRNA can include DNA in the spacer sequence, the gRNA core, or the extension arm. In some embodiments, a PEgRNA comprises DNA in the spacer sequence. In some embodiments, the entire spacer sequence of a PEgRNA is a DNA sequence. In some embodiments, the PEgRNA comprises DNA in the gRNA core, for example, in a stem region of the gRNA core. In some embodiments, the PEgRNA comprises DNA in the extension arm, for example, in the editing template. An editing template that comprises a DNA sequence may serve as a DNA synthesis template for a DNA polymerase in a prime editor, for example, a DNA-dependent DNA polymerase. Accordingly, the PEgRNA may be a chimeric polynucleotide that comprises RNA in the spacer, gRNA core, and / or the PBS sequences and DNA in the editing template.

[0460] Components of a PEgRNA may be arranged in a modular fashion. In some embodiments, the spacer and the extension arm comprising a primer binding site sequence (PBS) and an editing template, e.g. embodiments, a In some embodiments, the gRNA core of a PEgRNA of this disclosure may be located in between a spacer and an extension arm of the PEgRNA. In some embodiments, the gRNA some em , a gRNA core, an editing template, spacer, and a gRNA core.

[0461] In some embodiments, a PEgRNA comprises a single polynucleotide molecule that comprises the spacer sequence, the gRNA core, and the extension arm. In some embodiments, a PEgRNA comprises multiple polynucleotide molecules, for example, two polynucleotide molecules. In some embodiments, a PEgRNA comprise a first polynucleotide molecule that comprises the spacer and a portion of the gRNA core, and a second polynucleotide molecule that comprises the rest of the gRNA core and the extension arm. In some embodiments, the gRNA core portion in the first polynucleotide molecule and the gRNA core portion in the second polynucleotide molecule are at least partly complementary to each other. In some embodiments, the PEgRNA may comprise a first polynucleotideWSGR Docket No. 59761-791.601 comprising the spacer and a first portion of a gRNA core comprising, which may be also be referred to as a crRNA. In some embodiments, the PEgRNA comprise a second polynucleotide comprising a second portion of the gRNA core and the extension arm, wherein the second portion of the gRNA core may also be referred to as a trans-activating crRNA, or tracr RNA. In some embodiments, the crRNA portion and the tracr RNA portion of the gRNA core are at least partially complementary to each other. In some embodiments, the partially complementary portions of the crRNA and the tracr RNA form a lower stem, a bulge, and an upper stem, as exemplified in FIG. 3.

[0462] In some embodiments, a spacer sequence comprises a region that has substantial complementarity to a search target sequence on the target strand of a double stranded target DNA, e.g., an RHO gene. In some embodiments, the spacer sequence of a PEgRNA is identical or substantially identical to a protospacer sequence on the edit strand of the target gene (except that the protospacer sequence comprises thymine and the spacer sequence may comprise uracil). In some embodiments, the spacer sequence is at least about 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to a search target sequence in the target gene. In some embodiments, the spacer comprises is substantially complementary to the search target sequence.

[0463] In some embodiments, the length of the spacer varies from about 10 to about 100 nucleotides. In some embodiments, the spacer is 16 nucleotides, 17 nucleotides, 18 nucleotides, 19 nucleotides, 20 nucleotides, 21 nucleotides, 22 nucleotides, 23 nucleotides, 24 nucleotides, or 25 nucleotides in length. In some embodiments, the spacer is from 15 nucleotides to 30 nucleotides in length, 15 to 25 nucleotides in length, 18 to 22 nucleotides in length, 10 to 20 nucleotides in length, or 20 to 30 nucleotides in length. In some embodiments, the spacer is 16 to 22 nucleotides in length, e.g., about 16, 17, 18, 19, 20, 21, or 22 nucleotides in length.

[0464] As used herein in a PEgRNA or a nick guide RNA sequence, or fragments thereof such as a spacer, PBS, or RTT sequence, unless indicated otherwise, it should be appreciated that the letter “T” or “thymine” indicates a nucleobase in a DNA sequence that encodes the PEgRNA or guide RNA sequence, and is intended to refer to a uracil (U) nucleobase of the PEgRNA or guide RNA or any chemically modified uracil nucleobase known in the art, such as 5-methoxyuracil.

[0465] The extension arm of a PEgRNA may comprise a primer binding site (PBS) and an editing template (e.g., an RTT). The extension arm may be partially complementary to the spacer. In some embodiments, the editing template (e.g., RTT) is partially complementary to the spacer. In some embodiments, the editing template (e.g., RTT) and the primer binding site (PBS) are each partially complementary to the spacer.

[0466] An extension arm of a PEgRNA may comprise a primer binding site sequence (PBS, or PBS sequence) that comprises complementarity to and can hybridize with a f DNA in the target gene (e.g., the RHO gene) generated by nicking with a prime editor at the nick site on the PAM strand.WSGR Docket No. 59761-791.601

[0467] The length of the PBS sequence may vary depending on, e.g., the prime editor components, the search target sequence and other components of the PEgRNA.

[0468] In some embodiments, the PBS is about 3 to 19 nucleotides in length. in some embodiments, the PBS is about 3 to 17 nucleotides in length. In some embodiments, the PBS is about 4 to 16 nucleotides, about 6 to 16 nucleotides, about 6 to 18 nucleotides, about 6 to 20 nucleotides, about 8 to 20 nucleotides, about 10 to 20 nucleotides, about 12 to 20 nucleotides, about 14 to 20 nucleotides, about 16 to 20 nucleotides, or about 18 to 20 nucleotides in length. In some embodiments, the PBS is 8 to 17 nucleotides in length. In some embodiments, the PBS is 8 to 16 nucleotides in length. In some embodiments, the PBS is 8 to 15 nucleotides in length. In some embodiments, the PBS is 8 to 14 nucleotides in length. In some embodiments, the PBS is 8 to 13 nucleotides in length. In some embodiments, the PBS is 8 to 12 nucleotides in length. In some embodiments, the PBS is 8 to 11 nucleotides in length. In some embodiments, the PBS is 8 to 10 nucleotides in length. In some embodiments, the PBS is 8 or 9 nucleotides in length. In some embodiments, the PBS is 16 or 17 nucleotides in length. In some embodiments, the PBS is 15 to 17 nucleotides in length. In some embodiments, the PBS is 14 to 17 nucleotides in length. In some embodiments, the PBS is 13 to 17 nucleotides in length. In some embodiments, the PBS is 12 to 17 nucleotides in length. In some embodiments, the PBS is 11 to 17 nucleotides in length. In some embodiments, the PBS is 10 to 17 nucleotides in length. In some embodiments, the PBS is 9 to 17 nucleotides in length. In some embodiments, the PBS is about 7 to 15 nucleotides in length. In some embodiments, the PBS is 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides in length. In some embodiments, the PBS is 8 to 14 nucleotides in length. For example, the PBS can be 8, 9, 10, 11, 12, 13, or 14 nucleotides in length. In some embodiments, the PBS is 11 or 12 nucleotides in length. In some embodiments, the PBS is 11 to 13 nucleotides in length. In some embodiments, the PBS is 11 to 14 nucleotides in length.

[0469] The PBS may be complementary or substantially complementary to a DNA sequence in the edit strand of the target gene. By annealing with the edit strand at a free hydroxy group, e.g., generated by prime editor nicking, the PBS may initiate synthesis of a new single stranded DNA encoded by the editing template at the nick site. In some embodiments, the PBS is at least about 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to a region of the edit strand of the target gene (e.g., the RHO gene). In some embodiments, the PBS is perfectly complementary, or 100% complementary, to a region of the edit strand of the target gene (e.g., the RHO gene).

[0470] An extension arm of a PEgRNA may comprise an editing template that serves as a DNA synthesis template for the DNA polymerase in a prime editor during prime editing.

[0471] The length of an editing template may vary depending on, e.g., the prime editor components, the search target sequence and other components of the PEgRNA. In some embodiments, the editing template serves as a DNA synthesis template for a reverse transcriptase, and the editing template is referred to as a reverse transcription editing template (RTT).WSGR Docket No. 59761-791.601

[0472] The editing template (e.g., RTT), in some embodiments, is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length. In some embodiments, the RTT is 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length. In some embodiments, the RTT is 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 nucleotides in length. In some embodiments, the RTT is 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 nucleotides in length. In some embodiments, the RTT is 10 to 110 nucleotides in length. In some embodiments, the RTT is 10 to 109, 10 to 108, 10 to 107, 10 to 106, 10 to 105, 10 to 104, 10 to 103, 10 to 102, or 10 to 101 nucleotides in length. In some embodiments, the RTT is at least 8 and no more than 50 nucleotides in length. In some embodiments, the RTT is at least 8 and no more than 25 nucleotides in length. In some embodiments, the RTT is about 10 to about 20 nucleotides in length. In some embodiments, the RTT is about 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides in length. In some embodiments, the RTT is 11 to 17 nucleotides in length. In some embodiments, the RTT is 12 to 17 nucleotides in length. In some embodiments, the RTT is 12 to 16 nucleotides in length. In some embodiments, the RTT is 13 to 17 nucleotides in length. In some embodiments, the RTT is 11, 12, 13, 14, 15, 16, or 17 nucleotides in length. In some embodiments the RTT is 12 nucleotides in length. In some embodiments the RTT is 16 nucleotides in length. In some embodiments the RTT is 17 nucleotides in length.

[0473] In some embodiments, the editing template (e.g., RTT) sequence is about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, or 99% complementary to the editing target sequence on the edit strand of the target gene. In some embodiments, the editing template sequence (e.g., RTT) is substantially complementary to the editing target sequence. In some embodiments, the editing template sequence (e.g., RTT) is complementary to the editing target sequence except at positions of the intended nucleotide edits to be incorporated int the target gene. In some embodiments, the editing template comprises a nucleotide sequence comprising about 85% to about 95% complementarity to an editing target sequence in the edit strand in the target gene (e.g., the RHO gene). In some embodiments, the editing template comprises about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% complementarity to an editing target sequence in the edit strand of the target gene (e.g., the RHO gene).

[0474] An intended nucleotide edit in an editing template of a PEgRNA may comprise various types of alterations as compared to the target gene sequence. In some embodiments, the nucleotide edit is a single nucleotide substitution as compared to the target gene sequence. In some embodiments, the nucleotide edit is a deletion as compared to the target gene sequence. In some embodiments, the nucleotide edit is an insertion as compared to the target gene sequence. In some embodiments, the editing template comprises one to ten intended nucleotide edits as compared to the target gene sequence. In some embodiments, the editing template comprises one or more intended nucleotide edits as compared to the target geneWSGR Docket No. 59761-791.601 sequence. In some embodiments, the editing template comprises two or more intended nucleotide edits as compared to the target gene sequence. In some embodiments, the editing template comprises three or more intended nucleotide edits as compared to the target gene sequence. In some embodiments, the editing template comprises four or more, five or more, or six or more intended nucleotide edits as compared to the target gene sequence. In some embodiments, the editing template comprises two single nucleotide substitutions, insertions, deletions, or any combination thereof, as compared to the target gene sequence. In some embodiments, the editing template comprises three single nucleotide substitutions, insertions, deletions, or any combination thereof, as compared to the target gene sequence. In some embodiments, the editing template comprises four, five, or six single nucleotide substitutions, insertions, deletions, or any combination thereof, as compared to the target gene sequence. In some embodiments, a nucleotide substitution comprises an adenine (A)-to-thymine (T) substitution. In some embodiments, a nucleotide substitution comprises an A-to-guanine (G) substitution. In some embodiments, a nucleotide substitution comprises an A-to-cytosine (C) substitution. In some embodiments, a nucleotide substitution comprises a T-A substitution. In some embodiments, a nucleotide substitution comprises a T-G substitution. In some embodiments, a nucleotide substitution comprises a T-C substitution. In some embodiments, a nucleotide substitution comprises a G-to-A substitution. In some embodiments, a nucleotide substitution comprises a G-to-T substitution. In some embodiments, a nucleotide substitution comprises a G-to-C substitution. In some embodiments, a nucleotide substitution comprises a C-to-A substitution. In some embodiments, a nucleotide substitution comprises a C-to-T substitution. In some embodiments, a nucleotide substitution comprises a C-to-G substitution.

[0475] In some embodiments, a nucleotide insertion is at least 1, at least 2, at least 3, at least 4, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, or at least 20 nucleotides in length. In some embodiments, a nucleotide insertion is from 1 to 2 nucleotides, from 1 to 3 nucleotides, from 1 to 4 nucleotides, from 1 to 5 nucleotides, form 2 to 5 nucleotides, from 3 to 5 nucleotides, from 3 to 6 nucleotides, from 3 to 8 nucleotides, from 4 to 9 nucleotides, from 5 to 10 nucleotides, from 6 to 11 nucleotides, from 7 to 12 nucleotides, from 8 to 13 nucleotides, from 9 to 14 nucleotides, from 10 to 15 nucleotides, from 11 to 16 nucleotides, from 12 to 17 nucleotides, from 13 to 18 nucleotides, from 14 to 19 nucleotides, from 15 to 20 nucleotides in length. In some embodiments, a nucleotide insertion is a single nucleotide insertion. In some embodiments, a nucleotide insertion comprises insertion of two nucleotides.

[0476] The editing template of a PEgRNA may comprise one or more intended nucleotide edits, compared to the RHO gene to be edited. Position of the intended nucleotide edit(s) relevant to other components of the PEgRNA, or to particular nucleotides (e.g., mutations) in the RHO target gene may vary. In some embodiments, the nucleotide edit is in a region of the PEgRNA corresponding to orWSGR Docket No. 59761-791.601 homologous to the protospacer sequence. In some embodiments, the nucleotide edit is in a region of the PEgRNA corresponding to a region of the RHO gene outside of the protospacer sequence.

[0477] By “upstream” and “downstream” it is intended to define relevant positions at least two regions -to- upstream of a second sequence in a DNA molecule where the first sequence is positioned 5’ to the second sequence. Accordingly, the second sequence is downstream of the first sequence.

[0478] In some embodiments, the position of a nucleotide edit incorporation in the target gene can be determined based on position of the nick site. In some embodiments, position of an intended nucleotide edit is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, or 150 nucleotides apart from the nick site. In some embodiments, position of an intended nucleotide edit is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, or 150 nucleotides downstream of the nick site on the PAM strand (or the non-target strand, or the edit strand) of the double stranded target DNA. In some embodiments, position of the intended nucleotide edit in the editing template may be referred to by aligning the editing template with the partially complementary editing target sequence on the edit strand, and referring to nucleotide positions on the editing strand where the intended nucleotide edit is incorporated. Accordingly, in some embodiments, a nucleotide edit in an editing template is at a position corresponding to a position about 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, or 150 nucleotides apart from the nick site. In some embodiments, a nucleotide edit in an editing template is at a position corresponding to a position about 0 to 2 nucleotides, 0 to 4 nucleotides, 0 to 6 nucleotides, 0 to 8 nucleotides, 0 to 10 nucleotides, 2 to 4 nucleotides, 2 to 6 nucleotides, 2 to 8 nucleotides, 2 to 10 nucleotides, 2 to 12 nucleotides, 4 to 6 nucleotides, 4 to 8 nucleotides, 4 to 10 nucleotides, 4 to 12 nucleotides, 4 to 14 nucleotides, 6 to 8 nucleotides, 6 to 10 nucleotides, 6 to 12 nucleotides, 6 to 14 nucleotides, 6 to16 nucleotides, 8 to 10 nucleotides, 8 to 12 nucleotides, 8 to 14 nucleotides, 8 to 16 nucleotides, 8 to 18 nucleotides, 10 to 12 nucleotides, 10 to 14 nucleotides, 10 to 16 nucleotides, 10 to 18 nucleotides, 10 to 20 nucleotides, 12 to 14 nucleotides, 12 to 16 nucleotides, 12 to 18 nucleotides, 12 to 20 nucleotides, 12 to 22 nucleotides, 14 to 16 nucleotides, 14 to 18 nucleotides, 14 to 20 nucleotides, 14 to 22 nucleotides, 14 to 24 nucleotides, 16 to 18 nucleotides, 16 to 20 nucleotides, 16 to 22 nucleotides, 16 to 24 nucleotides, 16 to 26 nucleotides, 18 to 20 nucleotides, 18 to 22 nucleotides, 18 to 24 nucleotides, 18 to 26 nucleotides, 18 to 28 nucleotides, 20 to 22 nucleotides, 20 to 24 nucleotides, 20 to 26 nucleotides, 20 to 28 nucleotides, 20 to 30 nucleotides, 30 to 40 nucleotides, 40 to 50 nucleotides, 50 to 60 nucleotides, 60 to 70 nucleotides, 70 to 80 nucleotides, 80 to 90 nucleotides, 90 to 100 nucleotides, 100 to 110 nucleotides, 110 to 120 nucleotides, 120 to 130 nucleotides, 130 to 140 nucleotides, or 140 toWSGR Docket No. 59761-791.601 150 nucleotides apart from the nick site. In some embodiments, when referred to in the context of the PAM strand (or the non-target strand, or the edit strand), a nucleotide edit in an editing template is at a position corresponding to a position about 0 to 2 nucleotides, 0 to 4 nucleotides, 0 to 6 nucleotides, 0 to 8 nucleotides, 0 to 10 nucleotides, , 2 to 4 nucleotides, 2 to 6 nucleotides, 2 to 8 nucleotides, 2 to 10 nucleotides, 2 to 12 nucleotides, 4 to 6 nucleotides, 4 to 8 nucleotides, 4 to 10 nucleotides, 4 to 12 nucleotides, 4 to 14 nucleotides, 6 to 8 nucleotides, 6 to 10 nucleotides, 6 to 12 nucleotides, 6 to 14 nucleotides, 6 to16 nucleotides, 8 to 10 nucleotides, 8 to 12 nucleotides, 8 to 14 nucleotides, 8 to 16 nucleotides, 8 to 18 nucleotides, 10 to 12 nucleotides, 10 to 14 nucleotides, 10 to 16 nucleotides, 10 to 18 nucleotides, 10 to 20 nucleotides, 12 to 14 nucleotides, 12 to 16 nucleotides, 12 to 18 nucleotides, 12 to 20 nucleotides, 12 to 22 nucleotides, 14 to 16 nucleotides, 14 to 18 nucleotides, 14 to 20 nucleotides, 14 to 22 nucleotides, 14 to 24 nucleotides, 16 to 18 nucleotides, 16 to 20 nucleotides, 16 to 22 nucleotides, 16 to 24 nucleotides, 16 to 26 nucleotides, 18 to 20 nucleotides, 18 to 22 nucleotides, 18 to 24 nucleotides, 18 to 26 nucleotides, 18 to 28 nucleotides, 20 to 22 nucleotides, 20 to 24 nucleotides, 20 to 26 nucleotides, 20 to 28 nucleotides, 20 to 30 nucleotides, 30 to 40 nucleotides, 40 to 50 nucleotides, 50 to 60 nucleotides, 60 to 70 nucleotides, 70 to 80 nucleotides, 80 to 90 nucleotides, 90 to 100 nucleotides, 100 to 110 nucleotides, 110 to 120 nucleotides, 120 to 130 nucleotides, 130 to 140 nucleotides, or 140 to 150 nucleotides downstream from the nick site. The relative positions of the intended nucleotide edit(s) and nick site may be referred to by numbers. For example, in some embodiments, the nucleotide immediately downstream of the nick site on a PAM strand (or the non-target strand, or the edit strand) may be referred to as at position 0. The nucleotide immediately upstream of the nick site on the PAM strand (or the non-target strand, or the edit strand) may be referred to as at position -1. The nucleotides downstream of position 0 on the PAM strand may be referred to as at positions +1, +2, +3, +4, … +n, and the nucleotides upstream of position -1 on the PAM strand may be referred to as at positions -2, -3, -4, …, -n. Accordingly, in some embodiments, the nucleotide in the editing template that corresponds to position 0 when the editing template is aligned with the partially complementary editing target sequence by complementarity may also be referred to as position 0 in the editing template, the nucleotides in the editing template corresponding to the nucleotides at positions +1, +2, +3, +4, …, +n on the PAM strand of the double stranded target DNA may also be referred to as at positions +1, +2, +3, +4, …, +n in the editing template, and the nucleotides in the editing template corresponding to the nucleotides at positions -1, -2, -3, -4, …, -n on the PAM strand on the double stranded target DNA may also be referred to as at positions -1, -2, -3, -4, …, -n on the editing template, even though when the PEgRNA is viewed as a -1, -2, -3, -4, …- e. In some embodiments, an intended nucleotide edit is at position +n of the editing template relative to position 0. Accordingly, the intended nucleotide edit may be incorporated at position +n of the PAM strand of the double stranded target DNA (and subsequently, the target strand of the double stranded target DNA) by prime editing. The corresponding positions of theWSGR Docket No. 59761-791.601 intended nucleotide edit incorporated in the RHO gene may also be referred to based on the nicking position generated by a prime editor based on sequence homology and complementarity. For example, in embodiments, the distance between the nucleotide edit to be incorporated into the RHO gene and the nick site (also referred to as the “nick to edit distance”) may be determined by the position of the nick site and the position of the nucleotide(s) corresponding to the intended nucleotide edit(s), for example, by identifying sequence complementarity between the spacer and the search target sequence and sequence complementarity between the editing template and the editing target sequence. In certain embodiments, the position of the nucleotide edit can be in any position downstream of the nick site on the edit strand (or the PAM strand). As used herein, the distance between the nick site and the nucleotide edit, for example, where the nucleotide edit comprises an insertion or deletion, refers to the 5’ most position of the nucleotide edit for a nick that creates a 3’ free end on the edit strand (i.e., the “near position” of the nucleotide edit to the nick site). In some embodiments, the nick-to-edit distance is 2 to 106 nucleotides. In some embodiments, the nick-to-edit distance is 2 to 105, 2 to 104, 2 to 103, 2 to 102, 2 to 101, 2 to 100, 2 to 99, 2 to 98, or 2 to 97 nucleotides. In some embodiments, the nick-to-edit distance is 2 to 90, 2 to 80, 2 to 70, 2 to 60, 2 to 50, 2 to 40, or 2 to 30 nucleotides. In some embodiments, the nick-to-edit distance is 2 to 25, 2 to 20, 2 to 15, or 2 to 10 nucleotides. In some embodiments, the nick-to-edit distance is 2, 3, 4, 5, 6, or 7 nucleotides in length. In some embodiments, the nick-to-edit distance is 28 nucleotides. In some embodiments, the nick-to-edit distance is 22 nucleotides. In some embodiments, the nick-to-edit distance is 21 nucleotides. In some embodiments, the nick-to-edit distance is 17 nucleotides. In some embodiments, the nick-to-edit distance is 16 nucleotides. In some embodiments, the nick-to-edit distance is 4 nucleotides.

[0479] The RTT length and the nick-to-edit distance relate to the length of the portion of the RTT that is upstream of (i.e. 5’ to) the 5’-most edit in the RTT and is complementary to the edit strand. In some embodiments, the editing template comprises at least 4 contiguous nucleotides of complementarity with the edit strand wherein the at least 4 nucleotides contiguous are located upstream of the 5’ most edit in the editing template. In some embodiments, the editing template comprises at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or more contiguous nucleotides of complementarity with the edit strand wherein the at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or more contiguous nucleotides are located upstream of the 5’ most edit in the editing template. In some embodiments, the editing template comprises 20-25, 25-30, 30-35, 35-40, 45-45, or 45-50 contiguous nucleotides of complementarity with the edit strand wherein the 20-25, 25-30, 30-35, 35-40, 45-45, or 45-50 or more contiguous nucleotides are located upstream of the 5’ most edit in the editing template. In some embodiments, the editing template comprises 9-14 contiguous nucleotides of complementarity with the edit strand wherein the 9- 14 contiguous nucleotides are located upstream of the 5’ most edit in the editing template. In some embodiments, the editing template comprises 6-10 contiguous nucleotides of complementarity with the edit strand wherein the 6-10 contiguous nucleotides are located upstream of the 5’ most edit in the editingWSGR Docket No. 59761-791.601 template. In some embodiments, the editing template comprises 10 contiguous nucleotides of complementarity with the edit strand wherein the 10 contiguous nucleotides are located upstream of the 5’ most edit in the editing template. In some embodiments, the editing template comprises 9 contiguous nucleotides of complementarity with the edit strand wherein the 9 contiguous nucleotides are located upstream of the 5’ most edit in the editing template.

[0480] When referred to within the PEgRNA, positions of the one or more intended nucleotide edits may be referred to relevant to components of the PEgRNA. For example, an intended nucleotide edit may be 5’ or 3’ to the PBS. In some embodiments, a PEgRNA comprises the structure, from 5’ to 3’: a spacer, a gRNA core, an editing template, and a PBS. In some embodiments, the intended nucleotide edit is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 nucleotides upstream to the 5’ most nucleotide of the PBS. In some embodiments, the intended nucleotide edit is 0 to 2 nucleotides, 0 to 4 nucleotides, 0 to 6 nucleotides, 0 to 8 nucleotides, 0 to 10 nucleotides, 2 to 4 nucleotides, 2 to 6 nucleotides, 2 to 8 nucleotides, 2 to 10 nucleotides, 2 to 12 nucleotides, 4 to 6 nucleotides, 4 to 8 nucleotides, 4 to 10 nucleotides, 4 to 12 nucleotides, 4 to 14 nucleotides, 6 to 8 nucleotides, 6 to 10 nucleotides, 6 to 12 nucleotides, 6 to 14 nucleotides, 6 to16 nucleotides, 8 to 10 nucleotides, 8 to 12 nucleotides, 8 to 14 nucleotides, 8 to 16 nucleotides, 8 to 18 nucleotides, 10 to 12 nucleotides, 10 to 14 nucleotides, 10 to 16 nucleotides, 10 to 18 nucleotides, 10 to 20 nucleotides, 12 to 14 nucleotides, 12 to 16 nucleotides, 12 to 18 nucleotides, 12 to 20 nucleotides, 12 to 22 nucleotides, 14 to 16 nucleotides, 14 to 18 nucleotides, 14 to 20 nucleotides, 14 to 22 nucleotides, 14 to 24 nucleotides, 16 to 18 nucleotides, 16 to 20 nucleotides, 16 to 22 nucleotides, 16 to 24 nucleotides, 16 to 26 nucleotides, 18 to 20 nucleotides, 18 to 22 nucleotides, 18 to 24 nucleotides, 18 to 26 nucleotides, 18 to 28 nucleotides, 20 to 22 nucleotides, 20 to 24 nucleotides, 20 to 26 nucleotides, 20 to 28 nucleotides, or 20 to 30 nucleotides upstream to the 5’ most nucleotide of the PBS.

[0481] The corresponding positions of the intended nucleotide edit incorporated in the target gene may also be referred to based on the nicking position generated by a prime editor based on sequence homology and complementarity. For example, in some embodiments, the distance between the nucleotide edit to be incorporated into the target RHO gene and the nick site (also referred to as the “nick to edit distance”) may be determined by the position of the nick site and the position of the nucleotide(s) corresponding to the intended nucleotide edit(s), for example, by identifying sequence complementarity between the spacer and the search target sequence and sequence complementarity between the editing template and the editing target sequence. In certain embodiments, the position of the nucleotide edit can be in any position downstream of the nick site on the edit strand (or the PAM strand) generated by the prime editor, such that the distance between the nick site and the intended nucleotide edit is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some embodiments, the position of the nucleotide edit is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,WSGR Docket No. 59761-791.601 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some embodiments, the position of the nucleotide edit is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides upstream of the nick site on the edit strand. In some embodiments, the position of the nucleotide edit is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides downstream of the nick site on the edit strand. In some embodiments, the position of the nucleotide edit is 0 base pair from the nick site on the edit strand, that is, the editing position is at the same position as the nick site. As used herein, the distance between the nick site and the nucleotide edit, for example, where the nucleotide edit e “near position” of the nucleotide edit to the nick site). Similarly, as used herein, the distance between the nick site and a PAM position edit, for example, where the nucleotide edit comprises an insertion, deletion, or substitution of two or more contiguous sequence.

[0482] In some embodiments, the editing template extends beyond a nucleotide edit to be incorporated to the target RHO gene sequence. For example, in some embodiments, the editing template comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 nucleotides.

[0483] In some embodiments, the editing template can comprise a second edit relative to a target sequence. The second edit can be designed to mutate or otherwise silence a PAM sequence such that a corresponding nucleic acid guided nuclease or CRISPR nuclease is no longer able to cleave the target sequence (such edits referred to as “PAM silencing edits).

[0484] Without wishing to be bound by any particular theory, PAM silencing edits may prevent the Cas, e.g., Cas9, nickase, from re-nicking the edit strand before the edit is incorporated in the target strand, therefore improving prime editing efficiency. In some embodiments, a PAM silencing edit is a synonymous edit that does not alter the amino acid sequence encoded by the RHO gene after incorporation of the edit. In some embodiments, a PAM silencing edit is at a position corresponding to a coding region, e.g., an exon, of a RHO gene. In some embodiments, a PAM silencing edit is at a position corresponding to a non-coding region, e.g., an intron, of a RHO gene. In some embodiments, the edits in an intron of a RHO gene is not at a position that corresponds to intron-exon junction and the edit does not affect transcript splicing.

[0485] In some embodiments, the length of the editing template is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 nucleotides longer than the nick to edit distance. In someWSGR Docket No. 59761-791.601 embodiments, for example, the nick to edit distance is 8 nucleotides, and the editing template is 10 to 15, 10 to 20, 10 to 25, 10 to 30, 10 to 35, 10 to 40, 10 to 45, 10 to 50, 10 to 55, 10 to 60, 10 to 65, 10 to 70, 10 to 75, or 10 to 80 nucleotides in length. In some embodiments, the nick to edit distance is 22 nucleotides, and the editing template is 24 to 28, 24 to 30, 24 to 32, 24 to 34, 24 to 36, 24 to 37, 24 to 38, 24 to 40, 24 to 45, 24 to 50, 24 to 55, 24 to 60, 24 to 65, 24 to 70, 24 to 75, 24 to 80, 24 to 85, 24 to 90, 24 to 95, 24 to 100, 24 to 105, 24 to 100, 24 to 105, or 24 to 110 nucleotides in length.

[0486] In some embodiments, the editing template comprises an adenine at the first nucleobase position (e.g. -spacer-gRNA core-RTT-PBS- the “first base”). In some embodiments, the editing template comprises a guanine at the first nucleobase position (e.g. -spacer-gRNA core-RTT-PBS- nucleobase is the “first base”). In some embodiments, the editing template comprises an uracil at the first nucleobase position (e.g. -spacer-gRNA core-RTT-PBS- most nucleobase is the “first base”). In some embodiments, the editing template comprises a cytosine at the first nucleobase position (e.g. -spacer-gRNA core-RTT-PBS- not comprise a cytosine at the first nucleobase position (e.g. -spacer-gRNA core-RTT-PBS-

[0487] The editing template of a PEgRNA may encode a new single stranded DNA (e.g., by reverse transcription) to replace an editing target sequence in the target gene. In some embodiments, the editing target sequence in the edit strand of the target gene is replaced by the newly synthesized strand, and the nucleotide edit(s) are incorporated in the region of the target gene. In some embodiments, the target gene is an RHO gene. In some embodiments, the editing template of the PEgRNA encodes a newly synthesized single stranded DNA that comprises a wild type RHO gene sequence. In some embodiments, the newly synthesized DNA strand replaces the editing target sequence in the target RHO gene, wherein the editing target sequence (or the endogenous sequence complementary to the editing target sequence on the target strand of the RHO gene) comprises a mutation or a nucleotide alteration compared to a wild type RHO gene. In some embodiments, the mutation is associated with retinal degenerative disease, such as retinitis pigmentosa.

[0488] In some embodiments, the newly synthesized single stranded DNA encoded by the editing target sequence replaces the editing target sequence, and corrects the mutation in the editing target sequence of the RHO gene.

[0489] In some embodiments, the editing target sequence comprises a mutation in exon 5 of the RHO gene as compared to a wild type RHO gene. In some embodiments, the editing target sequence comprises a mutation that is located at position 1033 of the coding sequence of the rhodopsin protein. In some embodiments, the editing target sequence comprises a c.1033G->C mutation (on the sense strand) or a C- >G mutation (on the antisense strand) at position 1033 of the coding sequence of the rhodopsin protein.WSGR Docket No. 59761-791.601 In some embodiments, the editing target sequence comprises a mutation that is located at position 1040 of the coding sequence of the rhodopsin protein. In some embodiments, the editing target sequence comprises a c.1040C->T mutation (on the sense strand) or a G->A mutation (on the antisense strand) at position 1040 of the coding sequence of the rhodopsin protein. In some embodiments, the editing target sequence comprises a mutation in a region from c.1030 to c.1045 of the coding sequence of the rhodopsin protein.

[0490] In some embodiments, the editing template comprises one or more intended nucleotide edits compared to the sequence on the target strand of the RHO gene that is complementary to the editing target sequence. In some embodiments, the editing template encodes a single stranded DNA that comprises one or more intended nucleotide edits compared to the editing target sequence. In some embodiments, the single stranded DNA replaces the editing target sequence by prime editing, thereby incorporating the one or more intended nucleotide edits. In some embodiments, the one or more intended nucleotide edits comprises a C-G substitution at a position corresponding to position 1033 of the coding sequence of the rhodopsin protein compared to the editing target sequence. In some embodiments, the one or more intended nucleotide edits comprises a G-C substitution in the anti-sense strand at a position corresponding to position 1033 of the coding sequence of the rhodopsin protein compared to the editing target sequence. In some embodiments, the one or more intended nucleotide edits comprises a T-C substitution at a position corresponding to position 1040 of the coding sequence of the rhodopsin protein compared to the editing target sequence. In some embodiments, the one or more intended nucleotide edits comprises a A-G substitution in the anti-sense strand at a position corresponding to position 1040 of the coding sequence of the rhodopsin protein compared to the editing target sequence. In some embodiments, incorporation of the one or more intended nucleotide edits corrects the mutation in the editing target sequence to wild type nucleotides at corresponding positions in the RHO gene. As used herein, “correcting” a mutation means restoring a wild type sequence at the place of the mutation in the double stranded target DNA, e.g. target gene, by prime editing. In some embodiments, the editing template comprises and / or encodes a wild type RHO gene sequence.

[0491] In some embodiments, the editing target sequence comprises a mutation that is located between positions 129528639 -129535344 GRCh38.p13. In some embodiments, the editing target sequence comprises a mutation that is located between positions 129528701 and 129528901 of human chromosome 13. In some embodiments, the editing target sequence comprises position 129528801in human chromosome 13.

[0492] In some embodiments, incorporation of the one or more intended nucleotide edits does not correct the mutation in the editing target sequence to wild type sequence, but allows for expression of a functional rhodopsin protein encoded by the RHO gene. For example, in some embodiments, incorporation of the one or more intended nucleotide edits results in one or more codons that are different from a wild type codon but encode one or more amino acids same as the wild type rhodopsin protein. InWSGR Docket No. 59761-791.601 some embodiments, incorporation of the one or more intended nucleotide edits results in one or more codons that encode one or more amino acids different from the wild type rhodopsin protein, but allows for expression of a functional rhodopsin protein. Exemplary amino acid sequence of wild type rhodopsin protein is provided in SEQ ID NO: 943. Exemplary mRNA / cDNA sequence of wild type rhodopsin protein is provided in SEQ ID NO: 944.

[0493] Wild-type rhodopsin protein sequence (SEQ ID NO: 943) MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQ HKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLV VLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYY TLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV IAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCG KNPLGDDEASATVSKTETSQVAPA

[0494] Wild-type rhodopsin mRNA / cDNA sequence (SEQ ID NO: 944) agagtcatccagctggagccctgagtggctgagctcaggccttcgcagcattcttgggtgggagcagccacgggtcagccacaagggccacagccat gaatggcacagaaggccctaacttctacgtgcccttctccaatgcgacgggtgtggtacgcagccccttcgagtacccacagtactacctggctgagcc atggcagttctccatgctggccgcctacatgtttctgctgatcgtgctgggcttccccatcaacttcctcacgctctacgtcaccgtccagcacaagaagct gcgcacgcctctcaactacatcctgctcaacctagccgtggctgacctcttcatggtcctaggtggcttcaccagcaccctctacacctctctgcatggata cttcgtcttcgggcccacaggatgcaatttggagggcttctttgccaccctgggcggtgaaattgccctgtggtccttggtggtcctggccatcgagcggt acgtggtggtgtgtaagcccatgagcaacttccgcttcggggagaaccatgccatcatgggcgttgccttcacctgggtcatggcgctggcctgcgccg cacccccactcgccggctggtccaggtacatccccgagggcctgcagtgctcgtgtggaatcgactactacacgctcaagccggaggtcaacaacga gtcttttgtcatctacatgttcgtggtccacttcaccatccccatgattatcatctttttctgctatgggcagctcgtcttcaccgtcaaggaggccgctgccca gcagcaggagtcagccaccacacagaaggcagagaaggaggtcacccgcatggtcatcatcatggtcatcgctttcctgatctgctgggtgccctacg ccagcgtggcattctacatcttcacccaccagggctccaacttcggtcccatcttcatgaccatcccagcgttctttgccaagagcgccgccatctacaac cctgtcatctatatcatgatgaacaagcagttccggaactgcatgctcaccaccatctgctgcggcaagaacccactgggtgacgatgaggcctctgcta ccgtgtccaagacggagacgagccaggtggccccggcctaagacctgcctaggactctgtggccgactataggcgtctcccatcccctacaccttccc ccagccacagccatcccaccaggagcagcgcctgtgcagaatgaacgaagtcacataggctccttaattttttttttttttttaagaaataattaatgaggctc ctcactcacctgggacagcctgagaagggacatccaccaagacctactgatctggagtcccacgttccccaaggccagcgggatgtgtgcccctcctc ctcccaactcatctttcaggaacacgaggattcttgctttctggaaaagtgtcccagcttagggataagtgtctagcacagaatggggcacacagtaggtg cttaataaatgctggatggatgcaggaaggaatggaggaatgaatgggaagggagaacatatctatcctctcagaccctcgcagcagcagcaactcata cttggctaatgatatggagcagttgtttttccctccctgggcctcactttcttctcctataaaatggaaatcccagatccctggtcctgccgacacgcagctac tgagaagaccaaaagaggtgtgtgtgtgtctatgtgtgtgtttcagcactttgtaaatagcaagaagctgtacagattctagttaatgttgtgaataacatcaa ttaatgtaactagttaattactatgattatcacctcctgatagtgaacattttgagattgggcattcagatgatggggtttcacccaaccttggggcaggttttta aaaattagctaggcatcaaggccagaccagggctgggggttgggctgtaggcagggacagtcacaggaatgcagaatgcagtcatcagacctgaaa aaacaacactgggggagggggacggtgaaggccaagttcccaatgagggtgagattgggcctggggtctcacccctagtgtggggccccaggtccc gtgcctccccttcccaatgtggcctatggagagacaggcctttctctcagcctctggaagccacctgctcttttgctctagcacctgggtcccagcatctag agcatggagcctctagaagccatgctcacccgcccacatttaattaacagctgagtccctgatgtcatccttatctcgaagagcttagaaacaaagagtggWSGR Docket No. 59761-791.601 gaaattccactgggcctaccttccttggggatgttcatgggccccagtttccagtttcccttgccagacaagcccatcttcagcagttgctagtccattctcc attctggagaatctgctccaaaaagctggccacatctctgaggtgtcagaattaagctgcctcagtaactgctcccccttctccatataagcaaagccaga agctctagctttacccagctctgcctggagactaaggcaaattgggccattaaaagctcagctcctatgttggtattaacggtggtgggttttgttgctttcac actctatccacaggatagattgaaactgccagcttccacctgatccctgaccctgggatggctggattgagcaatgagcagagccaagcagcacagagt cccctggggctagaggtggaggaggcagtcctgggaatgggaaaaacccca

[0495] A guide RNA core (also referred to herein as the gRNA core, gRNA scaffold, or gRNA backbone sequence) of a PEgRNA may contain a polynucleotide sequence that binds to a DNA binding domain (e.g., Cas9) of a prime editor. The gRNA core may interact with a prime editor as described herein, for example, by association with a DNA binding domain, such as a DNA nickase of the prime editor.

[0496] One of skill in the art will recognize that different prime editors having different DNA binding domains from different DNA binding proteins may require different gRNA core sequences specific to the DNA binding protein. In some embodiments, the gRNA core is capable of binding to a Cas9-based prime editor. In some embodiments, the gRNA core is capable of binding to a Cpf1-based prime editor. In some embodiments, the gRNA core is capable of binding to a Cas12b-based prime editor.

[0497] In some embodiments, the gRNA core comprises regions and secondary structures involved in binding with specific CRISPR Cas proteins. For example, in a Cas9 based prime editing system, the gRNA core of a PEgRNA may comprise one or more regions of a base paired “lower stem” adjacent to the spacer sequence and a base paired “upper stem” following the lower stem, where the lower stem and upper stem may be connected by a “bulge” comprising unpaired RNAs. The gRNA core may further comprise a “nexus” distal from the spacer sequence, followed by a hairpin structure, e.g. , as exemplified in FIG. 3. In some embodiments, the gRNA core comprises modified nucleotides as compared to a wild type gRNA core in the lower stem, upper stem, and / or the hairpin. For example, nucleotides in the lower stem, upper stem, an / or the hairpin regions may be modified, deleted, or replaced. In some embodiments, RNA nucleotides in the lower stem, upper stem, an / or the hairpin regions may be replaced with one or more DNA sequences. In some embodiments, the gRNA core comprises unmodified or wild type RNA sequences in the nexus and / or the bulge regions. In some embodiments, the gRNA core does not include long stretches of A-T pairs, for example, a GUUUU- AAAAC pairing element. In some embodiments, a prime editing system comprises a prime editor and a PEgRNA, wherein the prime editor comprises a SpCas9 nickase variant thereof, and the gRNA core of the PEgRNA comprises the sequence capable of binding to a SpCas9. Any gRNA core sequences known in the art are also contemplated in the prime editing compositions described herein.

[0498] In some embodiments, the PEgRNA and / or ngRNA comprises a gRNA core that comprises a nucleic acid sequence selected from the Table 10 below. In some embodiments, the PEgRNA and / or ngRNA comprises a gRNA core that comprises a nucleic acid sequence that has at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to anyWSGR Docket No. 59761-791.601 one of the sequences in Table 10. In some embodiments, PEgRNA and / or ngRNA comprises a gRNA core that comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 differences e.g., mutations e.g., deletions, substitutions and / or insertions compared to any one of sequences in Table 10.

[0499] Table: 10: lists exemplary nucleic acid sequences of gRNA core (gRNA scaffold). The sequences in Table 10 below are annotated with SEQ ID NO as required by ST.26 standard. Although all the sequences provided in Table 10 are RNA sequences, “T” is used instead of a “U” in the sequences for consistency with the ST.26 standard.

[0500] Table 10. Exemplary nucleic acid sequences of gRNA core (gRNA scaffold)WSGR Docket No. 59761-791.601

[0501] In some embodiments, the PEgRNA and / or ngRNA comprises a nucleic acid sequence selected from the Table 11 below at the 3’ end. In some embodiments, the PEgRNA and / or ngRNA comprises a nucleic acid sequence that has at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of the sequences provided in Table 11 at the 3’ end. In some embodiments, the PEgRNA and / or ngRNA comprises a nucleic acid sequence selected from the group consisting of the sequences provided in Table 11. Table: 11: lists exemplary nucleic acid sequences of 3’ motif (e.g., Univ. 3’ motif) of PEgRNA or ngRNA. The sequences in Table 11 below are annotated with SEQ ID NO as required by ST.26 standard. Although all the sequences provided in Table 11 are RNA sequences, “T” is used instead of a “U” in the sequences for consistency with the ST.26 standard.

[0502] Table 11. Exemplary nucleic acid sequences of 3’ motif (e.g., Univ. 3’ motif) of PEgRNA or ngRNA.

[0503] In some embodiments, a PEgRNA comprises a linker. In some embodiments, the secondary structure or a 3’ motif is linked to one or more other component of a PEgRNA via a linker. For example, in some embodiments, the secondary structure is at the 3’ end of the PEgRNA (e.g., a RTT, or a PBS) and is linked to the 3’ end of a PBS via a linker. For example, in some embodiments, a 3’ motif is at the 3’ end of the PEgRNA and is linked to the 3’ end of a PEgRNA (e.g., a RTT or a PBS) via a linker. In some embodiments, the secondary structure or a 5’ motif is at the 5’ end of the PEgRNA and is linked to the 5’ end of a spacer via a linker. In some embodiments, the linker is a nucleotide linker that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides in length. In some embodiments, the linker is 5 to 10 nucleotides in length. In some embodiments, the linker is 10 to 20 nucleotides in length. In some embodiments, the linker is 15 to 25 nucleotides in length. In some embodiments, the linker is 8 nucleotides in length.

[0504] In some embodiments, the linker is designed to minimize base pairing between the linker and another component of the PEgRNA. In some embodiments, the linker is designed to minimize base pairing between the linker and the spacer. In some embodiments, the linker is designed to minimize base pairing between the linker and the PBS. In some embodiments, the linker is designed to minimize base pairing between the linker and the editing template. In some embodiments, the linker is designed to minimize base pairing between the linker and the sequence of the RNA secondary structure. In some embodiments, the linker is optimized to minimize base pairing between the linker and another component of the PEgRNA, in order of the following priority: spacer, PBS, editing template and then scaffold. InWSGR Docket No. 59761-791.601 some embodiments, base paring probability is calculated using ViennaRNA 2.0 ,as described in Lorenz, R. et al. ViennaRNA package 2.0. Algorithms Mol. Biol. 6, incorporated by reference in its entirety herein, under standard parameters (37 °C, 1 M NaCl, 0.05 M MgCl2).

[0505] Table 33. Exemplary nucleic acid sequences of linkers of PEgRNAs or ngRNAs.WSGR Docket No. 59761-791.601

[0506] modifier region. In some embodiments, a PEgRNA comprises at least one nucleotide that is not part of a spacer, a gRNA core, or an extension arm. The optional sequence modifiers could be positioned within or In certain embodiments, the PEgRNA comprises secondary RNA structure, such as, but not limited to, aptamers, hairpins, stem / loops, toeloops, and / or RNA-binding protein recruitment domains (e.g., the MS2 aptamer which recruits and binds to the MS2cp protein). In some embodiments, a PEgRNA comprises a short a -GAAANNNNN- the spacer. In some embodiments, the secondary structure is positioned within the extension arm. In some embodiments, the secondary structure is positioned within the gRNA core. In some embodiments, the secondary structure is positioned between the spacer and the gRNA core, between the gRNA core and the extension arm, or between the spacer and the extension arm. In some embodiments, the secondary structure is positioned between the PBS and the editing template. In some embodiments the secondary RNA structures, the PEgRNA may comprise a chemical linker or a poly(N) linker or tail, where “N” can be any nucleobase. In some embodiments, the chemical linker may function to prevent reverse transcription of the gRNA core.

[0507] A PEgRNA may also comprise a tag sequence in addition to the spacer, gRNA core, primer binding site, and editing template referred to as a “COMP-tag”. In some embodiments, the tag sequence comprises a region of complementarity to the editing template. In some embodiments, the tag sequence comprises a region of complementarity to the PBS. In some embodiments, the tag sequence comprises a region of complementarity to the editing template and / or the PBS. In some embodiments, the tag sequence comprises a region of complementarity to the editing template and does not have substantial complementarity to the PBS. In some embodiments, the tag sequence comprises a region of complementarity to the editing template and does not have complementarity to the PBS. In some embodiments, the tag sequence and the editing template each comprises a region of complementarity to each other, wherein the 3’ end of the region of complementarity in the editing template is at a position 1, some embodiments, the region of complementarity in the tag sequence is at a 5’ portion of the tagWSGR Docket No. 59761-791.601 sequence. In some embodiments, the tag sequence does not have substantial complementarity to the spacer. In some embodiments, the tag does not have complementarity to the spacer. In some embodiments, the tag sequence is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 nucleotides in length. In some embodiments, the tag sequence is at least 4, at least 6, at least 8 nucleotides in length. The tag, or Comp-tag, may be attached to the rest of the pegRNA via a linker sequence. Exemplary Tag sequences can be found in Table 34.

[0508] Table 34. Exemplary nucleic acid sequences of COMP-tags.

[0509] In some embodiments, a prime editing system or composition further comprises a nick guide polynucleotide, such as a nick guide RNA (ngRNA). In some embodiments, a ngRNA comprises a spacer (referred to as a ngRNA spacer or ng spacer) and a gRNA core, wherein the spacer of the ngRNAWSGR Docket No. 59761-791.601 comprises a region of complementarity to the edit strand, and wherein the gRNA core can interact with a Cas, e.g., Cas9, of a prime editor. Without wishing to be bound by any particular theory, an ngRNA may bind to the edit strand and direct the Cas nickase to generate a nick on the non-edit strand (or target strand). In some embodiments, the nick on the non-edit strand directs endogenous DNA repair machinery to use the edit strand as a template for repair of the non-edit strand, which may increase efficiency of prime editing. In some embodiments, the non-edit strand is nicked by a prime editor localized to the non- edit strand by the ngRNA. Accordingly, also provided herein are PEgRNA systems comprising at least one PEgRNA and at least one ngRNA.

[0510] A prime editing system comprising a PEgRNA (or one or more polynucleotide encoding the PEgRNA) and a prime editor protein (or one or more polynucleotides encoding the prime editor), may be referred to as a PE2 prime editing system and the corresponding editing approach referred to as PE2 approach or PE2 strategy. A PE2 system does not contain a ngRNA. A prime editing system comprising a PEgRNA (or one or more polynucleotide encoding the PEgRNA), a prime editor protein (or one or more polynucleotides encoding the prime editor), and a ngRNA (or one or more polynucleotides encoding the ngRNA) may be referred to as a “PE3” prime editing system. In some embodiments, an ngRNA spacer sequence is complementary to a portion of the edit strand that includes the intended nucleotide edit, and may hybridize with the edit strand only after the edit has been incorporated on the edit strand. Such ngRNA may be referred to a “PE3b” ngRNA, and the prime editing system a PE3b prime editing system.

[0511] In some embodiments, a PEgRNA or a nick guide RNA (ngRNA) can be chemically synthesized, or can be assembled or cloned and transcribed from a DNA sequence, e.g., a plasmid DNA sequence, or by any RNA oligonucleotide synthesis method known in the art. In some embodiments, DNA sequence For example, in some embodiments, a DNA sequence that encodes a PEgRNA (or nick guide RNA) (or embodiments, a DNA sequence that encodes a PEgRNA (or nick guide RNA) may be designed to append DNA sequence that encodes a PEgRNA (or nick guide RNA) may be designed to append the sequence sequence that encodes a PEgRNA (or nick guide RNA) may be designed to append the sequence TTT, nick guide RNA) may comprise an appended sequence UUU, UUUU, UUUUU, UUUUUU, or In some embodiments, a PEgRNA or ngRNA may include a modifyingWSGR Docket No. 59761-791.601 ID NO: 949). In some embodiments, a PEgRNA or a ngRNA comprises the sequence TTTT (sequence end. In some embodiments, a PEgRNA or a ngRNA comprises the sequence comprises a 3’ terminator sequence (e.g., TTTT; sequence number 950) at the 3’ end. In some embodiments, a PEgRNA or a ngRNA comprises a transcription adaptation sequence (e.g., TTTTTTT sequence number 951) at the 3’ end. The sequences in sequence number 950, and sequence number 951 are annotated with a sequence number as required by ST.26 standard. Although the sequences set forth in sequence number 950, and sequence number 951 are RNA sequences, “T” is used instead of a “U” in the sequences for consistency with the ST.26 standard.

[0512] In some embodiments, the ng search target sequence is located on the non-target strand, within 10 base pairs to 100 base pairs of an intended nucleotide edit incorporated by the PEgRNA on the edit strand. In some embodiments, the ng target search target sequence is within 10 bp, 20 bp, 30 bp, 40 bp, 50 bp, 60 bp, 70 bp, 80 bp, 90 bp, 91 bp, 92 bp, 93 bp, 94 bp, 95 bp, 96 bp, 97 bp, 98 bp, 99 bp, or 100 bp of an intended nucleotide edit incorporated by the PEgRNA on the edit strand. In some embodiments, the quence are within 1, 2, 3, 4, 5, sequence and the PEgRNA search target sequence are within 10 bp, 20 bp, 30 bp, 40 bp, 50 bp, 60 bp, 70 bp, 80 bp, 90 bp, 91 bp, 92 bp, 93 bp, 94 bp, 95 bp, 96 bp, 97 bp, 98 bp, 99 bp, or 100 bp apart from each other.

[0513] In some embodiments, an ng spacer sequence is complementary to, and may hybridize with the second search target sequence only after an intended nucleotide edit has been incorporated on the edit strand, by the editing template of a PEgRNA. In some embodiments, such a prime editing system maybe referred to as a “PE3b” prime editing system or composition. In some embodiments, the ngRNA comprises a spacer sequence that matches only the edit strand after incorporation of the nucleotide edits, but not the endogenous target gene sequence on the edit strand. Accordingly, in some embodiments, an intended nucleotide edit is incorporated within the ng search target sequence.

[0514] A ngRNA protospacer may be in close proximity to the PEgRNA spacer, or may be upstream or downstream of the PEgRNA spacer. In some embodiments, the distance generated by the PEgRNA nick site and the ngRNA nick site (referred to as the nick-to-nick distance) is about 3 to about 100 nucleotides. In some embodiments, the distance generated by the PEgRNA nick site and the ngRNA nick site (referred to as the nick-to-nick distance) is about 4-90, 4-80, 4-70, 4-60, 4-50, 4-40, 4-30, 4-20, or 4-10 nucleotides. In some embodiments, the distance generated by the PEgRNA nick site and the ngRNA nick site (referred to as the nick-to-nick distance) is about 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80,80- 90, or 90-100 nucleotides. In some embodiments, the nick-to-nick distance is about 4-88 nucleotides. In some embodiments, the nick-to-nick distance is about 4-72 nucleotides. In some embodiments, the nick-WSGR Docket No. 59761-791.601 to-nick distance is about 4-61 nucleotides. In some embodiments, the nick-to-nick distance is about 61-72 nucleotides. In some embodiments, the nick-to-nick distance is about 61-88 nucleotides. In some embodiments, the nick-to-nick distance is about 72-88 nucleotides. In some embodiments, the nick-to- nick distance is about 4-7 nucleotides. In some embodiments, the nick-to-nick distance is 4, 5, 6, or 7 nucleotides. In some embodiments, the nick-to-nick distance is about 41-96 nucleotides. In some embodiments, the nick-to-nick distance is about 41-82 nucleotides. In some embodiments, the nick-to- nick distance is about 41-44 nucleotides. In some embodiments, the nick-to-nick distance is about 44-82 nucleotides. In some embodiments, the nick-to-nick distance is about 44-96 nucleotides. In some embodiments, the nick-to-nick distance is about 82-96 nucleotides. In some embodiments, the nick-to- nick distance is 41, 44, 82, or 96 nucleotides. In some embodiments, the intended nucleotide edit is incorporated within about 1-10 nucleotides of the position corresponding to the PAM of the ng search target sequence.

[0515] The gRNA core of a PEgRNA or ngRNA can be any gRNA scaffold sequence that is capable of interacting with a Cas protein that recognizes the corresponding PAM of the PEgRNA or ngRNA. In some embodiments, gRNA core of a PEgRNA or a ngRNA comprises a nucleic acid sequence selected from SEQ ID Nos: 854-859.

[0516] In some embodiments, a PEgRNA (or ngRNA) comprises an additional secondary structure at the 5’ end. In some embodiments, a PEgRNA (or ngRNA) comprises an additional secondary structure at the 3’ end.

[0517] In some embodiments, the secondary structure comprises a pseudoknot. In some embodiments, the secondary structure comprises a pseudoknot derived from a virus. In some embodiments, the secondary structure comprises a pseudoknot of a Moloney murine leukemia virus (M-MLV) genome (a mpknot). In some embodiments, the secondary structure comprises a nucleotide sequence selected from the group consisting of sequences provided in Table 12, or a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity therewith.

[0518] In some embodiments, the secondary structure comprises a quadruplex. In some embodiments, the secondary structure comprises a G-quadruplex.

[0519] In some embodiments, the secondary structure comprises a P4-P6 domain of a Group I intron.

[0520] In some embodiments, the secondary structure comprises a riboswitch aptamer. In some embodiments, the secondary structure comprises a riboswitch aptamer derived from a prequeosine-1 riboswitch aptamer. In some embodiments, the secondary structure comprises a modified prequeosine-1 riboswitch aptamer.

[0521] In some embodiments, the PEgRNA comprises a RNA secondary structure and / or a linker disclosed in Nelson et al. Engineered pegRNAs improve prime editing efficiency. Nat Biotechnol. (2021), the entirety of which is incorporated herein by reference.

[0522] Exemplary secondary structure sequences are provided in Table 12.WSGR Docket No. 59761-791.601

[0523] Table 12. Illustrative sequences for secondary structures. The sequences in Table 12 are annotated with SEQ ID NO as required by ST.26 standard. Although all the sequences provided in Table 12 are RNA sequences, “T” is used instead of a “U” in the sequences for consistency with the ST.26 standard.WSGR Docket No. 59761-791.601

[0524] In some embodiments, a PEgRNA is transcribed from a nucleotide encoding the PEgRNA, for example, a DNA plasmid encoding the PEgRNA. In some embodiments, the PEgRNA comprises a self- cleaving element. In some embodiments, the self-cleaving element improves transcription and / or processing of the PEgRNA when transcribed form the nucleotide encoding the PEgRNA. In some embodiments, the PEgRNA comprises a hairpin or a RNA quadruplex. In some embodiments, the PEgRNA comprises a self-cleaving ribozyme element, for example, a hammerhead, a pistol, a hatchet, a hairpin, a VS, a twister, or a twister sister ribozyme. In some embodiments, the PEgRNA comprises a HDV ribozyme. In some embodiments, the PEgRNA comprises a hairpin recognized by Csy4. In some embodiments, the PEgRNA comprises an ENE motif. In some embodiments, the PEgRNA comprises an element for nuclear expression (ENE) from MALAT1 lnc RNA. In some embodiments, the PEgRNA comprises an ENE element from Kaposi’s sarcoma-associated herpesvirus (KSHV). In some embodiments, the PEgRNA comprises a 3’ box of a U1 snRNA. In some embodiments, the PEgRNA forms a circular RNA.

[0525] In some embodiments, the PEgRNA comprises a RNA secondary structure or a motif that improves binding to the DNA-RNA duple or enhances PEgRNA activity. In some embodiments, the PEgRNA comprises a sequence derived from a native nucleotide element involved in reverse transcription, e.g., initiation of retroviral transcription. In some embodiments, the PEgRNA comprises a sequence of, or derived from, a primer binding site of a substrate of a reverse transcriptase, a polypurine tract (PPT), or a kissing loop. In some embodiments, the PEgRNA comprises a dimerization motif, a kissing loop, or a GNRA tetraloop – tetraloop receptor pair that results in circularization of the PEgRNA. In some embodiments, the PEgRNA comprises a RNA secondary structure of a motif that results in physical separation of the spacer and the PBS of the PEgRNA, thereby prevents occlusion of the spacer and improves PEgRNA activity. In some embodiments, the PEgRNA comprises a secondary structure or motif, e.g., a 5’ or 3’ extension in the spacer region that form a toehold or hairpin, wherein the secondary structure or motif competes favorably against annealing between the spacer and the PBS of the PEgRNA, thereby prevents occlusion of the spacer and improves PEgRNA activity.WSGR Docket No. 59761-791.601

[0526] In some embodiments, a PEgRNA additionally comprises a sequence provided in Table 13. In some embodiments, a PEgRNA comprises the sequence GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUGCUUCGGCAUGGCGA AUGGGAC (SEQ ID No: 979) at the 3’ end. In some embodiments, a PEgRNA comprises the structure [spacer]-[gRNA core]-[editing template]-[PBS]- GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUGCUUCGGCAUGGCGA AUGGGAC (SEQ ID NO: 979), or [spacer]-[gRNA core]-[editing template]-[PBS]- GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUGCUUCGGCAUGGCGA AUGGGAC-(U)n (SEQ ID NO: 980), wherein n is an integer between 3 and 7. The structure derived from hepatitis D virus (HDV) is italicized.

[0527] In some embodiments, the PEgRNA comprises the sequence GGUGGGAGACGUCCCACC (SEQ ID No: 981) at the 5’ end and / or the sequence UGGGAGACGUCCCACC (SEQ ID NO: 982) at the 3’ end. In some embodiments, the PEgRNA comprises the following structure (M-MLV kissing loop): GGUGGGAGACGUCCCACC (SEQ ID NO: 981)-[spacer]-[gRNA core]-[editing template]-[PBS]- UGGGAGACGUCCCACC (SEQ ID NO: 982), or GGUGGGAGACGUCCCACC (SEQ ID NO: 981)- [spacer]-[gRNA core]-[editing template]-[PBS]-UGGGAGACGUCCCACC-(U)n (SEQ ID NO: 983), wherein n is an integer between 3 and 7. The kissing loop structure is italicized.

[0528] In some embodiments, the PEgRNA comprises the sequence GAGCAGCAUGGCGUCGCUGCUCAC (SEQ ID No: 984) at the 5’ end and / or the sequence CCAUCAGUUGACACCCUGAGG (SEQ ID No: 985) at the 3’ end. In some embodiments, the PEgRNA comprises the following structure (VS ribozyme kissing loop):

[0529] GAGCAGCAUGGCGUCGCUGCUCAC (SEQ ID NO: 984)-[spacer]-[gRNA core]-[editing template]-[PBS]- CCAUCAGUUGACACCCUGAGG (SEQ ID NO: 985), or GAGCAGCAUGGCGUCGCUGCUCAC (SEQ ID NO: 984)-[spacer]-[gRNA core]-[editing template]- [PBS]- CCAUCAGUUGACACCCUGAGG-(U)n (SEQ ID NO: 986), wherein n is an integer between 3 and 7. (VS ribozyme kissing loop)

[0530] In some embodiments, the PEgRNA comprises the sequence GCAGACCUAAGUGGUGACAUAUGGUCUG (SEQ ID No: 987) at the 5’ end and / or the sequence CAUGCGAUUAGAAAUAAUCGCAUG (SEQ ID No: 988) at the 3’ end. In some embodiments, the PEgRNA comprises the following structure (tetraloop and receptor): GCAGACCUAAGUGGUGACAUAUGGUCUG (SEQ ID NO: 987)-[spacer]-[gRNA core]-[editing template]-[PBS]- CAUGCGAUUAGAAAUAAUCGCAUG (SEQ ID NO: 988), or GCAGACCUAAGUGGUGACAUAUGGUCUG (SEQ ID NO: 987)-[spacer]-[gRNA core]-[editing template]-[PBS]- CAUGCGAUUAGAAAUAAUCGCAUG-(U)n (SEQ ID NO: 989), wherein n is an integer between 3 and 7. The tetraloop / tetraloop receptor structure is italicized.WSGR Docket No. 59761-791.601

[0531] In some embodiments, the PEgRNA comprises the sequence GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUGCUUCGGCAUGGCG AAUGGGAC (SEQ ID No: 979) or UCUGCCAUCAAAGCUGCGACCGUGCUCAGUCUGGUGGGAGACGUCCCACCGGCCGGCAUG GUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUGCUUCGGCAUGGCGAAUGGGAC (SEQ ID No: 990).

[0532] Example sequences of components within PEgRNA are provided in Table 13. In some embodiments, the PEgRNA comprises a nucleic acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 91% identical, at least about 92% identical, at least about 93% identical, at least about 94% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to a sequence in Table 13. In some embodiments, the PEgRNA comprises a nucleic acid sequence that has no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 differences e.g., mutations e.g., deletions, substitutions and / or insertions compared to any one of the nucleic acid sequences set forth in Table 13.

[0533] Table 13. Exemplary sequences of components within PEgRNA.WSGR Docket No. 59761-791.601

[0534] In some embodiments, a PEgRNA comprises a gRNA core that comprises a modified direct repeat compared to the sequence of a naturally occurring CRISPR-Cas guide RNA scaffold, for example, a Cas9 gRNA scaffold. In some embodiments, the PEgRNA comprises a “flip and extension (F+E)” gRNA core, wherein one or more base pairs in a direct repeat is modified. In some embodiments, the PEgRNA comprises a first direct repeat (the first paring element or the lower stem), wherein a Uracil is changed to a Adenine (such that in the stem region, a U-A base pair is changed to a A-U base pair). In some embodiments, the PEgRNA comprises a first direct repeat wherein the fourth U-A base pair in the stem is changed to a A-U base pair. In some embodiments, the PEgRNA comprises a first direct repeat wherein one or more U-A base pair is changed to a G-C or C-G base pair. For example, in some embodiments, the PEgRNA comprises a first direct repeat comprising a modification to a GUUUU- AAAAC pairing element, wherein one or more of the U-A base pairs is changed to a A-U base pair, a G- C base pair, or a C-G base pair. In some embodiments, the PEgRNA comprises an extended first direct repeat.

[0535] A PEgRNA and / or an ngRNA of this disclosure, in some embodiments, may include modified nucleotides, e.g., chemically modified DNA or RNA nucleobases, and may include one or more nucleobase analogs (e.g., modifications which might add functionality, such as temperature resilience). In some embodiments, PEgRNAs and / or ngRNAs as described herein may be chemically modified. The phrase “chemical modifications,” as used herein, can include modifications which introduce chemistries which differ from those seen in naturally occurring DNA or RNAs, for example, covalent modifications such as the introduction of modified nucleotides, (e.g., nucleotide analogs, or the inclusion of pendant groups which are not naturally found in DNA or RNA molecules).

[0536] In some embodiments, the PEgRNAs provided in the disclosure may further comprise nucleotides added to the 5’ of the PEgRNAs. In some embodiments, the PEgRNA further comprises 1, 2, or 3 additional nucleotides added to the 5’ end. The additional nucleotides can be guanine, cytosine, adenine, or uracil. In some embodiments, the additional nucleotide at the 5’ end of the PEgRNA is a guanine or cytosine. In some embodiments, the additional nucleotides can be chemically or biologically modified.

[0537] In some embodiments, the PEgRNAs provided in the disclosure may further comprise nucleotides to the 3’ of the PEgRNAs. In some embodiments, the PEgRNA further comprises 1, 2, or 3 additional nucleotides to the 3’ end. The additional nucleotides can be guanine, cytosine, adenine, or uracil. In some embodiments, the additional nucleotides at the 3’ end of the PEgRNA is a polynucleotide comprising at least 1 uracil. In some embodiments, the additional nucleotides can be chemically or biologically modified.

[0538] In some embodiments, a PEgRNA or ngRNA is produced by transcription from a template nucleotide, for example, a template plasmid. In some embodiments, a polynucleotide encoding the PEgRNA or ngRNA is appended with one or more additional nucleotides that improves PEgRNA orWSGR Docket No. 59761-791.601 ngRNA function or expression, e.g., expression from a plasmid that encodes the PEgRNA or ngRNA. In some embodiments, a polynucleotide encoding a PEgRNA or ngRNA is appended with one or more additional nucleotides at the 5’ end or at the 3’ end. In some embodiments, the polynucleotide encoding the PEgRNA or ngRNA is appended with a guanine at the 5’ end, for example, if the first nucleotide at the 5’ end of the spacer is not a guanine. In some embodiments, a polynucleotide encoding the PEgRNA or ngRNA is appended with nucleotide sequence CACC at the 5’ end. In some embodiments, the polynucleotide encoding the PEgRNA or ngRNA is appended with an additional nucleotide adenine at the 3’ end, for example, if the last nucleotide at the 3’ end of the PBS is a Thymine. In some embodiments, the polynucleotide encoding the PEgRNA or ngRNA is appended with additional nucleotide sequence TTTTTT, TTTTTTT, TTTTT, or TTTT at the 3’ end. In some embodiments, the PEgRNA or ngRNA comprises the appended nucleotides from the transcription template. In some embodiments, the PEgRNA or ngRNA further comprises one or more nucleotides at the 5’ end or the 3’ end in addition to spacer, PBS, and RTT sequences. in some embodiments, the PEgRNA or ngRNA further comprises a guanine at the 5’ end, for example, when the first nucleotide at the 5’ end of the spacer is not a guanine. In some embodiments, the PEgRNA or ngRNA further comprises nucleotide sequence CACC at the 5’ end. In some embodiments, the PEgRNA or ngRNA further comprises an adenine at the 3’ end, for example, if the last nucleotide at the 3’ end of the PBS is a thymine. In some embodiments, the PEgRNA or ngRNA further comprises nucleotide sequence UUUUUUU, UUUUUU, UUUUU, or UUUU at the 3’ end.

[0539] In some embodiments, the PEgRNAs and / or ngRNAs provided in this disclosure may have undergone a chemical or biological modifications. Modifications may be made at any position within a PEgRNA or ngRNA, and may include modification to a nucleobase or to a phosphate backbone of the PEgRNA or ngRNA. In some embodiments, chemical modifications can be a structure guided modifications. In some embodiments, a chemical modification is at the 5’ end and / or the 3’ end of a PEgRNA. In some embodiments, a chemical modification is at the 5’ end and / or the 3’ end of a ngRNA. In some embodiments, a chemical modification may be within the spacer sequence, the extension arm, the editing template sequence, or the primer binding site of a PEgRNA. In some embodiments, a chemical modification may be within the spacer sequence or the gRNA core of a PEgRNA or a ngRNA. In some embodiments, a chemical modification may be within the 3’ most nucleotides of a PEgRNA or ngRNA. In some embodiments, a chemical modification may be within the 3’ most end of a PEgRNA or ngRNA some embodiments, a PEgRNA or ngRNA comprises 3 contiguous chemically modified nucleotides at ification may be within the 5’ most end of a PEgRNA or ngRNA. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more chemically modified nucleotides at the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more chemically modified nucleotides at the 5’ end. In some embodiments, aWSGR Docket No. 59761-791.601 PEgRNA or ngRNA comprises 1, 2, 3, 4, or 5 or more chemically modified nucleotides at the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, or 5 more chemically modified nucleotides at the 5’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, or 3 or more chemically modified nucleotides at the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, or 3 more chemically modified nucleotides at the 5’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more contiguous chemically modified nucleotides at the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more contiguous chemically modified nucleotides at the 5’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, or 5 contiguous chemically modified nucleotides at the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, or 5 contiguous chemically modified nucleotides at the 5’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, or 3 contiguous chemically modified nucleotides at the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, or 3 contiguous chemically modified nucleotides at the 5’ end. In some embodiments, a PEgRNA or ngRNA comprises 3 contiguous chemically modified nucleotides at the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, 5, or more chemically modified nucleotides near the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 3 contiguous chemically modified nucleotides at the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 3 contiguous chemically modified nucleotides at the 5’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, 5, or more chemically modified nucleotides near the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, 5, or more contiguous chemically modified nucleotides near the 3’ end. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, 5, or more chemically modified nucleotides near the 3’ end, where the 3’ most nucleotide is not modified, and the 1, 2, 3, 4, 5, or more chemically modified nucleotides precede the 3’ most nucleotide in a 5’-to-3’ order. In some embodiments, a PEgRNA or ngRNA comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 or more chemically modified nucleotides near the 3’ end, where the 3’ most nucleotide is not modified, and the 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 or more chemically modified nucleotides precede the 3’ most nucleotide in a 5’-to-3’ order.

[0540] In some embodiments, a PEgRNA or ngRNA comprises one or more chemical modified nucleotides in the gRNA core. As exemplified in FIG. 3, the gRNA core of a PEgRNA may comprise one or more regions of a base paired lower stem, a base paired upper stem, where the lower stem and upper stem may be connected by a bulge comprising unpaired RNAs. The gRNA core may further comprise a nexus distal from the spacer sequence. In some embodiments, the gRNA core comprises one or more chemically modified nucleotides in the lower stem, upper stem, and / or the hairpin regions. In some embodiments, all of the nucleotides in the lower stem, upper stem, and / or the hairpin regions are chemically modified.WSGR Docket No. 59761-791.601

[0541] -O-thionocarbamate- pr -O- -O- -O- -O-methyl (M) RNA, a -O-methyl -O- -F RNA, a phosphorothioate bond modification, any other chemical modifications known in the art, or any combination thereof. A chemical modification may also include, for example, the incorporation of non-nucleotide linkages or modified nucleotides into the PEgRNA and / or ngRNA (e.g., modifications to one or both of the 3' and 5' ends of a guide RNA molecule). Such modifications can include the addition of bases to an RNA sequence, complexing the RNA with an agent (e.g., a protein or a complementary nucleic acid molecule), and inclusion of elements which change the structure of an RNA molecule (e.g., which form secondary structures). Prime Editing Compositions

[0542] Disclosed herein, in some embodiments, are compositions, systems, and methods using a prime editing composition. The term “prime editing composition” or “prime editing system” refers to compositions involved in the method of prime editing as described herein. A prime editing composition may include a prime editor, e.g., a prime editor fusion protein, and a PEgRNA. A prime editing composition may further comprise additional elements, such as second strand nicking ngRNAs. Components of a prime editing composition may be combined to form a complex for prime editing, or may be kept separately, e.g., for administration purposes.

[0543] In some embodiments, a prime editing composition comprises a prime editor fusion protein complexed with a PEgRNA and optionally complexed with a ngRNA. In some embodiments, the prime editing composition comprises a prime editor comprising a DNA binding domain and a DNA polymerase domain associated with each other through a PEgRNA. For example, the prime editing composition may comprise a prime editor comprising a DNA binding domain and a DNA polymerase domain linked to each other by an RNA-protein recruitment aptamer RNA sequence, which is linked to a PEgRNA. In some embodiments, a prime editing composition comprises a PEgRNA and a polynucleotide, a polynucleotide construct, or a vector that encodes a prime editor fusion protein.

[0544] In some embodiments, a prime editing composition comprises a PEgRNA, a ngRNA, and a polynucleotide, a polynucleotide construct, or a vector that encodes a prime editor fusion protein. In some embodiments, a prime editing composition comprises multiple polynucleotides, polynucleotide constructs, or vectors, each of which encodes one or more prime editing composition components. In some embodiments, the PEgRNA of a prime editing composition is associated with the DNA binding domain, e.g., a Cas9 nickase, of the prime editor. In some embodiments, the PEgRNA of a prime editingWSGR Docket No. 59761-791.601 composition complexes with the DNA binding domain of a prime editor and directs the prime editor to the target DNA.

[0545] In some embodiments, a prime editing composition comprises one or more polynucleotides that encode prime editor components and / or PEgRNA or ngRNAs. In some embodiments, a prime editing composition comprises a polynucleotide encoding a fusion protein comprising a DNA binding domain and a DNA polymerase domain. In some embodiments, a prime editing composition comprises (i) a polynucleotide encoding a fusion protein comprising a DNA binding domain and a DNA polymerase domain, and (ii) a PEgRNA or a polynucleotide encoding the PEgRNA. In some embodiments, a prime editing composition comprises (i) a polynucleotide encoding a fusion protein comprising a DNA binding domain and a DNA polymerase domain, (ii) a PEgRNA or a polynucleotide encoding the PEgRNA, and (iii) an ngRNA or a polynucleotide encoding the ngRNA. In some embodiments, a prime editing composition comprises (i) a polynucleotide encoding a DNA binding domain of a prime editor, e.g., a Cas9 nickase, (ii) a polynucleotide encoding a DNA polymerase domain of a prime editor, e.g., a reverse transcriptase, and (iii) a PEgRNA or a polynucleotide encoding the PEgRNA. In some embodiments, a prime editing composition comprises (i) a polynucleotide encoding a DNA binding domain of a prime editor, e.g., a Cas9 nickase, (ii) a polynucleotide encoding a DNA polymerase domain of a prime editor, e.g., a reverse transcriptase, (iii) a PEgRNA or a polynucleotide encoding the PEgRNA, and (iv) an ngRNA or a polynucleotide encoding the ngRNA.

[0546] In some embodiments, the polynucleotide encoding the DNA biding domain or the polynucleotide encoding the DNA polymerase domain further encodes an additional polypeptide domain, e.g., an RNA-protein recruitment domain, such as a MS2 coat protein domain. In some embodiments, a prime editing composition comprises (i) a polynucleotide encoding a N-terminal half of a prime editor fusion protein and an intein-N and (ii) a polynucleotide encoding a C-terminal half of a prime editor fusion protein and an intein-C. In some embodiments, a prime editing composition comprises (i) a polynucleotide encoding a N-terminal half of a prime editor fusion protein and an intein-N (ii) a polynucleotide encoding a C-terminal half of a prime editor fusion protein and an intein-C, (iii) a PEgRNA or a polynucleotide encoding the PEgRNA, and / or (iv) an ngRNA or a polynucleotide encoding the ngRNA. In some embodiments, a prime editing composition comprises (i) a polynucleotide encoding a N-terminal portion of a DNA binding domain and an intein-N, (ii) a polynucleotide encoding a C-terminal portion of the DNA binding domain, an intein-C, and a DNA polymerase domain. In some embodiments, the DNA binding domain is a Cas protein domain, e.g., a Cas9 nickase. In some embodiments, the prime editing composition comprises (i) a polynucleotide encoding a N-terminal portion of a DNA binding domain and an intein-N, (ii) a polynucleotide encoding a C-terminal portion of the DNA binding domain, an intein-C, and a DNA polymerase domain, (iii) a PEgRNA or a polynucleotide encoding the PEgRNA, and / or (iv) a ngRNA or a polynucleotide encoding the ngRNA.WSGR Docket No. 59761-791.601

[0547] In some embodiments, a prime editing system comprises one or more polynucleotides encoding one or more prime editor polypeptides, wherein activity of the prime editing system may be temporally regulated by controlling the timing in which the vectors are delivered. For example, in some embodiments, a polynucleotide encoding the prime editor and a polynucleotide encoding a PEgRNA may be delivered simultaneously. For example, in some embodiments, a polynucleotide encoding the prime editor and a polynucleotide encoding a PEgRNA may be delivered sequentially.

[0548] In some embodiments, a polynucleotide encoding a component of a prime editing system may further comprise an element that is capable of modifying the intracellular half-life of the polynucleotide and / or modulating translational control. In some embodiments, the polynucleotide is a RNA, for example, an mRNA. In some embodiments, the half-life of the polynucleotide, e.g., the RNA may be increased. In some embodiments, the half-life of the polynucleotide, e.g., the RNA may be decreased. In some embodiments, the element may be capable of increasing the stability of the polynucleotide, e.g., the RNA. In some embodiments, the element may be capable of decreasing the stability of the In some embodiments, the element may include a polyadenylation signal (PA). In some embodiments, the element may include a cap, e.g., an upstream mRNA or PEgRNA end. In some embodiments, the RNA may comprise no PA such that it is subject to quicker degradation in the cell after transcription.

[0549] In some embodiments, the element may include at least one AU-rich element (ARE). The AREs may be bound by ARE binding proteins (ARE-BPs) in a manner that is dependent upon tissue type, cell type, timing, cellular localization, and environment. In some embodiments the destabilizing element may promote RNA decay, affect RNA stability, or activate translation. In some embodiments, the ARE may comprise 50 to 150 nucleotides in length. In some embodiments, the ARE may comprise at least one copy of the sequence AUUUA. In some embodiments, at least one ARE may be added to the the RNA. In some embodiments, the element may be a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE). In further embodiments, the element is a modified and / or truncated WPRE sequence that is capable of enhancing expression from the transcript. In some embodiments, the WPRE selected from other RNA sequence motifs that are enriched in either fast- or slow-decaying transcripts. In some embodiments, the polynucleotide, e.g., a vector, encoding the PE or the PEgRNA may be self- destroyed via cleavage of a target sequence present on the polynucleotide, e.g., a vector. The cleavage may prevent continued transcription of a PE or a PEgRNA.

[0550] Polynucleotides encoding prime editing composition components can be DNA, RNA, or any combination thereof. In some embodiments, a polynucleotide encoding a prime editing composition component is an expression construct. In some embodiments, a polynucleotide encoding a prime editing composition component is a vector. In some embodiments, the vector is a DNA vector. In some embodiments, the vector is a plasmid. In some embodiments, the vector is a virus vector, e.g., a retroviralWSGR Docket No. 59761-791.601 vector, adenoviral vector, lentiviral vector, herpesvirus vector, or an adeno-associated virus vector (AAV).

[0551] In some embodiments, polynucleotides encoding polypeptide components of a prime editing composition are codon optimized by replacing at least one codon (e.g., about or more than about 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons) of the native sequence with codons that are more frequently or most frequently used in the genes of that host cell while maintaining the native amino acid sequence. In some embodiments, a polynucleotide encoding a polypeptide component of a prime editing composition ime editing composition component is a messenger RNA (mRNA). In some embodiments, the mRNA comprises a

[0552] Unless otherwise indicated, references to nucleotide positions in human chromosomes are as set forth in human genome assembly consortium Human build 38 (GRCh38), GenBank accession GCF_000001405.38.

[0553] Provided herein in some embodiments are example sequences for PEgRNAs, including PEgRNA spacers, PBS, RTT, and ngRNA spacers for a prime editing system comprising a nuclease that recognizes the PAM sequence “NG.” In some embodiments, a PAM motif on the edit strand comprises an “NG” motif, wherein N is any nucleotide.

[0554] Exemplary combinations of PEgRNA components, e.g., spacer, PBS, and edit template / RTT, exemplary full-length PEgRNAs, as well as combinations of PEgRNA and corresponding ngRNA(s) are provided in Tables 14-20. Tables 14-20 each contain three columns. The left column is the sequence number. The middle column provides the sequence of the component, labeled with a SEQ ID NO where required by ST.26 standard. Although all the sequences provided in Tables 14-20 are RNA sequences, “T” is used instead of a “U” in the sequences for consistency with the ST.26 standard. The right column contains a description of the sequence. All of the RTT and full-length PEgRNAs in Tables 14-20 are designed to be capable of correcting c.1033G>C and c.1040C>T mutations in the RHO gene, mutations which result in V345L and P347L mutations respectively in the encoded rhodopsin protein. However, the disclosed RTT and full-length PEgRNA are also capable of correcting other mutations in the RHO gene that are found in the portion of the gene that shares homology or complementarity with the edit template / RTT. Such other mutations may include, for example: c.1033G>A (p.Val345Met), c.1030C>T (p.Gln344Ter), c.1040C>A (p.Pro347Gln), c.1040C>G (p.Pro347Arg), c.1039C>G (p.Pro347Ala), c.1039C>T (p.Pro347Ser), c.1045T>G (p.Ter349Glu), c.1034T>G (p.Val345Gly), c.1045T>C (p.Ter349Gln), c.1028G>A (p.Ser343Asn), c.1033G>T (p.Val345Leu), c.1031A>C (p.Gln344Pro), c.1039C>A (p.Pro347Thr), c.1034T>C (p.Val345Ala), c.1034T>A (p.Val345Glu), c.1040del (p.Pro347fs), or a combination thereof. These mutations, which occur at the c-terminus of exon 5 of theWSGR Docket No. 59761-791.601 RHO gene cause rhodopsin protein mislocalization and are associated with early onset, severe retinal degeneration.

[0555] The PEgRNAs exemplified in Tables 14-20 comprise: (a) a spacer comprising at its 3’ end a sequence corresponding to a listed PEgRNA spacer sequence; (b) a gRNA core capable of complexing with a Cas9 protein, and (c) an extension arm comprising: (i) an editing template comprising at its 3’ end any RTT sequence from the same table as the PEgRNA spacer, and (ii) a primer binding site (PBS) comprising at its 5’ end any PBS sequence from the same table as the PEgRNA spacer. The PEgRNA spacer can be, for example, 17-22 nucleotides in length. The PEgRNA spacers in Tables 14-20 are annotated with their PAM sequence(s), enabling the selection of a prime editor comprising an appropriate Cas9 protein. The editing template can be referred to as a reverse transcription template (RTT). The editing template can encode wildtype RHO gene sequence (annotated as simply RTT in Tables 14-20). Alternatively, the editing template can encode one or more synonymous mutations relative to the wildtype RHO gene. The one or more synonymous mutations can be PAM silencing mutations. RTT encoding synonymous PAM silencing mutations are annotated as such in Tables 14-20. In some of Tables 14-20, RTT are further annotated with a * followed by a number code. As described below, a PE3 or PE3b ngRNA spacer annotated with the same * and number code as an RTT was designed to have perfect complementarity to the edit strand post-edit by a PEgRNA containing the RTT. The PBS can be, for example, 5 to 19 nucleotides in length.

[0556] In some embodiments, the spacer comprises a nucleic acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 91% identical, at least about 92% identical, at least about 93% identical, at least about 94% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any one of the nucleic acid sequences set forth in Tables 14-20. In some embodiments, the spacer comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 differences e.g., mutations e.g., deletions, substitutions and / or insertions compared to any one of the nucleic acid sequences set forth in Tables 14-20.

[0557] In some embodiments, the PBS comprises a nucleic acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 91% identical, at least about 92% identical, at least about 93% identical, at least about 94% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any one of the nucleic acid sequences set forth in Tables 14-20. In some embodiments, the PBS comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 differences e.g., mutations e.g., deletions, substitutions and / or insertions compared to any one of the nucleic acid sequences set forth in Tables 14-20.WSGR Docket No. 59761-791.601

[0558] In some embodiments, the RTT comprises a nucleic acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 91% identical, at least about 92% identical, at least about 93% identical, at least about 94% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any one of the nucleic acid sequences set forth in Tables 14-20. In some embodiments, the RTT comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 differences e.g., mutations e.g., deletions, substitutions and / or insertions compared to any one of the nucleic acid sequences set forth in Tables 14-20. In some embodiments, the editing template encodes one or more synonymous mutations relative to a wild type Rhodopsin gene. In some embodiments, the editing template encodes a wild type amino acid sequence of a Rhodopsin protein.

[0559] In embodiments, the PEgRNA comprises a nucleic acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 91% identical, at least about 92% identical, at least about 93% identical, at least about 94% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any one of the nucleic acid sequences set forth in Tables 14-20. In some embodiments, the PEgRNA comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 differences e.g., mutations e.g., deletions, substitutions and / or insertions compared to any one of the nucleic acid sequences set forth in Tables 14-20. In some embodiments, the editing template encodes one or more synonymous mutations relative to a wild type Rhodopsin gene. In some embodiments, the editing template encodes a wild type amino acid sequence of a Rhodopsin protein.

[0560] The PEgRNA provided in Tables 14-20 can comprise, from 5’ to 3’, the spacer, the gRNA core, the edit template, and the PBS. The 3’ end of the edit template can be contiguous with the 5’ end of the PBS. The PEgRNA can comprise multiple RNA molecules or can be a single RNA molecule. Any PEgRNA exemplified in Tables 14-20 may comprise, or further comprise, a 3’ motif at the 3’ end of the extension arm, such as a universal motif, a sequence specific motif, or a series of 1, 2, 3, 4, 5, 6, 7 or more U nucleotides. In some embodiments, a universal or structural 3’ motif is used that is capable of forming a tertiary structure on its own (e.g., a hairpin, a pseudoknot, or other RNA structure). In some embodiments, a sequence specific motif is used that is designed to hybridize with a portion of the RTT while not covering the PBS. Whether a universal or sequence specific motif is used, it can be connected to the 3’ of the PBS via a linker sequence. In some embodiments, the PEgRNA comprises 4 U nucleotides at its 3’ end. Without being bound by theory, such 3’ motifs are believed to increase PEgRNA stability. The PEgRNA may be chemically synthesized and may alternatively or additionally comprise one or more chemical modifications, such as phosphorothioate (PS) bond(s), 2’-O-methylated (2’-Ome) nucleotides, or a combination thereof. In some embodiments, the PEgRNA comprise 3’WSGR Docket No. 59761-791.601 mN*mN*mN*N and 5’mN*mN*mN* modifications, where m indicates that the nucleotide contains a 2’-O-Me modification and a * indicates the presence of a phosphorothioate bond. In some embodiments, the PEgRNA comprises 3’ mU*mU*mU*U and 5’mN*mN*mN* modifications, where m indicates that the nucleotide contains a 2’-O-Me modification, U indicat...

Claims

WSGR Docket No. 59761-791.601 CLAIMS WHAT IS CLAIMED IS:

1. A prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 678; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 678, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

2. A prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 678; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end any one of SEQ ID NOs: 698-701, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO:

678.

3. The PEgRNA of any one of claims 1-2, wherein the spacer is from 17-22 nucleotides in length.

4. The PEgRNA of any one of claims 1-3, wherein the spacer comprises at its 3’ end any one of SEQ ID NOs: 679-682, or 147.

5. The PEgRNA of claim 4, wherein the spacer comprises at its 3’ end SEQ ID NO:

147.

6. The PEgRNA of claim 4, wherein the spacer comprises at its 3’ end SEQ ID NO:

681.

7. The PEgRNA of any one of claims 1-6, wherein the editing template comprises SEQ ID NO: 698 at its 3’ end and encodes a AGG-to-GGT PAM silencing edit.

8. The PEgRNA of claim 7, wherein the editing template comprises at its 3’ end SEQ ID NOs: 702, 706, 710, 714, 718, 722, 726, 730, 734, 738, 742, 746, 750, 754, 758, 762, 766, 770, 774, 778, 782, 786, 790, 794, or 798.WSGR Docket No. 59761-791.601 9. The PEgRNA of any one of claims 1-6, wherein the editing template comprises SEQ ID NO: 699 at its 3’ end.

10. The PEgRNA of claim 9, wherein the editing template comprises at its 3’ end any one of SEQ ID NOs: 703, 707, 711, 715, 719, 723, 727, 731, 735, 739, 743, 747, 751, 755, 759 ,763, 767, 771, 775, 779, 783, 787, 791, 795, or 799.

11. The PEgRNA of claim 10, wherein the editing template comprises at its 3’ end SEQ ID NO:

711.

12. The PEgRNA of any one of claims 1-6, wherein the editing template comprises SEQ ID NO: 700 at its 3’ end and encodes a AGG-to-GGC PAM silencing edit.

13. The PEgRNA of claim 12, wherein the editing template comprises at its 3’ end SEQ ID NOs: 704, 708, 712, 716, 720, 724, 728, 732, 736, 740, 744, 748, 752, 756, 760, 764, 768, 772, 776, 780, 784, 788, 792, 796, or 800.

14. The PEgRNA of claim 13, wherein the editing template comprises at its 3’ end SEQ ID NO:

712.

15. The PEgRNA of any one of claims 1-6, wherein the editing template comprises SEQ ID NO: 701 at its 3’ end and encodes a AGG-to-GGA PAM silencing edit.

16. The PEgRNA of claim 15, wherein the editing template comprises at its 3’ end SEQ ID NOs: 705, 709, 713, 717, 721, 725, 729, 733, 737, 741, 745, 749, 753, 757, 761, 765, 769, 773, 777, 781, 785, 789, 793, 797, or 801.

17. The PEgRNA of claim 16, wherein the editing template comprises at its 3’ end SEQ ID NO:

713.

18. The PEgRNA of any one of claims 1-17, wherein the editing template has a length of 40 nucleotides or less.

19. The PEgRNA of claim 18, wherein the editing template is 15 to 40 nucleotides in length.

20. The PEgRNA of any one of claims 1-19, wherein the PBS comprises at its 5’end a sequence corresponding to sequence number 683.

21. The PEgRNA of claim 20, wherein the PBS comprises any one of sequence numbers 684, 685, 686, 687, 688, 689, 690, 691, 692, 693, 694, 695, 696, or 697.

22. The PEgRNA of claim 21, wherein the PBS comprises a sequence of sequence number or SEQ ID NO:

690.

23. The PEgRNA of claim 21, wherein the PBS comprises a sequence of sequence number or SEQ ID NO:

692.

24. The PEgRNA of any one of claims 1-23, wherein the PBS is 5 to 19 nucleotides in length.

25. The PEgRNA of any one of claims 1-24, comprising a PEgRNA sequence selected from any one of SEQ ID NOs: 802-845, 1064-1132, 1151-1219, 1238-1306, 1325-1393, 1417, 1418, 1422, 1423, 1427, 1428, 1432, 1433, 1460-1469, 1482, 1483, 1491-1511, 1535, 1536, 1538-1544, 1570, 1596, or 1597.

26. The PEgRNA of claim 25, wherein the PEgRNA comprises a sequence of SEQ ID NO:

815.

27. The PEgRNA of claim 25, wherein the PEgRNA comprises a sequence of SEQ ID NO:

813.

28. The PEgRNA of claim 25, wherein the PEgRNA comprises a sequence of SEQ ID NO: 826.WSGR Docket No. 59761-791.601 29. The PEgRNA of claim 25, wherein the PEgRNA comprises a sequence of SEQ ID NO: 1100.

30. The PEgRNA of claim 25, wherein the PEgRNA comprises a sequence of SEQ ID NO: 1596.

31. The PEgRNA of claim 25, wherein the PEgRNA comprises a sequence of SEQ ID NO: 1363.

32. The PEgRNA of claim 25, wherein the PEgRNA comprises a sequence of SEQ ID NO: 1597.

33. The PEgRNA of any one of claims 1-25, wherein the spacer comprises a sequence of SEQ ID NO: 147, the editing template comprises a sequence of SEQ ID NO: 713, and the PBS comprises a sequence of SEQ ID NO:

690.

34. The PEgRNA of any one of claims 1-25, wherein the spacer comprises a sequence of SEQ ID NO: 147, the editing template comprises a sequence of SEQ ID NO: 711, and the PBS comprises a sequence of SEQ ID NO:

690.

35. The PEgRNA of any one of claims 1-25, wherein the spacer comprises a sequence of SEQ ID NO: 147, the editing template comprises a sequence of SEQ ID NO: 712, and the PBS comprises a sequence of SEQ ID NO:

692.

36. The PEgRNA of any one of claims 1-35, wherein the gRNA core comprises a sequence of SEQ ID NO:

854.

37. The PEgRNA of any one of claims 1-35, wherein the gRNA core comprises a sequence of SEQ ID NO:

858.

38. The PEgRNA of any one of claims 1-35, wherein the gRNA core comprises a sequence of SEQ ID NO:

859.

39. The PEgRNA of any one of claims 1-38, wherein the PEgRNA comprises a 3’ motif.

40. The PEgRNA of claim 39, wherein the PEgRNA comprises a linker between the PBS and the 3’ motif.

41. The PEgRNA of claim 40, wherein the linker comprises a sequence of sequence number 1000.

42. The PEgRNA of claim 39 or 40, wherein the 3' motif comprises a sequence of SEQ ID NO:

948.

43. The PEgRNA of any one of claims 1-38, wherein the PEgRNA further comprises a COMP-tag.

44. The PEgRNA of claim 43, wherein the PEgRNA comprises a linker between the PBS and the COMP-tag.

45. The PEgRNA of claim 44, wherein the linker comprises a sequence of sequence number 1018.

46. The PEgRNA of claim 43 or 44, wherein the COMP-tag comprises a sequence of sequence number 1052.

47. The PEgRNA of any one of claims 39-42, wherein the spacer comprises a sequence of SEQ ID NO: 147, the editing template comprises a sequence of SEQ ID NO: 712, the PBS comprises a sequence of SEQ ID NO: 692, the gRNA core comprises a sequence of SEQ ID NO: 858, the 3’ motif comprises a sequence of SEQ ID NO: 948, and the linker between the PBS and the 3’ motif comprises a sequence of sequence number 1000.WSGR Docket No. 59761-791.601 48. The PEgRNA of any one of claims 43-46, wherein the spacer comprises a sequence of SEQ ID NO: 147, the editing template comprises a sequence of SEQ ID NO: 712, the PBS comprises a sequence of SEQ ID NO: 692, the gRNA core comprises a sequence of SEQ ID NO: 859, the COMP -tag comprises a sequence of sequence number 1052, and the linker between the PBS and the 3’ motif comprises a sequence of sequence number 1018.

49. A prime editing system comprising: (a) the PEgRNA or the nucleic acid of any one of claims 1-48, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 307, 308, 309, 191, 311, 312, 507, 313, 508, 509, or 314; and (ii) an ngRNA core capable of binding a Cas9 protein.

50. The prime editing system of claim 49, wherein the spacer of the ngRNA comprises at its 3’ end any one of SEQ ID NOs: 307, 308, 309, 191, 311, 312, 507, 313, 508, 509, or 314.

51. The prime editing system of claims 49 or 50, wherein the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO:

307.

52. The prime editing system of claims 49 or 50, wherein the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO:

308.

53. The prime editing system of claims 49 or 50, wherein the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO:

314.

54. The prime editing system of claims 49 or 50, wherein the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO:

509.

55. The prime editing system of claims 49 or 50, wherein the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO:

313.

56. The prime editing system of any one of claims 49-55, wherein the ngRNA comprises a sequence selected from any one of SEQ ID NOs: 333-339, or 846-849.

57. The prime editing system of claim 56, wherein the ngRNA comprises a sequence of SEQ ID NO:

849.

58. The prime editing system of claim 56, wherein the ngRNA comprises a sequence of SEQ ID NO:

334.

59. The prime editing system of claim 56, wherein the ngRNA comprises a sequence of SEQ ID NO:

336.

60. The prime editing system of claim 56, wherein the ngRNA comprises a sequence of SEQ ID NO:

846.

61. The prime editing system of claim 56, wherein the ngRNA comprises a sequence of SEQ ID NO: 337.WSGR Docket No. 59761-791.601 62. The prime editing system of any one of claims 49-61, wherein the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 713, and the PBS of SEQ ID NO: 690; and the ngRNA comprises the spacer of SEQ ID NO:

307.

63. The prime editing system of any one of claims 49-61, wherein the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 713, and the PBS of SEQ ID NO: 690; and the ngRNA comprises the spacer of SEQ ID NO:

308.

64. The prime editing system of any one of claims 49-61, wherein the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 713, and the PBS of SEQ ID NO: 690; and the ngRNA comprises the spacer of SEQ ID NO:

314.

65. The prime editing system of any one of claims 49-61, wherein the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 713, and the PBS of SEQ ID NO: 690; and the ngRNA comprises the spacer of SEQ ID NO:

509.

66. The prime editing system of any one of claims 49-61, wherein the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 711, and the PBS of SEQ ID NO: 690; and the ngRNA comprises the spacer of SEQ ID NO:

313.

67. The prime editing system of any one of claims 49-61, wherein the PEgRNA comprises: the spacer of SEQ ID NO: 147, the editing template of SEQ ID NO: 712, and the PBS of SEQ ID NO: 692; and the ngRNA comprises the spacer of SEQ ID NO:

314.

68. The prime editing system of any one of claims 49-67, wherein the ngRNA core or the gRNA core comprises a sequence of SEQ ID NO:

854.

69. The prime editing system of claim 49, wherein the PEgRNA comprises a sequence of SEQ ID NO: 815 and the ngRNA comprises a sequence of SEQ ID NO:

849.

70. The prime editing system of claim 49, wherein the PEgRNA comprises a sequence of SEQ ID NO: 815 and the ngRNA comprises a sequence of SEQ ID NO:

334.

71. The prime editing system of claim 49, wherein the PEgRNA comprises a sequence of SEQ ID NO: 815 and the ngRNA comprises a sequence of SEQ ID NO:

336.

72. The prime editing system of claim 49, wherein the PEgRNA comprises a sequence of SEQ ID NO: 815 and the ngRNA comprises a sequence of SEQ ID NO:

846.

73. The prime editing system of claim 49, wherein the PEgRNA comprises a sequence of SEQ ID NO: 813 and the ngRNA comprises a sequence of SEQ ID NO:

337.

74. The prime editing system of claim 49, wherein the PEgRNA comprises a sequence of SEQ ID NO: 826 and the ngRNA comprises a sequence of SEQ ID NO:

336.

75. The prime editing system of claim 49, wherein the PEgRNA comprises a sequence of SEQ ID NO: 1100 and the ngRNA comprises a sequence of SEQ ID NO:

336.

76. The prime editing system of claim 49, wherein the PEgRNA comprises a sequence of SEQ ID NO: 1363 and the ngRNA comprises a sequence of SEQ ID NO: 336.WSGR Docket No. 59761-791.601 77. The prime editing system of claim 49, wherein the PEgRNA comprises a sequence of SEQ ID NO: 1596 and the ngRNA comprises a sequence of SEQ ID NO:

336.

78. The prime editing system of claim 49, wherein the PEgRNA comprises a sequence of SEQ ID NO: 1597 and the ngRNA comprises a sequence of SEQ ID NO:

336.

79. A prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 542; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 542, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

80. A prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 542; b. a gRNA core capable of binding to a Cas9 protein, and c. an extension arm comprising: i. an editing template comprising at its 3’ end any one of SEQ ID NOs: 562-565, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO:

542.

81. The PEgRNA of any claim 79 or 80, wherein the spacer is from 17-22 nucleotides in length.

82. The PEgRNA of any one of claims 79-81, wherein the spacer comprises at its 3’ end any one of SEQ ID NOs: 543, 544, 132, 545, or 546.

83. The PEgRNA of claim 82, wherein the spacer comprises at its 3’ end SEQ ID NO:

132.

84. The PEgRNA of any one of claims 79-83, wherein the editing template comprises SEQ ID NO: 562 at its 3’ end and encodes a AGG-to-ATG PAM silencing edit.

85. The PEgRNA of claim 84, wherein the editing template comprises at its 3’ end SEQ ID NOs: 566, 570, 574, 578, 582, 586, 590, 594, 598, 602, 606, 610, 614, 618, 622, 626, 630, 634, 638, or 642.

86. The PEgRNA of claim 85, wherein the editing template comprises at its 3’ end SEQ ID NO: 566.WSGR Docket No. 59761-791.601 87. The PEgRNA of any one of claims 79-83, wherein the editing template comprises SEQ ID NO: 563 at its 3’ end.

88. The PEgRNA of claim 87, wherein the editing template comprises at its 3’ end SEQ ID NOs: 567, 571, 575, 579, 583, 587, 591, 595, 599, 603, 607, 611, 615, 619, 623, 627, 631, 635, 639, or 643.

89. The PEgRNA of any one of claims 79-83, wherein the editing template comprises SEQ ID NO: 564 at its 3’ end and encodes a AGG-to-ACG PAM silencing edit.

90. The PEgRNA of claim 89, wherein the editing template comprises at its 3’ end SEQ ID NOs: 568, 572, 576, 580, 584, 588, 592, 596, 600, 604, 608, 612, 616, 620, 624, 628, 632, 636, 640, or 644.

91. The PEgRNA of any one of claims 79-83, wherein the editing template comprises SEQ ID NO: 565 at its 3’ end and encodes a AGG-to-AAG PAM silencing edit.

92. The PEgRNA of claim 91, wherein the editing template comprises at its 3’ end SEQ ID NOs: 569, 573, 577, 581, 585, 589, 593, 597, 601, 605, 609, 613, 617, 621, 625, 629, 633, 637, 641, or 645.

93. The PEgRNA of any one of claims 79-83, wherein the editing template has a length of 40 nucleotides or less.

94. The PEgRNA of claim 93, wherein the editing template is 20 to 40 nucleotides in length.

95. The PEgRNA of any one of claims 79-94, wherein the PBS comprises at its 5’end a sequence corresponding to sequence number 547.

96. The PEgRNA of claim 95, wherein the PBS comprises any one of sequence numbers 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, or 561.

97. The PEgRNA of claim 96, wherein the PBS comprises a sequence of sequence number 550.

98. The PEgRNA of any one of claims 79-97, wherein the PBS is 5 to 19 nucleotides in length.

99. The PEgRNA of any one of claims 79-98, comprising a PEgRNA sequence selected from any one of SEQ ID NOs: 646-677, 1133-1150, 1220-1237, 1307-1324, 1394-1411, 1437, 1438, 1470-1473, 1476, 1477, 1513, 1514, 1545, 1546, or 1584-1595.

100. The PEgRNA of claim 99, wherein the PEgRNA sequence comprises a sequence of SEQ ID NO: 1584.

101. The PEgRNA of any one of claims 79-100, wherein the spacer comprises a sequence of SEQ ID NO: 132, the editing template comprises a sequence of SEQ ID NO: 566, and the PBS comprises a sequence of SEQ ID NO:

550.

102. The PEgRNA of any one of claims 79-101, wherein the gRNA core comprises a sequence of SEQ ID NO:

859.

103. The PEgRNA of any one of claims 79-102, wherein the PEgRNA comprises a 3’ motif.

104. The PEgRNA of claim 103, wherein the PEgRNA comprises a linker between the PBS and the 3’ motif.

105. The PEgRNA of claim 104, wherein the linker comprises a sequence of sequence number 999.

106. The PEgRNA of claim 103 or 104, wherein the 3’ motif comprises a sequence of SEQ ID NO: 948.WSGR Docket No. 59761-791.601 107. The PEgRNA of any one of claims 103-106, wherein the spacer comprises a sequence of SEQ ID NO: 132, the editing template comprises a sequence of SEQ ID NO: 712, the PBS comprises a sequence of sequence number 550, the gRNA core comprises a sequence of SEQ ID NO: 859, the 3’motif comprises a sequence of SEQ ID NO: 948, and the linker between the PBS and the 3’ motif comprises a sequence of sequence number 999.

108. A prime editing system comprising: (a) the PEgRNA or the nucleic acid of any one of claims 79- 107, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 307, 308, 309, 191, 311, 312, 313, or 314; and (ii) an ngRNA core capable of binding a Cas9 protein.

109. The prime editing system of claim 108, wherein the spacer of the ngRNA comprises at its 3’ end any one of SEQ ID NOs: 307, 308, 309, 191, 311, 312, 313, or 314.

110. The prime editing system of claim 97, wherein the spacer of the ngRNA comprises at its 3’ end a sequence of SEQ ID NO:

314.

111. The prime editing system of any one of claims 108-110, wherein the ngRNA comprises a sequence selected from any one of SEQ ID NOs: 333-339.

112. The prime editing system of claim 111, wherein the ngRNA comprises a sequence of SEQ ID NO:

336.

113. The prime editing system of any one of claims 108-112, wherein the PEgRNA comprises: the spacer of SEQ ID NO: 132, the editing template of SEQ ID NO: 566, and the PBS of SEQ ID NO: 550; and the ngRNA comprises the spacer of SEQ ID NO:

314.

114. The prime editing system of claim 108, wherein the PEgRNA comprises a sequence of SEQ ID NO: 1584 and the ngRNA comprises a sequence of SEQ ID NO:

336.

115. The prime editing system of any one of claims 108-114, wherein the ngRNA core or the gRNA core comprises a sequence of SEQ ID NO:

854.

116. A prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 1; and b. a gRNA core capable of binding to a Cas9 protein; c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 1, wherein the first strand and second strand are complementary to each other,WSGR Docket No. 59761-791.601 wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

117. A prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 1; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end any one of SEQ ID NOs: 22-25, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO:

1.

118. The PEgRNA of claim 116 or 117, wherein the spacer is from 17-22 nucleotides in length.

119. The PEgRNA of any one of claims 116-118, wherein the spacer comprises at its 3’ end any one of SEQ ID NOs: 2-6.

120. The PEgRNA of claim 119, wherein the spacer comprises at its 3’ end SEQ ID NO:

4.

121. The PEgRNA of any one of claims 116-120, wherein the editing template comprises SEQ ID NO: 22 at its 3’ end and encodes a TGG-to-TTG PAM silencing edit.

122. The PEgRNA of claim 121, wherein the editing template comprises at its 3’ end SEQ ID NOs: 26, 30, 34, 38, 42, 46, 50, 54, 58, 62, 66, 70, 74, 78, 82, 86, 90, 94, 98, 102, 106, 110, 114, 118, 122, or 126.

123. The PEgRNA of any one of claims 116-120, wherein the editing template comprises SEQ ID NO: 23 at its 3’ end.

124. The PEgRNA of claim 123, wherein the editing template comprises at its 3’ end SEQ ID NOs: 27, 31, 35, 39, 43, 47, 51, 55, 59, 63, 67, 71, 75, 79, 83, 87, 91, 95, 99, 103, 107, 111, 115, 119, 123, or 127.

125. The PEgRNA of any one of claims 116-120, wherein the editing template comprises SEQ ID NO: 24 at its 3’ end and encodes a TGG-to-TCG PAM silencing edit.

126. The PEgRNA of claim 125, wherein the editing template comprises at its 3’ end SEQ ID NOs: 28, 32, 36, 40, 44, 48, 52, 56, 60, 64, 68, 72, 76, 80, 84, 88, 92, 96, 100, 104, 108, 112, 116, 120, 124, or 128.

127. The PEgRNA of any one of claims 116-120, wherein the editing template comprises SEQ ID NO: 25 at its 3’ end and encodes a TGG-to-TAG PAM silencing edit.

128. The PEgRNA of claim 127, wherein the editing template comprises at its 3’ end SEQ ID NOs: 29, 33, 37, 41, 45, 49, 53, 57, 61, 65, 69, 73, 77, 81, 85, 89, 93, 97, 101, 105, 109, 113, 117, 121, or 125.

129. The PEgRNA of any one of claims 116-128, wherein the editing template has a length of 40 nucleotides or less.

130. The PEgRNA of claim 129, wherein the editing template is 14 to 40 nucleotides in length.WSGR Docket No. 59761-791.601 131. The PEgRNA of any one of claims 116-130, wherein the PBS comprises at its 5’end a sequence corresponding to sequence number 7.

132. The PEgRNA of claim 131, wherein the PBS comprises any one of sequence numbers 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22.

133. The PEgRNA of any one of claims 116-132, wherein the PBS is 5 to 19 nucleotides in length.

134. The PEgRNA of any one of claims 116-133, comprising a PEgRNA sequence selected from any one of SEQ ID NOs: 156-187.

135. A prime editing system comprising: (a) the PEgRNA or the nucleic acid of any one of claims 116- 134, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 130-155; and (ii) an ngRNA core capable of binding a Cas9 protein.

136. The prime editing system of claim 135, wherein the spacer of the ngRNA comprises at its 3’ end any one of SEQ ID NOs: 130-155.

137. A prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 188; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 188, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

138. A prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 188; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end any one of SEQ ID NOs: 209, 210, 211, or 212, andWSGR Docket No. 59761-791.601 ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO:

188.

139. The PEgRNA of claim 137 or 138, wherein the spacer is from 17-22 nucleotides in length.

140. The PEgRNA of any one of claims 137-139, wherein the spacer comprises at its 3’ end any one of SEQ ID NOs: 189, 190, 191, 192, or 193.

141. The PEgRNA of claim 140, wherein the spacer comprises at its 3’ end SEQ ID NO:

191.

142. The PEgRNA of any one of claims 137-141, wherein the editing template comprises SEQ ID NO: 209 at its 3’ end and encodes a CGG-to-CTG PAM silencing edit.

143. The PEgRNA of claim 142, wherein the editing template comprises at its 3’ end SEQ ID NOs: 213, 217, 221, 225, 229, 233, 237, 241, 245, 249, or 253.

144. The PEgRNA of any one of claims 137-141, wherein the editing template comprises SEQ ID NO: 210 at its 3’ end.

145. The PEgRNA of claim 144, wherein the editing template comprises at its 3’ end SEQ ID NOs: 214, 218, 222, 226, 230, 234, 238, 242, 246, 250, or 254.

146. The PEgRNA of any one of claims 137-141, wherein the editing template comprises SEQ ID NO: 211 at its 3’ end and encodes a CGG-to-CCG PAM silencing edit.

147. The PEgRNA of claim 146, wherein the editing template comprises at its 3’ end SEQ ID NOs: 215, 219, 223, 227, 231, 235, 239, 243, 247, 251, or 255.

148. The PEgRNA of any one of claims 137-141, wherein the editing template comprises SEQ ID NO: 212 at its 3’ end and encodes a CGG-to-CAG PAM silencing edit.

149. The PEgRNA of claim 148, wherein the editing template comprises at its 3’ end SEQ ID NOs: 216, 220, 224, 228, 232, 236, 240, 244, 248, 252, or 256.

150. The PEgRNA of any one of claims 137-149, wherein the editing template has a length of 40 nucleotides or less.

151. The PEgRNA of claim 150, wherein the editing template is 29 to 40 nucleotides in length.

152. The PEgRNA of any one of claims 137-151, wherein the PBS comprises at its 5’end a sequence corresponding to sequence number 194.

153. The PEgRNA of claim 152, wherein the PBS comprises any one of sequence numbers 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, or 208.

154. The PEgRNA of any one of claims 137-153, wherein the PBS is 5 to 19 nucleotides in length.

155. The PEgRNA of any one of claims 137-154, comprising a PEgRNA sequence selected from any one of SEQ ID NOs: 261-272.

156. A prime editing system comprising: (a) the PEgRNA or the nucleic acid of any one of claims 137- 155, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises:WSGR Docket No. 59761-791.601 (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 130, 131, 257, 258, 259, 260, 132, 133, 134, 135, 136, 137, 138, 139, 140, 142, 145, 146, 147, 148, 150, 151, 152, 153, 154, or 155; and (ii) an ngRNA core capable of binding a Cas9 protein.

157. The prime editing system of claim 156, wherein the spacer of the ngRNA comprises at its 3’ end any one of SEQ ID NOs: 130, 131, 257, 258, 259, 260, 132, 133, 134, 135, 136, 137, 138, 139, 140, 142, 145, 146, 147, 148, 150, 151, 152, 153, 154, or 155.

158. A prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 273; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 273, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

159. A prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 273; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end SEQ ID NO: 293, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO:

273.

160. The PEgRNA of claim 158 or 159, wherein the spacer is from 17-22 nucleotides in length.

161. The PEgRNA of any one of claims 158-160, wherein the spacer comprises at its 3’ end any one of SEQ ID NOs: 274, 275, 148, 276, or 277.

162. The PEgRNA of claim 161, wherein the spacer comprises at its 3’ end SEQ ID NO:

148.

163. The PEgRNA of any one of claims 158-161, wherein the editing template comprises SEQ ID NO: 293 at its 3’ end.WSGR Docket No. 59761-791.601 164. The PEgRNA of claim 163, wherein the editing template comprises at its 3’ end any one of SEQ ID NOs: 294-306.

165. The PEgRNA of any one of claims 158-164, wherein the editing template has a length of 40 nucleotides or less.

166. The PEgRNA of claim 165, wherein the editing template is 27 to 40 nucleotides in length.

167. The PEgRNA of any one of claims 158-166, wherein the PBS comprises at its 5’end a sequence corresponding to sequence number 278.

168. The PEgRNA of claim 167, wherein the PBS comprises any one of sequence numbers 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, or 292.

169. The PEgRNA of any one of claims 158-168, wherein the PBS is 5 to 19 nucleotides in length.

170. The PEgRNA of any one of claims 158-169, comprising a PEgRNA sequence selected from any one of SEQ ID NOs: 315-332.

171. A prime editing system comprising: (a) the PEgRNA or the nucleic acid of any one of claims 158- 170, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 307, 308, 309, 310, 191, 311, 312, 313, or 314; and (ii) an ngRNA core capable of binding a Cas9 protein.

172. The prime editing system of claim 171, wherein the spacer of the ngRNA comprises at its 3’ end SEQ ID NOs: 307, 308, 309, 310, 191, 311, 312, 313, or 314.

173. The prime editing system of claim 171 or 172, wherein the ngRNA comprises a sequence selected from any one of SEQ ID NOs: 333-339.

174. A prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 340; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 340, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.WSGR Docket No. 59761-791.601 175. A prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 340; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end SEQ ID NO: 360, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO:

340.

176. The PEgRNA of claim 174 or 175, wherein the spacer is from 17-22 nucleotides in length.

177. The PEgRNA of any one of claims 174-176, wherein the spacer comprises at its 3’ end any one of SEQ ID NOs: 341, 342, 131, 343, or 344.

178. The PEgRNA of claim 177, wherein the spacer comprises at its 3’ end SEQ ID NO:

131.

179. The PEgRNA of any one of claims 174-178, wherein the editing template comprises SEQ ID NO: 360 at its 3’ end.

180. The PEgRNA of claim 179, wherein the editing template comprises at its 3’ end SEQ ID NOs: 361- 369.

181. The PEgRNA of any one of claims 174-180, wherein the editing template has a length of 40 nucleotides or less.

182. The PEgRNA of claim 181, wherein the editing template is 31 to 40 nucleotides in length.

183. The PEgRNA of any one of claims 174-182, wherein the PBS comprises at its 5’end a sequence corresponding to sequence number 345.

184. The PEgRNA of 183, wherein the PBS comprises any one of sequence numbers 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, or 359.

185. The PEgRNA of any one of claims 174-184, wherein the PBS is 9 to 19 nucleotides in length.

186. The PEgRNA of any one of claims 174-185, comprising a PEgRNA sequence selected from any one of SEQ ID NOs: 370-377.

187. A prime editing system comprising: (a) the PEgRNA or the nucleic acid of any one of claims 174- 186, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 308, 309, 310, 191, 311, 312, 313, or 314; and (ii) an ngRNA core capable of binding a Cas9 protein.

188. The prime editing system of claim 187, wherein the spacer of the ngRNA comprises at its 3’ end any one of SEQ ID NOs: 308, 309, 310, 191, 311, 312, 313, or 314.

189. The prime editing system of claim 187 or 188, wherein the ngRNA comprises a sequence selected from any one of SEQ ID NOs: 333-339.WSGR Docket No. 59761-791.601 190. A prime editing guide RNA (PEgRNA) or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer that is complementary to a search target sequence on a first strand of a RHO gene wherein the spacer comprises at its 3’ end SEQ ID NO: 378; and b. a gRNA core capable of binding to a Cas9 protein; c. an extension arm comprising: i. an editing template that comprises a region of complementarity to an editing target sequence on a second strand of the RHO gene, and ii. a primer binding site (PBS) that comprises at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO: 378, wherein the first strand and second strand are complementary to each other, wherein the editing target sequence on the second strand comprises or is complementary to a portion of the RHO gene comprising a mutation in a region from c.1030 to c.1045, and wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein in the region from c.1030 to c.1045.

191. A prime editing guide RNA (PEgRNA), or a nucleic acid encoding the PEgRNA, wherein the PEgRNA comprises: a. a spacer comprising at its 3’ end SEQ ID NO: 378; b. a gRNA core capable of binding to a Cas9 protein; and c. an extension arm comprising: i. an editing template comprising at its 3’ end any one of SEQ ID NOs: 399-402, and ii. a primer binding site (PBS) comprising at its 5’ end a sequence that is a reverse complement of nucleotides 10-14 of SEQ ID NO:

378.

192. The PEgRNA of claim 190 or 191, wherein the spacer is from 17-22 nucleotides in length.

193. The PEgRNA of any one of claims 190-192, wherein the spacer comprises at its 3’ end any one of SEQ ID NOs: 379, 380, 381, 382, or 383.

194. The PEgRNA of claim 193, wherein the spacer comprises at its 3’ end SEQ ID NO:

381.

195. The PEgRNA of any one of claims 190-192, wherein the editing template comprises SEQ ID NO: 399 at its 3’ end and encodes a GGG-to-GTG PAM silencing edit.

196. The PEgRNA of claim 195, wherein the editing template comprises at its 3’ end SEQ ID NOs: 403, 407, 411, 415, 419, 423, 427, 431, 435, 439, 443, 447, 451, 455, 459, 463, 467, 471, 475, 479, 483, 487, 491, 495, 499, or 503.

197. The PEgRNA of any one of claims 190-192, wherein the editing template comprises SEQ ID NO: 400 at its 3’ end.WSGR Docket No. 59761-791.601 198. The PEgRNA of claim 197, wherein the editing template comprises at its 3’ end SEQ ID NOs: 404, 408, 412, 416, 420, 424, 428, 432, 436, 440, 444, 448, 452, 456, 460, 464, 468, 472, 476, 480, 484, 488, 492, 496, 500, or 504.

199. The PEgRNA of any one of claims 190-198, wherein the editing template comprises SEQ ID NO: 401 at its 3’ end and encodes a GGG-to-GCG PAM silencing edit.

200. The PEgRNA of claim 199, wherein the editing template comprises at its 3’ end SEQ ID NOs: 405, 409, 413, 417, 421, 425, 429, 433, 437, 441, 445, 449, 453, 457, 461, 465, 469, 473, 477, 481, 485, 489, 493, 497, 501, or 505.

201. The PEgRNA of any one of claims 190-198, wherein the editing template comprises SEQ ID NO: 402 at its 3’ end and encodes a GGG-to-GAG PAM silencing edit.

202. The PEgRNA of claim 201, wherein the editing template comprises at its 3’ end SEQ ID NOs: 406, 410, 414, 418, 422, 426, 430, 434, 438, 442, 446, 450, 454, 458, 462, 466, 470, 474, 478, 482, 486, 490, 494, 498, 502, or 506.

203. The PEgRNA of any one of claims 190-202, wherein the editing template has a length of 40 nucleotides or less.

204. The PEgRNA of claim 203, wherein the editing template is 14 to 40 nucleotides in length.

205. The PEgRNA of any one of claims 190-204, wherein the PBS comprises at its 5’end a sequence corresponding to sequence number 384.

206. The PEgRNA of claim 205, wherein the PBS comprises any one of sequence numbers 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, or 398.

207. The PEgRNA of any one of claims 190-206, wherein the PBS is 5 to 19 nucleotides in length.

208. The PEgRNA of any one of claims 190-207, comprising a PEgRNA sequence selected from any one of SEQ ID NOs: 510-541.

209. A prime editing system comprising: (a) the PEgRNA or the nucleic acid of any one of claims 190- 208, and (b) a ngRNA, or a nucleic acid encoding the ngRNA, wherein the ngRNA comprises: (i) a spacer comprising at its 3’ end a sequence corresponding to nucleotides 4-20 of SEQ ID NOs: 307, 308, 309, 191, 311, 312, 507, 313, 508, 509, or 314; and (ii) an ngRNA core capable of binding a Cas9 protein.

210. The prime editing system of claim 209, wherein the spacer of the ngRNA comprises at its 3’ end SEQ ID NOs: 307, 308, 309, 191, 311, 312, 507, 313, 508, 509, or 314.

211. The prime editing system of claim 209 or 210, wherein the ngRNA comprises a sequence selected from any one of SEQ ID NOs: 333-339.

212. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, or 190-208, comprising from 5’ to 3’, the spacer, the gRNA core, the editing template, and the PBS.

213. The PEgRNA of claim 212, wherein the spacer, the gRNA core, the editing template, and the PBS form a contiguous sequence in a single molecule.WSGR Docket No. 59761-791.601 214. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, or 190-208, wherein the gRNA core comprises a sequence of any one of SEQ ID NOs: 854-859.

215. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, or 190-208, further comprising 3’ mN*mN*mN*N and 5’mN*mN*mN* modifications, where m indicates that the nucleotide contains a 2’-O-Me modification and a * indicates the presence of a phosphorothioate bond.

216. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, or 190-208, further comprising 3’ mT*mT*mT*T and 5’mN*mN*mN* modifications, where m indicates that the nucleotide contains a 2’-O-Me modification, a * indicates the presence of a phosphorothioate bond, and a T indicates the presence of an additional uridine nucleotide.

217. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the spacer selected from any one of Tables 14-20 further comprises a G at the 5’ end.

218. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the PEgRNA selected from any one of Tables 14-20, further comprises a G at the 5’ end.

219. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the spacer comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from any one of Tables 14-20.

220. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the editing template comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from any one of Tables 14-20.

221. The PEgRNA of claim 220, wherein the editing template encodes one or more synonymous mutations relative to a wild type Rhodopsin gene.

222. The PEgRNA of claim 220, wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein.

223. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the PBS comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from any one of Tables 14-20.

224. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the gRNA core comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from Table 10.

225. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the PEgRNA comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from any one of Tables 14-20.

226. The PEgRNA of claim 225, wherein the editing template encodes one or more synonymous mutations relative to a wild type Rhodopsin gene.WSGR Docket No. 59761-791.601 227. The PEgRNA of claim 225, wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein.

228. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the spacer comprises no more than 1, 2, 3, 4, or 5 mutations, deletions, substitutions, or insertions compared to a sequence selected from any one of Tables 14-20.

229. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the editing template comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 mutations, deletions, substitutions, or insertions compared to a sequence selected from any one of Tables 14-20.

230. The PEgRNA of claim 229, wherein the editing template encodes one or more synonymous mutations relative to a wild type Rhodopsin gene.

231. The PEgRNA of claim 229, wherein the editing template encodes a wild type amino acid sequence of a Rhodopsin protein.

232. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the PBS comprises no more than 1, 2, 3, 4, or 5 mutations, deletions, substitutions, or insertions compared to a sequence selected from any one of Tables 14-20.

233. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the gRNA core comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 mutations, deletions, substitutions, or insertions compared to a sequence selected from Table 10.

234. The PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-216, wherein the PEgRNA comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 mutations, deletions, substitutions, or insertions compared to a sequence selected from any one of Tables 14-20.

235. The prime editing system of any one of claims 49-78, 108-115, 135, 136, 156, 157, 171-173, 187- 189, or 209-211, wherein the ngRNA comprises a sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a sequence selected from any one of Tables 14-20.

236. The prime editing system of any one of claims 49-78, 108-115, 135, 136, 156, 157, 171-173, 187- 189, or 209-211, wherein the ngRNA comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 mutations, deletions, substitutions, or insertions compared to a sequence selected from any one of Tables 14-20.

237. The prime editing system of any one of claims 49-78, 108-115, 135, 136, 156, 157, 171-173, 187- 189, or 209-211, further comprising: (c) a prime editor comprising a Cas9 nickase having a nuclease inactivating mutation in the HNH domain, or a nucleic acid encoding the Cas9 nickase, and a reverse transcriptase, or a nucleic acid encoding the reverse transcriptase.WSGR Docket No. 59761-791.601 238. The prime editing system of claim 237, wherein the prime editor is a fusion protein.

239. The prime editing system of any one of claims 49-78, 108-115, 135, 136, 156, 157, 171-173, 187- 189, 209-211, 235-238, further comprising: (c) an N-terminal extein comprising an N-terminal fragment of a prime editor fusion protein and an N-intein or a polynucleotide encoding the N-terminal extein; and (d) a C-terminal extein comprising a C-terminal fragment of the prime editor fusion protein and a C- intein, or a polynucleotide encoding the C-terminal extein; wherein the N-intein and the C-intein of the N-terminal and C-terminal exteins are capable of self-excision to join the N-terminal fragment and the C- terminal fragment to form the prime editor fusion protein, and wherein the prime editor fusion protein comprises a Cas9 nickase and a reverse transcriptase (RT) domain.

240. A prime editing system comprising: (a) the PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-234, or the nucleotide encoding the PEgRNA; and (b) a prime editor comprising a Cas9 nickase having a nuclease inactivating mutation in the HNH domain, or a nucleic acid encoding the Cas9 nickase, and a reverse transcriptase, or a nucleic acid encoding the reverse transcriptase.

241. A prime editing system comprising: (a) the PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-234, or the nucleotide encoding the PEgRNA; (b) an N- terminal extein comprising an N-terminal fragment of a prime editor fusion protein and an N-intein or a polynucleotide encoding the N-terminal extein; and (c) a C-terminal extein comprising a C-terminal fragment of the prime editor fusion protein and a C-intein, or a polynucleotide encoding the C-terminal extein; wherein the N-intein and the C-intein of the N-terminal and C-terminal exteins are capable of self-excision to join the N-terminal fragment and the C-terminal fragment to form the prime editor fusion protein, and wherein the prime editor fusion protein comprises a Cas9 nickase and a reverse transcriptase (RT) domain.

242. The prime editing system of any one of claims 239-241, wherein the Cas9 nickase comprises an amino acid sequence having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 875 or SEQ ID NO:

876.

243. The prime editing system of any one of claims 239-242, wherein the reverse transcriptase comprises an amino acid sequence having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO:

872.

244. The prime editing system of claim 242 or 243, wherein the sequence identities are determined by Needleman-Wunsch alignment of two protein sequences with Gap Costs set to Existence: 11 Extension: 1 where percent identity is calculated by dividing the number of identities by the length of the global alignment.

245. A population of viral particles collectively comprising the one or more nucleic acids encoding the prime editing system of any one of claims 49-78, 108-115, 135, 136, 156, 157, 171-173, 187-189, 209- 211, 235-244.WSGR Docket No. 59761-791.601 246. The population of viral particles of claim 245, wherein the viral particles are AAV particles.

247. An LNP comprising the prime editing system of any one of claims 49-78, 108-115, 135, 136, 156, 157, 171-173, 187-189, 209-211, 235-244.

248. The LNP of claim 247, comprising the PEgRNA, the nucleic acid encoding the Cas9 nickase, and the nucleic acid encoding the reverse transcriptase.

249. The LNP of claim 248, wherein the nucleic acid encoding the Cas9 nickase and the nucleic acid encoding the reverse transcriptase are mRNA.

250. The LNP of claim 247 or 248, wherein the nucleic acid encoding the Cas9 nickase and the nucleic acid encoding the reverse transcriptase are the same molecule.

251. A method of correcting or editing a RHO gene, the method comprising contacting the RHO gene with: (a) the PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158-170, 174-186, 190-208, or 212-234 and a prime editor comprising a Cas9 nickase having a nuclease inactivating mutation in the HNH domain and a reverse transcriptase or (b) the prime editing system of any one of claims 49-78, 108- 115, 135, 136, 156, 157, 171-173, 187-189, 209-211, 235-244.

252. The method of claim 251, wherein the RHO gene comprises a mutation selected from the group consisting of: c.1033G>C (p.Val345Leu), c.1040C>T (p.Pro347Leu), c.1033G>A (p.Val345Met), c.1030C>T (p.Gln344Ter), c.1040C>A (p.Pro347Gln), c.1040C>G (p.Pro347Arg), c.1039C>G (p.Pro347Ala), c.1039C>T (p.Pro347Ser), c.1045T>G (p.Ter349Glu), c.1034T>G (p.Val345Gly), c.1045T>C (p.Ter349Gln), c.1028G>A (p.Ser343Asn), c.1033G>T (p.Val345Leu), c.1031A>C (p.Gln344Pro), c.1039C>A (p.Pro347Thr), c.1034T>C (p.Val345Ala), c.1034T>A (p.Val345Glu), and c.1040del (p.Pro347fs).

253. The method of claims 251 or 252, wherein the RHO gene is in a cell.

254. The method of claim 253, wherein the cell is a mammalian cell.

255. The method of claim 254, wherein the cell is a human cell.

256. The method of any one of claims 253-255, wherein the cell is a primary cell.

257. The method of any one of claims 253-256, wherein the cell is in a subject.

258. The method of claim 257, wherein the subject is a human.

259. The method of any one of claims 253-258, wherein the cell is from a subject having Retinitis pigmentosa.

260. The method of any one of claims 253-259, wherein contacting the RHO gene comprises contacting the cell with (i) the population of viral particles of claim 245 or 246 or (ii) the LNP of any one of claims 247-250.

261. A method for treating Retinitis pigmentosa in a subject in need thereof, the method comprising administering to the subject: (A) the PEgRNA of any one of claims 1-48, 79-107, 116-134, 137-155, 158- 170, 174-186, 190-208, or 212-234 and a prime editor comprising a Cas9 nickase having a nuclease inactivating mutation in the HNH domain and a reverse transcriptase, (B) the prime editing system of anyWSGR Docket No. 59761-791.601 one of claims 49-78, 108-115, 135, 136, 156, 157, 171-173, 187-189, 209-211, 235-244, (C) the population of viral particles of claim 245 or 246 or (D) the LNP of any one of claims 247-250.

262. The method of claim 261, wherein the subject comprises a mutation in a RHO gene, wherein the mutation is selected from the group consisting of: c.1033G>C (p.Val345Leu), c.1040C>T (p.Pro347Leu), c.1033G>A (p.Val345Met), c.1030C>T (p.Gln344Ter), c.1040C>A (p.Pro347Gln), c.1040C>G (p.Pro347Arg), c.1039C>G (p.Pro347Ala), c.1039C>T (p.Pro347Ser), c.1045T>G (p.Ter349Glu), c.1034T>G (p.Val345Gly), c.1045T>C (p.Ter349Gln), c.1028G>A (p.Ser343Asn), c.1033G>T (p.Val345Leu), c.1031A>C (p.Gln344Pro), c.1039C>A (p.Pro347Thr), c.1034T>C (p.Val345Ala), c.1034T>A (p.Val345Glu), and c.1040del (p.Pro347fs).

263. The method of any one of claims 251-262, wherein the method is performed ex vivo.

264. The method of any one of claims 251-262, wherein the method is performed in vivo.

265. The method of any one of claims 251-262, wherein the method is performed in vitro.

266. The method of any one of claims 251-262, wherein the method is performed ex vitro.

267. The method of any one of claims 251-260, wherein the correcting or editing the RHO gene results in a restoration of a wild type Rhodopsin protein sequence.

268. A cell generated by the method of any of claims 251-267.

269. A population of cells generated by the method of any one of claims 251-267.

270. A pharmaceutical composition comprising the cell of claim 268 or the population of cells of claim 269.

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