Novel cas nucleases and polynucleotides encoding the same

Abstract

The present disclosure provides novel CRISPR-associated (Cas) nucleases, as well as polynucleotides (e.g., DNA and RNA polynucleotides) encoding the same, host cells containing such nucleases and polynucleotides, and methods of using the foregoing compositions to effectuate genome editing.

Description

[0001] PATENT ATTORNEY DOCKET NO.50858-164WO2 NOVEL CAS NUCLEASES AND POLYNUCLEOTIDES ENCODING THE SAME SEQUENCE LISTING The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on December 18, 2024, is named “50858-164WO2_Sequence_Listing_12_18_24” and is 750,770 bytes in size. FIELD OF THE INVENTION The present invention relates to novel CRISPR-associated (Cas) nucleases, variants thereof, and polynucleotides encoding the same. BACKGROUND In recent years, genome editing has emerged as an important tool for research and medical applications. Early methods required complex engineering of nucleases, such as meganucleases, zinc finger fusion proteins, or transcription activator-like effector nucleases, tailored for each target sequence. This process was time-consuming and costly, posing scalability and efficiency challenges. A transformative breakthrough occurred with the development RNA-guided nucleases, particularly CRISPR-associated (Cas) proteins. These RNA-guided nucleases allow specific targeting of genetic sequences using guide RNA, streamlining genome editing by eliminating the need for custom-engineered nucleases. RNA-guided nucleases utilize CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA) to provide versatile genome editing options, from introducing mutations by way of non-homologous end-joining (NHEJ) to precise base editing when fused with deaminases. Programmable nucleases, core components of RNA-guided nucleases, bind and cleave nucleic acids with sequence-specificity. They exhibit activities such as cis cleavage or nickase activity, guided by specialized RNA molecules. These nucleases can be engineered to reduce catalytic activity while maintaining sequence specificity, expanding their utility. CRISPR systems in bacterial and archaeal adaptive immunity display diverse characteristics. Differences in size, PAM site, on-target activity, and cleavage pattern offer unique advantages for various applications, but can also represent limitations (e.g., low frequency of PAM sites in the target cell genome, or low expressability). There remains a need for new Cas nucleases to address evolving genome engineering demands. SUMMARY In a first aspect, the disclosure features a CRISPR-associated (Cas) nuclease containing a polypeptide having an amino acid sequence that is at least 60% identical to the amino acid sequence of any one of SEQ ID NOs: 1-53. In some embodiments, the amino acid sequence of the polypeptide is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 the amino acid sequence of any one of SEQ ID NOs: 1-53. In some embodiments, the amino acid sequence of the polypeptide differs from the amino acid sequence of any one of SEQ ID NOs: 1-53 by way of 100 or fewer amino acids, resulting from insertions, PATENT ATTORNEY DOCKET NO.50858-164WO2 deletions, or substitutions. In some embodiments, the amino acid sequence of the polypeptide differs from the amino acid sequence of any one of SEQ ID NOs: 1-53 by way of 90 or fewer, 85 or fewer, 80 or fewer, 75 or fewer, 70 or fewer, 65 or fewer, 60 or fewer, 55 or fewer, 50 or fewer, 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from insertions, deletions, or substitutions. In some embodiments, the amino acid sequence of the polypeptide differs from the amino acid sequence of any one of SEQ ID NOs: 1-53 only by way of 100 or fewer amino acids, resulting from substitutions. In some embodiments, the amino acid sequence of the polypeptide differs from the amino acid sequence of any one of SEQ ID NOs: 1-53 only by way of 90 or fewer, 85 or fewer, 80 or fewer, 75 or fewer, 70 or fewer, 65 or fewer, 60 or fewer, 55 or fewer, 50 or fewer, 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from substitutions. In some embodiments, the amino acid substitutions are conservative amino acid substitutions. In some embodiments, the Cas nuclease includes a RuvC domain. In some embodiments, the Cas nuclease includes a RuvC domain having an amino acid sequence that is at least 60% identical to the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, the amino acid sequence of the RuvC domain is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 the amino acid sequence of any one of SEQ ID NOs: 107- 148 and 503-508. In some embodiments, the amino acid sequence of the RuvC domain differs from the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508 by way of 50 or fewer amino acids, resulting from, resulting from insertions, deletions, or substitutions. In some embodiments, the amino acid sequence of the RuvC domain differs from the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508 by way of 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from insertions, deletions, or substitutions. In some embodiments, the amino acid sequence of the RuvC domain differs from the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508 only by way of 50 or fewer amino acids, resulting from substitutions. In some embodiments, the amino acid sequence of the RuvC domain differs from the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508 only by way of 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from substitutions. In some embodiments, the amino acid substitutions are conservative amino acid substitutions. In some embodiments, the Cas nuclease includes an HNH domain. In some embodiments, the Cas nuclease includes an HNH domain having an amino acid sequence that is at least 60% identical to the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510. In some embodiments, the amino acid sequence of the HNH domain is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 PATENT ATTORNEY DOCKET NO.50858-164WO2 least 98%, at least 99%, or 100% identical to the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510. In some embodiments, the amino acid sequence of the HNH domain differs from the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510 by way of 50 or fewer amino acids, resulting from insertions, deletions, or substitutions. In some embodiments, the amino acid sequence of the HNH domain differs from the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510 by way of 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from insertions, deletions, or substitutions. In some embodiments, the amino acid sequence of the HNH domain differs from the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510 only by way of 50 or fewer amino acids, resulting from substitutions. In some embodiments, the amino acid sequence of the HNH domain differs from the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510 only by way of 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from substitutions. In some embodiments, the amino acid substitutions are conservative amino acid substitutions. In some embodiments, the Cas nuclease has double-strand break activity toward a target DNA polynucleotide. In some embodiments, the Cas nuclease includes one or more mutations in a RuvC domain that render the RuvC domain inactive. In some embodiments, the Cas nuclease includes one or more mutations in an HNH domain that render the HNH domain inactive. In some embodiments, the Cas nuclease has single-stranded break activity toward a target DNA polynucleotide. In some embodiments, the Cas nuclease is catalytically inactive, and exhibits neither single-stranded break activity nor double-stranded break activity toward a target DNA polynucleotide. In some embodiments, the Cas nuclease is a fusion protein containing the polypeptide bound to one or more additional protein domains. In some embodiments, the one or more additional protein domains contains a peptide that localizes to one or more subcellular organelles. In some embodiments, the one or more additional protein domains contain a nuclear localization sequence (NLS). In some embodiments, the one or more additional protein domains includes a base editor domain. In some embodiments, the base editor domain is an adenosine deaminase domain or a cytidine deaminase domain. In some embodiments, the one or more additional protein domains includes a reverse transcriptase domain. In some embodiments, the Cas nuclease specifically binds a target DNA polynucleotide having a protospacer-adjacent motif (PAM) sequence set forth in Table 7. In some embodiments, the Cas nuclease has a TM-score of at least 0.80 compared to the three- dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, wherein the three-dimensional structure is calculated using Alphafold. In some embodiments, the Cas nuclease has a TM-score of at least 0.85 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, optionally wherein the Cas nuclease has a TM-score of at least 0.90 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, optionally wherein the Cas nuclease has a TM-score of at least 0.95 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, optionally wherein the Cas nuclease has a TM-score of at least 1.0 compared to the PATENT ATTORNEY DOCKET NO.50858-164WO2 three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, wherein the three- dimensional structure is calculated using Alphafold. In another aspect, the disclosure features a Cas nuclease having a TM-score of at least 0.80 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, wherein the three-dimensional structure is calculated using Alphafold. In some embodiments, the Cas nuclease has a TM-score of at least 0.85 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, optionally wherein the Cas nuclease has a TM-score of at least 0.90 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, optionally wherein the Cas nuclease has a TM-score of at least 0.95 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, optionally wherein the Cas nuclease has a TM-score of at least 1.0 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, wherein the three-dimensional structure is calculated using Alphafold. In another aspect, the disclosure features a nucleic acid encoding the Cas nuclease of any one of the foregoing aspects or embodiments of the invention. In some embodiments, the nucleic acid is a chemically modified nucleic acid. In some embodiments, the nucleic acid is DNA. In some embodiments, the nucleic acid is RNA. In some embodiments, the nucleic acid is linear. In some embodiments, the nucleic acid is circular. In some embodiments, the nucleic acid is RNA, such as an mRNA containing one or more, or all, of: (a) a 5’ untranslated region (UTR); (b) an open reading frame (ORF) encoding the Cas nuclease; (c) a 3’ UTR; and (d) a poly-adenylyl (polyA) tail. In some embodiments, the mRNA further includes a 5’ cap located 5’ relative to the 5’ UTR. In some embodiments, the open reading frame consists of nucleosides selected from the group consisting of adenosine, a modified adenosine, uridine, a modified uridine, guanosine, a modified guanosine, cytidine, and a modified cytidine. In some embodiments, the open reading frame consists of nucleosides selected from the group consisting of adenosine, uridine, a modified uridine, guanosine, and cytidine. In some embodiments, the modified uridine of the open reading frame is selected from the group consisting of 1-methylpseudouridine, pseudouridine, pyridin-4-one ribonucleoside, 5-aza-uridine, 6-aza- uridine, 2-thio-5-aza-uridine, 2-thio-uridine, 4-thio-uridine, 4-thio-pseudouridine, 2-thio-pseudouridine, 5- hydroxy-uridine, 5-aminoallyl-uridine, 5-halo-uridine, 3-methyl-uridine, 5-methoxy-uridine, uridine 5-oxyacetic acid, uridine 5-oxyacetic acid methyl ester, 5-carboxymethyl-uridine, 1-carboxymethyl-pseudouridine, 5- carboxyhydroxymethyl-uridine, 5-carboxyhydroxymethyl-uridine methyl ester, 5-methoxycarbonylmethyl- uridine, 5-methoxycarbonylmethyl-2-thio-uridine, 5-aminomethyl-2-thio-uridine, 5-methylaminomethyl-uridine, 5-methylaminomethyl-2-thio-uridine, 5-methylaminomethyl-2-seleno-uridine, 5-carbamoylmethyl-uridine, 5- carboxymethylaminomethyl-uridine, 5-carboxymethylaminomethyl-2-thio-uridine, 5-propynyl-uridine, 1- propynyl-pseudouridine, 5-taurinomethyl-uridine, 1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio- uridine, 1-taurinomethyl-4-thio-pseudouridine, 5-methyl-uridine, 5-methyl-2-thio-uridine, 1-methyl-4-thio- pseudouridine, 4-thio-1-methyl-pseudouridine, 3-methylpseudouridine, 2-thio-1-methyl-pseudouridine, 1- methyl-1-deaza-pseudouridine, 2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine, dihydropseudouridine, 5,6-dihydrouridine, 5-methyl-dihydrouridine, 2-thio-dihydrouridine, 2-thio- PATENT ATTORNEY DOCKET NO.50858-164WO2 dihydropseudouridine, 2-methoxy-uridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine, 4-methoxy-2- thio-pseudouridine, N1-methyl-pseudouridine, 3-(3-amino-3-carboxypropyl)uridine, 1-methyl-3-(3-amino-3- carboxypropyl)pseudouridine, 5-(isopentenylaminomethyl)uridine, 5-(isopentenylaminomethyl)-2-thio-uridine, α-thio-uridine, 2′-O-methyl-uridine, 5,2′-O-dimethyl-uridine, 2′-O-methyl-pseudouridine, 2-thio-2′-O-methyl- uridine, 5-methoxycarbonylmethyl-2′-O-methyl-uridine, 5-carbamoylmethyl-2′-O-methyl-uridine, 5- carboxymethylaminomethyl-2′-O-methyl-uridine, 3,2′-O-dimethyl-uridine, 5-(isopentenylaminomethyl)-2′-O- methyl-uridine, 1-thio-uridine, deoxythymidine, 2’‐F‐ara‐uridine, 2’‐F‐uridine, 2’‐OH‐ara‐uridine, 5‐(2‐ carbomethoxyvinyl) uridine, and 5‐[3‐(1‐E‐propenylamino)uridine. In some embodiments, the modified uridine of the open reading frame is 1-methylpseudouridine. In some embodiments, the modified cytidine of the open reading frame is selected from the group consisting of 5-aza-cytidine, 6-aza-cytidine, pseudoisocytidine, 3-methyl-cytidine, N4-acetyl-cytidine, 5- formyl-cytidine, N4-methyl-cytidine, 5-methyl-cytidine, 5-halo-cytidine, 5-hydroxymethyl-cytidine, 1-methyl- pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine, 2-thio-cytidine, 2-thio-5-methyl-cytidine, 4- thio-pseudoisocytidine, 4-thio-1-methyl-pseudoisocytidine, 4-thio-1-methyl-1-deaza-pseudoisocytidine, 1- methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5-methyl-zebularine, 5-aza-2-thio- zebularine, 2-thio-zebularine, 2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine, 4-methoxy- pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine, lysidine, α-thio-cytidine, 2′-O-methyl-cytidine, 5,2′-O-dimethyl-cytidine, N4-acetyl-2′-O-methyl-cytidine, N4,2′-O-dimethyl-cytidine, 5-formyl-2′-O-methyl- cytidine, N4,N4,2′-O-trimethyl-cytidine, 1-thio-cytidine, 2’‐F‐ara‐cytidine, 2’‐F‐cytidine, and 2’‐OH‐ara‐ cytidine. In some embodiments, the modified adenosine of the open reading frame is selected from the group consisting of 2-amino-purine, 2, 6-diaminopurine, 2-amino-6-halo-purine, 6-halo-purine, 2-amino-6-methyl- purine, 8-azido-adenosine, 7-deaza-adenine, 7-deaza-8-aza-adenine, 7-deaza-2-amino-purine, 7-deaza-8- aza-2-amino-purine, 7-deaza-2,6-diaminopurine, 7-deaza-8-aza-2,6-diaminopurine, 1-methyl-adenosine, 2- methyl-adenine, N6-methyl-adenosine, 2-methylthio-N6-methyl-adenosine, N6-isopentenyl-adenosine, 2- methylthio-N6-isopentenyl-adenosine, N6-(cis-hydroxyisopentenyl)adenosine, 2-methylthio-N6-(cis- hydroxyisopentenyl)adenosine, N6-glycinylcarbamoyl-adenosine, N6-threonylcarbamoyl-adenosine, N6- methyl-N6-threonylcarbamoyl-adenosine, 2-methylthio-N6-threonylcarbamoyl-adenosine, N6,N6-dimethyl- adenosine, N6-hydroxynorvalylcarbamoyl-adenosine, 2-methylthio-N6-hydroxynorvalylcarbamoyl-adenosine, N6-acetyl-adenosine, 7-methyl-adenine, 2-methylthio-adenine, 2-methoxy-adenine, α-thio-adenosine, 2′-O- methyl-adenosine, N6,2′-O-dimethyl-adenosine, N6,N6,2′-O-trimethyl-adenosine, 1,2′-O-dimethyl-adenosine, 2′-O-ribosyladenosine, 2-amino-N6-methyl-purine, 1-thio-adenosine, 8-azido-adenosine, 2’‐F‐ara‐adenosine, 2’‐F‐adenosine, 2’‐OH‐ara‐adenosine, and N6‐(19‐amino‐pentaoxanonadecyl)-adenosine. In some embodiments, the modified guanosine of the open reading frame is selected from the group consisting of inosine, 1-methyl-inosine, wyosine, methylwyosine, 4-demethyl-wyosine, isowyosine, wybutosine, peroxywybutosine, hydroxywybutosine, 7-deaza-guanosine, queuosine, epoxyqueuosine, galactosyl-queuosine, mannosyl-queuosine, 7-cyano-7-deaza-guanosine, 7-aminomethyl-7-deaza- guanosine, archaeosine, 7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine, 6-thio-7- deaza-8-aza-guanosine, 7-methyl-guanosine, 6-thio-7-methyl-guanosine, 7-methyl-inosine, 6-methoxy- guanosine, 1-methyl-guanosine, N2-methyl-guanosine, N2,N2-dimethyl-guanosine, N2,7-dimethyl- guanosine, N2, N2,7-dimethyl-guanosine, 8-oxo-guanosine, 7-methyl-8-oxo-guanosine, 1-methyl-6-thio- PATENT ATTORNEY DOCKET NO.50858-164WO2 guanosine, N2-methyl-6-thio-guanosine, N2,N2-dimethyl-6-thio-guanosine, α-thio-guanosine, 2′-O-methyl- guanosine, N2-methyl-2′-O-methyl-guanosine, N2,N2-dimethyl-2′-O-methyl-guanosine, 1-methyl-2′-O- methyl-guanosine, N2,7-dimethyl-2′-O-methyl-guanosine, 2′-O-methyl-inosine, 1,2′-O-dimethyl-inosine, 2′-O- ribosylguanosine, 1-thio-guanosine, O6-methyl-guanosine, 2’‐F‐ara‐guanosine, and 2’‐F‐guanosine. In another aspect, the disclosure features a synthetic composition containing the Cas nuclease or the nucleic acid of any one of the foregoing aspects or embodiments of the invention. In some embodiments, the composition further includes one or more carriers, diluents, or excipients. In some embodiments, the composition further includes a guide RNA (gRNA) containing (i) a CRISPR RNA (crRNA) and (ii) a trans activating RNA (tracrRNA). In some embodiments, the crRNA and the tracrRNA are separate RNA molecules. In some embodiments, the crRNA and the tracrRNA are present within a single RNA molecule (sgRNA). In some embodiments, the crRNA includes a polynucleotide having a nucleic acid sequence that is at least 60% identical to the nucleic acid sequence of any one of SEQ ID NOs: 216 and 292-319. In some embodiments, the nucleic acid sequence of the crRNA polynucleotide is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 the nucleic acid sequence of any one of SEQ ID NOs: 216 and 292-319. In some embodiments, the tracrRNA includes a polynucleotide having a nucleic acid sequence that is at least 60% identical to the nucleic acid sequence of any one of SEQ ID NOs: 163-215 and 270-291. In some embodiments, the nucleic acid sequence of the tracrRNA polynucleotide is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 the nucleic acid sequence of any one of SEQ ID NOs: 163-215 and 270-291. In some embodiments, the sgRNA includes a polynucleotide having a nucleic acid sequence that is at least 60% identical to the nucleic acid sequence of any one of SEQ ID NOs: 217-269 and 320-371. In some embodiments, the nucleic acid sequence of the sgRNA polynucleotide is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 the nucleic acid sequence of any one of SEQ ID NOs: 217-269 and 320-371. In some embodiments, the composition further includes a base editor enzyme. In some embodiments, the base editor enzyme is an adenosine deaminase or a cytidine deaminase. In some embodiments, the base editor enzyme is present as a fusion polypeptide with said Cas nuclease. In some embodiments, the base editor enzyme is present in a separate polypeptide from said Cas nuclease. In some embodiments, the base editor further includes a reverse transcriptase enzyme. In some embodiments, the reverse transcriptase enzyme is present as a fusion polypeptide with said Cas nuclease. In some embodiments, the reverse transcriptase enzyme is present in a separate polypeptide from said Cas nuclease. In some embodiments, the composition further includes a template DNA polynucleotide for homology-directed repair (HDR) of a target DNA polynucleotide. In some embodiments, the composition is a population of lipid nanoparticles (LNPs). In some embodiments, the LNPs contain one or more, or all, of (i) a neutral lipid; (ii) a cationic lipid; (iii) a PEGylated lipid; and (iv) a sterol. In some embodiments, the population of LNPs has a mean particle size of from 80 nm PATENT ATTORNEY DOCKET NO.50858-164WO2 to 160 nm. In some embodiments, the population of LNPs has a polydispersity index PDI of from 0.02 to 0.2 (e.g., 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, or 0.2). In some embodiments, the population of LNPs has a mean lipid to polynucleotide ratio (wt / wt) of from 10 to 20 (e.g., 10, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 16, 16.1, 16.2, 16.3, 16.4, 16.5, 16.6, 16.7, 16.8, 16.9, 17, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, or 20). In another aspect, the disclosure features a genetically engineered host cell containing the Cas nuclease, the nucleic acid, or the composition of any one of the foregoing aspects or embodiments of the invention. In some embodiments, the Cas nuclease is heterologous with respect to the host cell. In some embodiments, the host cell is a eukaryotic cell. In some embodiments, the eukaryotic cell is a mammalian cell. In some embodiments, the mammalian cell is a modified human cell. In another aspect, the disclosure features a method of modifying the nucleic acid sequence of a target DNA polynucleotide by contacting the target DNA polynucleotide with the Cas nuclease, the nucleic acid, or the composition of any one of the foregoing aspects or embodiments of the invention. In another aspect, the disclosure features method of introducing a single nucleotide substitution into a target DNA polynucleotide by contacting the target DNA polynucleotide with the Cas nuclease, the nucleic acid, or the composition of any one of the foregoing aspects or embodiments of the invention, wherein (i) the Cas nuclease includes a base editor domain or (ii) the composition further includes a base editor enzyme. In another aspect, the disclosure features method of replacing a target nucleic acid sequence with a template nucleic acid sequence in a target DNA polynucleotide by contacting the target DNA polynucleotide with the Cas nuclease, the nucleic acid, or the composition of any one of the foregoing aspects or embodiments of the invention, wherein (i) the Cas nuclease includes a reverse transcriptase domain or (ii) the composition further includes a reverse transcriptase enzyme. In another aspect, the disclosure features a kit containing the Cas nuclease, the nucleic acid, or the composition of any one of the foregoing aspects or embodiments of the invention. In some embodiments, the kit further includes a package insert instructing a user of the kit to conduct the method of any one of any of the foregoing aspects or embodiments of the invention. DEFINITIONS In order that the present disclosure can be more readily understood, certain terms are first defined. As used in this application, except as otherwise expressly provided herein, each of the following terms shall have the meaning set forth below. Additional definitions are set forth throughout the application. The present disclosure includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention includes embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process. PATENT ATTORNEY DOCKET NO.50858-164WO2 In this specification and the appended claims, the singular forms "a", "an" and "the" include plural referents unless the context clearly dictates otherwise. The terms "a" (or "an"), as well as the terms "one or more," and "at least one" can be used interchangeably herein. In certain aspects, the term "a" or "an" means "single." In other aspects, the term "a" or "an" includes "two or more" or "multiple." Furthermore, "and / or" where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. Thus, the term "and / or" as used in a phrase such as "A and / or B" herein is intended to include "A and B," "A or B," "A" (alone), and "B" (alone). Likewise, the term "and / or" as used in a phrase such as "A, B, and / or C" is intended to encompass each of the following aspects: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone). Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure is related. For example, the Concise Dictionary of Biomedicine and Molecular Biology, Juo, Pei-Show, 2nd ed., 2002, CRC Press; The Dictionary of Cell and Molecular Biology, 3rd ed., 1999, Academic Press; and the Oxford Dictionary of Biochemistry and Molecular Biology, Revised, 2000, Oxford University Press, provide one of skill with a general dictionary of many of the terms used in this disclosure. Wherever aspects are described herein with the language "comprising," otherwise analogous aspects described in terms of "consisting of" and / or "consisting essentially of" are also provided. Where ranges are given, endpoints are included. Furthermore, unless otherwise indicated or otherwise evident from the context and understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value or subrange within the stated ranges in different embodiments of the present disclosure, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise. Units, prefixes, and symbols are denoted in their Système International de Unites (SI) accepted form. Numeric ranges are inclusive of the numbers defining the range. Where a range of values is recited, it is to be understood that each intervening integer value, and each fraction thereof, between the recited upper and lower limits of that range is also specifically disclosed, along with each subrange between such values. The upper and lower limits of any range can independently be included in or excluded from the range, and each range where either, neither or both limits are included is also encompassed within the invention. Where a value is explicitly recited, it is to be understood that values which are about the same quantity or amount as the recited value are also within the scope of the present disclosure. Where a combination is disclosed, each subcombination of the elements of that combination is also specifically disclosed and is within the scope of the present disclosure. Conversely, where different elements or groups of elements are individually disclosed, combinations thereof are also disclosed. Where any element of an invention is disclosed as having a plurality of alternatives, examples of that invention in which each alternative is excluded singly or in any combination with the other alternatives are also hereby disclosed; more than one element of an invention can have such exclusions, and all combinations of elements having such exclusions are hereby disclosed. As used herein, the term “about” refers to a value that is no more than 10% above or below the value being described. For example, the term “about 5 nM” indicates a range of from 4.5 nM to 5.5 nM. PATENT ATTORNEY DOCKET NO.50858-164WO2 As used herein, the term "biocompatible" means compatible with living cells, tissues, organs or systems posing little to no risk of injury, toxicity or rejection by the immune system. As used herein, the term "biodegradable" means capable of being broken down into innocuous products by the action of living things. As used herein, the phrase "biologically active" refers to a characteristic of any substance that has activity in a biological system and / or organism. For instance, a substance that, when administered to an organism, has a biological effect on that organism, is considered to be biologically active. In particular embodiments, a nucleic acid of the present disclosure can be considered biologically active if even a portion of the nucleic acid is biologically active or mimics an activity considered biologically relevant. As used herein, the term "amino acid substitution" refers to the replacement of an amino acid residue present in a parent or reference polypeptide (e.g., a target polypeptide described herein) with another amino acid residue. An amino acid can be substituted in a parent or reference sequence, for example, via chemical peptide synthesis or through recombinant methods known in the art. Accordingly, a reference to a "substitution at position X" refers to the substitution of an amino acid present at position X with an alternative amino acid residue. In some aspects, substitution patterns can be described according to the scheme AnY, wherein A is the single letter code corresponding to the amino acid naturally or originally present at position n, and Y is the substituting amino acid residue. In some aspects, substitution patterns can be described according to the scheme An(YZ), wherein A is the single letter code corresponding to the amino acid residue substituting the amino acid naturally or originally present at position n, and Y and Z are alternative substituting amino acid residue. In the context of the present disclosure, substitutions (even when they referred to as amino acid substitution) may be conducted at the nucleic acid level, i.e., substituting an amino acid residue with an alternative amino acid residue may be conducted by substituting the codon encoding the first amino acid with a codon encoding the second amino acid. As used herein, the terms “conservative mutation,” “conservative substitution,” “conservative amino acid substitution,” and the like refer to a substitution of one or more amino acids for one or more different amino acids that exhibit similar physicochemical properties, such as polarity, electrostatic charge, and / or steric volume. These properties are summarized for each of the twenty naturally-occurring amino acids in Table 1 below. Table 1. Representative physicochemical properties of naturally-occurring amino acids PATENT ATTORNEY DOCKET NO.50858-164WO2 From this table it is appreciated that the conservative amino acid families include, e.g., (i) G, A, V, L, I, P, and M; (ii) D and E; (iii) C, S and T; (iv) H, K and R; (v) N and Q; and (vi) F, Y and W. A conservative mutation or substitution is therefore one that substitutes one amino acid for a member of the same amino acid family (e.g., a substitution of Ser for Thr or Lys for Arg). As used herein, the term “conjugate” refers to a compound formed by the chemical bonding of a reactive functional group of one molecule with an appropriately reactive functional group of another molecule. Conjugates may additionally be produced, e.g., as two polypeptide domains covalently bound to one another as part of a single polypeptide chain that is synthesized by the translation of a single RNA transcript encoding both polypeptides in frame with one another. As used herein, the term "sequence optimization" refers to a process or series of processes by which nucleobases in a reference nucleic acid sequence are replaced with alternative nucleobases, resulting in a nucleic acid sequence with improved properties, e.g., improved protein expression or decreased immunogenicity. In general, the goal in sequence optimization is to produce a synonymous nucleotide sequence than encodes the same polypeptide sequence encoded by the reference nucleotide sequence. Thus, there are no amino acid substitutions (as a result of codon optimization) in the polypeptide encoded by the codon optimized nucleotide sequence with respect to the polypeptide encoded by the reference nucleotide sequence. As used herein, the terms "codon substitution" or "codon replacement" in the context of sequence optimization refer to replacing a codon present in a reference nucleic acid sequence with another codon. A codon can be substituted in a reference nucleic acid sequence, for example, via chemical peptide synthesis PATENT ATTORNEY DOCKET NO.50858-164WO2 or through recombinant methods known in the art. Accordingly, references to a "substitution" or "replacement" at a certain location in a nucleic acid sequence (e.g., an mRNA) or within a certain region or subsequence of a nucleic acid sequence (e.g., an mRNA) refer to the substitution of a codon at such location or region with an alternative codon. As used herein, the terms "coding region" and "region encoding" and grammatical variants thereof, refer to an Open Reading Frame (ORF) in a nucleic acid that upon expression yields a polypeptide or protein. The term “complementarity sufficient to hybridize,” as used herein, refers to a nucleic acid sequence or a portion thereof that need not be fully complementary (e.g., 100% complementary) to a target region or a nucleic acid sequence or a portion thereof that has one or more nucleotide mismatches relative to the target region but that is still capable of hybridizing to the target region under specified conditions. For example, the nucleic acid may be, e.g., 95% complementary, 90%, complementary, 85% complementary, 80% complementary, 75% complementary, 70% complementary, 65% complementary, 60% complementary, 55% complementary, 50% complementary, or less, but still form sufficient base pairs with the target so as to hybridize across its length. As used herein, the term “contacting” means establishing a physical connection between two or more entities. For example, contacting a mammalian cell with a nanoparticle composition means that the mammalian cell and a nanoparticle are made to share a physical connection. Methods of contacting cells with external entities both in vivo and ex vivo are well known in the biological arts. For example, contacting a nanoparticle composition and a mammalian cell disposed within a mammal can be performed by varied routes of administration (e.g., intravenous, intramuscular, intradermal, and subcutaneous) and can involve varied amounts of nanoparticle compositions. Moreover, more than one mammalian cell can be contacted by a nanoparticle composition. As used herein, the term “delivering” means providing an entity to a destination. For example, delivering a nucleic acid to a subject can involve administering a nanoparticle composition including the nucleic acid to the subject (e.g., by an intravenous, intramuscular, intradermal, or subcutaneous route). Administration of a nanoparticle composition to a mammal or mammalian cell can involve contacting one or more cells with the nanoparticle composition. As used herein, "delivery agent" refers to any substance that facilitates, at least in part, the in vivo, in vitro, or ex vivo delivery of a nucleic acid to targeted cells. As used herein, "expression" of a nucleic acid sequence refers to one or more of the following events: (1) production of an mRNA template from a DNA sequence (e.g., by transcription); (2) processing of an mRNA transcript (e.g., by splicing, editing, 5′ cap formation, and / or 3′ end processing); (3) translation of an mRNA into a polypeptide or protein; and (4) post-translational modification of a polypeptide or protein. As used herein, the term “lipid nanoparticle” refers to a transfer vehicle including one or more lipids (e.g., cationic lipids, non-cationic lipids, and PEG-modified lipids). Exemplary lipid nanoparticles are formulated to deliver one or more mRNA to one or more target cells. Examples of suitable lipids include, for example, the phosphatidyl compounds (e.g., phosphatidylglycerol, phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingolipids, cerebrosides, and gangliosides). Lipid nanoparticles may contain a cationic lipid, or a lipid species with a net positive charge at a selected pH (e.g., physiological pH), to encapsulate and / or enhance the delivery of mRNA into the target cells. PATENT ATTORNEY DOCKET NO.50858-164WO2 As used herein, the term “helper lipid” refers to a compound or molecule that includes a lipidic moiety (for insertion into a lipid layer, e.g., lipid bilayer) and a polar moiety (for interaction with physiologic solution at the surface of the lipid layer). Typically, the helper lipid is a phospholipid. A function of the helper lipid is to “complement” the amino lipid and increase the fusogenicity of the bilayer and / or to help facilitate endosomal escape, e.g., of nucleic acid delivered to cells. Helper lipids are also believed to be a key structural component to the surface of the LNP. As used herein, the term “ionizable amino lipid” includes those lipids having one, two, three, or more fatty acid or fatty alkyl chains and a pH-titratable amino head group (e.g., an alkylamino or dialkylamino head group). An ionizable amino lipid is typically protonated (i.e., positively charged) at a pH below the pKa of the amino head group and is substantially not charged at a pH above the pKa. Such ionizable amino lipids include, but are not limited to DLin-MC3-DMA (MC3), (13Z,165Z)-N,N-dimethyl-3-nonydocosa-13-16-dien-1- amine (L608), and a compound of any one of Formula I, II, and II described herein (e.g., any one of Compound I-1, Compound I-2, Compound I-3, or Compound I-VI). As used herein, the terms “messenger RNA” or “mRNA” refer to any nucleic acid which encodes a polypeptide of interest and which is capable of being translated to produce the encoded polypeptide of interest in vitro, in vivo, in situ, or ex vivo. Traditionally, the basic components of an mRNA molecule include a coding region, a 5’UTR, a 3’UTR, a 5’ cap, and a poly-A tail. As used herein the term "modified" refers to a changed state or structure of a molecule of the present disclosure. Molecules can be modified in many ways, including chemically, structurally, and functionally. In some embodiments, the mRNA molecules of the present disclosure are modified by the introduction of non-natural nucleosides and / or nucleotides, e.g., as it relates to the natural ribonucleotides A, U, G, and / or C. Examples of “modified” nucleosides are provided herein. As used herein, the terms “modified messenger RNA” or “modified mRNA” refer to mRNA nucleic acids that include naturally occurring and / or non-naturally occurring modifications, for example, of a sugar, a nucleobase, or an internucleoside linkage (e.g., to a linking phosphate, to a phosphodiester linkage, or to the phosphodiester backbone). Non-natural modified nucleotides may be introduced during synthesis of post- synthesis of the nucleic acids to achieve desired functions or properties. The modifications may be present on an internucleoside linkage, purine or pyrimidine base, or sugar. The modification may be introduced with chemical synthesis or with a polymerase enzyme at the terminal of a chain or anywhere else in the chain. Any of the regions of a nucleic acid may be chemically modified. As used herein, "unmodified" refers to any substance, compound, or molecule prior to being changed in some way. Unmodified can, but does not always, refer to the wild type or native form of a biomolecule. Molecules can undergo a series of modifications whereby each modified molecule can serve as the "unmodified" starting molecule for a subsequent modification. Uracil is one of the four nucleobases in the nucleic acid of RNA, and it is represented by the letter U. Uracil can be attached to a ribose ring, or more specifically, a ribofuranose via an N1-glycosidic bond to yield the nucleoside uridine. The nucleoside uridine is also commonly abbreviated according to the one letter code of its nucleobase, i.e., U. Thus, in the context of the present disclosure, when a monomer in a nucleic acid sequence is U, such U is designated interchangeably as a "uracil" or a "uridine." The terms "uridine content" or "uracil content" are interchangeable and refer to the amount of uracil or uridine present in a certain nucleic acid sequence. Uridine content or uracil content can be expressed as PATENT ATTORNEY DOCKET NO.50858-164WO2 an absolute value (total number of uridine or uracil in the sequence) or relative (uridine or uracil percentage respect to the total number of nucleobases in the nucleic acid sequence). The terms "uridine-modified sequence" refers to a sequence optimized nucleic acid (e.g., a synthetic mRNA sequence) with a different overall or local uridine content (higher or lower uridine content) or with different uridine patterns (e.g., gradient distribution or clustering) with respect to the uridine content and / or uridine patterns of a candidate nucleic acid sequence. In the content of the present disclosure, the terms "uridine-modified sequence" and "uracil-modified sequence" are considered equivalent and interchangeable. A "high uridine codon" is defined as a codon comprising two or three uridines, a "low uridine codon" is defined as a codon comprising one uridine, and a "no uridine codon" is a codon without any uridines. In some embodiments, a uridine-modified sequence comprises substitutions of high uridine codons with low uridine codons, substitutions of high uridine codons with no uridine codons, substitutions of low uridine codons with high uridine codons, substitutions of low uridine codons with no uridine codons, substitution of no uridine codons with low uridine codons, substitutions of no uridine codons with high uridine codons, and combinations thereof. In some embodiments, a high uridine codon can be replaced with another high uridine codon. In some embodiments, a low uridine codon can be replaced with another low uridine codon. In some embodiments, a no uridine codon can be replaced with another no uridine codon. A uridine-modified sequence can be uridine enriched or uridine rarefied. As used herein, the terms "uridine enriched" and grammatical variants refer to the increase in uridine content (expressed in absolute value or as a percentage value) in a sequence optimized nucleic acid (e.g., a synthetic mRNA sequence) with respect to the uridine content of the corresponding candidate nucleic acid sequence. Uridine enrichment can be implemented by substituting codons in the candidate nucleic acid sequence with synonymous codons containing less uridine nucleobases. Uridine enrichment can be global (i.e., relative to the entire length of a candidate nucleic acid sequence) or local (i.e., relative to a subsequence or region of a candidate nucleic acid sequence). As used herein, the terms "uridine rarefied" and grammatical variants refer to a decrease in uridine content (expressed in absolute value or as a percentage value) in a sequence optimized nucleic acid (e.g., a synthetic mRNA sequence) with respect to the uridine content of the corresponding candidate nucleic acid sequence. Uridine rarefication can be implemented by substituting codons in the candidate nucleic acid sequence with synonymous codons containing less uridine nucleobases. Uridine rarefication can be global (i.e., relative to the entire length of a candidate nucleic acid sequence) or local (i.e., relative to a subsequence or region of a candidate nucleic acid sequence). As used herein, the term “initiation codon”, used interchangeably with the term “start codon”, refers to the first codon of an open reading frame that is translated by the ribosome and is comprised of a triplet of linked adenine-uracil-guanine nucleobases. The initiation codon is depicted by the first letter codes of adenine (A), uracil (U), and guanine (G) and is often written simply as “AUG”. Although natural mRNAs may use codons other than AUG as the initiation codon, which are referred to herein as “alternative initiation codons”, the initiation codons of nucleic acids described herein use the AUG codon. During the process of translation initiation, the sequence comprising the initiation codon is recognized via complementary base- pairing to the anticodon of an initiator tRNA (Met-tRNAiMet) bound by the ribosome. Open reading frames may contain more than one AUG initiation codon, which are referred to herein as “alternate initiation codons”. PATENT ATTORNEY DOCKET NO.50858-164WO2 The initiation codon plays an important role in translation initiation. The initiation codon is the first codon of an open reading frame that is translated by the ribosome. Typically, the initiation codon comprises the nucleotide triplet AUG, however, in some instances translation initiation can occur at other codons comprised of distinct nucleotides. The initiation of translation in eukaryotes is a multistep biochemical process that involves numerous protein-protein, protein-RNA, and RNA-RNA interactions between messenger RNA molecules (mRNAs), the 40S ribosomal subunit, other components of the translation machinery (e.g., eukaryotic initiation factors; eIFs). The current model of mRNA translation initiation postulates that the pre-initiation complex (alternatively “43S pre-initiation complex”; abbreviated as “PIC”) translocates from the site of recruitment on the mRNA (typically the 5′ cap) to the initiation codon by scanning nucleotides in a 5′ to 3′ direction until the first AUG codon that resides within a specific translation- promotive nucleotide context (the Kozak sequence) is encountered (Kozak (1989) J Cell Biol 108:229-241). Scanning by the PIC ends upon complementary base-pairing between nucleotides comprising the anticodon of the initiator Met-tRNAiMettransfer RNA and nucleotides comprising the initiation codon of the mRNA. Productive base-pairing between the AUG codon and the Met-tRNAiMetanticodon elicits a series of structural and biochemical events that culminate in the joining of the large 60S ribosomal subunit to the PIC to form an active ribosome that is competent for translation elongation. The term “Kozak sequence” (also referred to as “Kozak consensus sequence”) refers to a translation initiation enhancer element to enhance expression of a gene or open reading frame, and which in eukaryotes, is located in the 5′ UTR. The Kozak consensus sequence was originally defined as the sequence GCCRCC (SEQ ID NO: 373), where R = a purine, following an analysis of the effects of single mutations surrounding the initiation codon (AUG) on translation of the preproinsulin gene (Kozak (1986) Cell 44:283-292). Nucleic acids disclosed herein comprise a Kozak consensus sequence, or a derivative or modification thereof. (Examples of translational enhancer compositions and methods of use thereof, see U.S. Pat. No.5,807,707 to Andrews et al., incorporated herein by reference in its entirety; U.S. Pat. No. 5,723,332 to Chernajovsky, incorporated herein by reference in its entirety; U.S. Pat. No.5,891,665 to Wilson, incorporated herein by reference in its entirety.) As used herein, the term “nucleobase” (alternatively “nucleotide base” or “nitrogenous base”) refers to a purine or pyrimidine heterocyclic compound found in nucleic acids, including any derivatives or analogs of the naturally occurring purines and pyrimidines that confer improved properties (e.g., binding affinity, nuclease resistance, chemical stability) to a nucleic acid or a portion or segment thereof. Adenine, cytosine, guanine, thymine, and uracil are the nucleobases predominately found in natural nucleic acids. Other natural, non-natural, and / or synthetic nucleobases, as known in the art and / or described herein, can be incorporated into nucleic acids. Unless otherwise specified, the nucleobase sequence of a SEQ ID NO described herein encompasses both natural nucleobases and chemically modified nucleobases (e.g., a “U” designation in a SEQ ID NO encompasses both uracil and chemically modified uracil). As used herein, the term “nucleoside” refers to a compound containing a sugar molecule (e.g., a ribose in RNA or a deoxyribose in DNA), or derivative or analog thereof, covalently linked to a nucleobase (e.g., a purine or pyrimidine), or a derivative or analog thereof (also referred to herein as “nucleobase”), but lacking an internucleoside linking group (e.g., a phosphate group). As used herein, the term “nucleotide” refers to a nucleoside covalently bonded to an internucleoside linking group (e.g., a phosphate group), or any derivative, analog, or modification thereof that confers improved chemical and / or functional properties PATENT ATTORNEY DOCKET NO.50858-164WO2 (e.g., binding affinity, nuclease resistance, chemical stability) to a nucleic acid or a portion or segment thereof. As used herein, the term “open reading frame”, abbreviated as “ORF”, refers to a segment or region of an mRNA molecule that encodes a polypeptide. The ORF comprises a continuous stretch of non- overlapping, in-frame codons, beginning with the initiation codon and ending with a stop codon, and is translated by the ribosome. As used herein, the term “translational regulatory activity” (used interchangeably with “translational regulatory function”) refers to a biological function, mechanism, or process that modulates (e.g., regulates, influences, controls, varies) the activity of the translational apparatus, including the activity of the PIC and / or ribosome. In some aspects, the desired translation regulatory activity promotes and / or enhances the translational fidelity of mRNA translation. In some aspects, the desired translational regulatory activity reduces and / or inhibits leaky scanning. As used herein, the terms "nucleic acid" and “nucleic acid” are used interchangeably. In their broadest sense, these terms include any compound and / or substance that comprises a polymer of nucleotides. Exemplary nucleic acids or nucleic acids encoding PNEs of the disclosure include, but are not limited to, ribonucleic acids (RNAs), deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), locked nucleic acids (LNAs, including LNA having a β- D-ribo configuration, α-LNA having an α-L-ribo configuration (a diastereomer of LNA), 2′-amino-LNA having a 2′-amino functionalization, and 2′-amino- α-LNA having a 2′-amino functionalization), ethylene nucleic acids (ENA), cyclohexenyl nucleic acids (CeNA) or hybrids or combinations thereof. Nucleic acid molecules of the disclosure may be, for example, triple-, double-, or single-stranded deoxyribonucleic acid ("DNA"), as well as triple-, double- and single-stranded ribonucleic acid ("RNA"). This term also includes modified, for example, by alkylation, and / or by capping, and unmodified forms of the corresponding unmodified nucleic acid. In particular aspects, the nucleic acid comprises an mRNA. In other aspect, the mRNA is a synthetic mRNA. In some aspects, the synthetic mRNA comprises at least one unnatural nucleobase. In some aspects, all nucleobases of a certain class have been replaced with unnatural nucleobases (e.g., all uridines in a nucleic acid disclosed herein can be replaced with an unnatural nucleobase, e.g., 1-methylpseudouridine). In some aspects, the nucleic acid (e.g., a synthetic RNA or a synthetic DNA) comprises only natural nucleobases, i.e., A (adenosine), G (guanosine), C (cytidine), and T (thymidine) in the case of a synthetic DNA, or A, C, G, and U (uridine) in the case of a synthetic RNA. The skilled artisan will appreciate that the T bases in the codon maps disclosed herein are present in DNA, whereas the T bases would be replaced by U bases in corresponding RNAs. For example, a codon- nucleotide sequence disclosed herein in DNA form, e.g., a vector or an in-vitro translation (IVT) template, would have its T bases transcribed as U based in its corresponding transcribed mRNA. In this respect, both codon-optimized DNA sequences (comprising T) and their corresponding mRNA sequences (comprising U) are considered codon-optimized nucleotide sequence of the present disclosure. A skilled artisan would also understand that equivalent codon-maps can be generated by one or more bases with non-natural bases. Thus, e.g., a TTC codon (DNA map) would correspond to a UUC codon (RNA map), which in turn would correspond to a ΨΨC codon (RNA map in which U has been replaced with pseudouridine). Standard A-T and G-C base pairs form under conditions which allow the formation of hydrogen bonds between the N3-H and C4-oxy of thymidine and the N1 and C6-NH2, respectively, of adenosine and PATENT ATTORNEY DOCKET NO.50858-164WO2 between the C2-oxy, N3 and C4-NH2, of cytidine and the C2-NH2, N′—H and C6-oxy, respectively, of guanosine. Thus, for example, guanosine (2-amino-6-oxy-9-β-D-ribofuranosyl-purine) can be modified to form isoguanosine (2-oxy-6-amino-9-β-D-ribofuranosyl-purine). Such modification results in a nucleoside base which will no longer effectively form a standard base pair with cytosine. However, modification of cytosine (1-β-D-ribofuranosyl-2-oxy-4-amino-pyrimidine) to form isocytosine (1-β-D-ribofuranosyl-2-amino-4- oxy-pyrimidine-) results in a modified nucleotide which will not effectively base pair with guanosine but will form a base pair with isoguanosine (U.S. Pat. No.5,681,702 to Collins et al.). Isocytosine is available from Sigma Chemical Co. (St. Louis, Mo.); isocytidine can be prepared by the method described by Switzer et al. (1993) Biochemistry 32:10489-10496 and references cited therein; 2′-deoxy-5-methyl-isocytidine can be prepared by the method of Tor et al., 1993, J. Am. Chem. Soc.115:4461-4467 and references cited therein; and isoguanine nucleotides can be prepared using the method described by Switzer et al., 1993, supra, and Mantsch et al., 1993, Biochem.14:5593-5601, or by the method described in U.S. Pat. No.5,780,610 to Collins et al. Other nonnatural base pairs can be synthesized by the method described in Piccirilli et al., 1990, Nature 343:33-37, for the synthesis of 2,6-diaminopyrimidine and its complement (1-methylpyrazolo- [4,3]pyrimidine-5,7-(4H,6H)-dione. Other such modified nucleotide units which form unique base pairs are known, such as those described in Leach et al. (1992) J. Am. Chem. Soc.114:3675-3683 and Switzer et al., supra. Nucleotides are referred to by their commonly accepted single-letter codes. Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation. Nucleobases are referred to herein by their commonly known one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Accordingly, A represents adenine, C represents cytosine, G represents guanine, T represents thymine, U represents uracil. In accordance with the compositions and methods disclosed herein, nucleic acids or nucleic acids may be “enriched” in certain nucleosides. As used in this context, the term “enriched” refers to a nucleic acid in which at least 50% of the nucleosides within the nucleic acid are the same. For example, a nucleic acid is said to be “enriched” in uridine if at least 50% (e.g., 51%, 52%, 53%, 54%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100%) of the nucleosides in the nucleic acid are uridine nucleosides. In another example, a nucleic acid is said to be “enriched” in a modified uridine nucleoside (e.g., in 1-methylpseudouridine) if at least 50% (e.g., 51%, 52%, 53%, 54%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100%) of the nucleosides in the nucleic acid are the modified uridine nucleoside (e.g., 1-methylpseudouridine). As used herein, polynucleotides that are “enriched” for certain nucleoside residues may be separated from one another by way of a spacer. In this context, a “spacer” refers to a nucleic acid that does not code for a polypeptide (i.e., does not contain a start codon operably linked to a continuous segment of amino acid-encoding codons) and that is not enriched with the same nucleoside as the enriched nucleic acid(s) adjacent to the spacer. In some embodiments, a spacer may be enriched for a different nucleoside as the enriched nucleic acid(s) adjacent to the spacer. Spacers may be, for example, from 5 to 100 nucleosides in length, such as from 10 to 40 nucleosides in length (e.g., 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 nucleosides in length). The terms "polypeptide," "peptide," and "protein" are used interchangeably herein to refer to polymers of amino acids of any length. The polymer can comprise modified amino acids. The terms also PATENT ATTORNEY DOCKET NO.50858-164WO2 encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component. Also included within the definition are, for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids such as homocysteine, ornithine, p-acetylphenylalanine, D-amino acids, and creatine), as well as other modifications known in the art. The term, as used herein, refers to proteins, polypeptides, and peptides of any size, structure, or function. Polypeptides include encoded nucleic acid products, naturally occurring polypeptides, synthetic polypeptides, homologs, orthologs, paralogs, fragments and other equivalents, variants, and analogs of the foregoing. A polypeptide can be a monomer or can be a multi-molecular complex such as a dimer, trimer or tetramer. They can also comprise single chain or multichain polypeptides. Most commonly disulfide linkages are found in multichain polypeptides. The term polypeptide can also apply to amino acid polymers in which one or more amino acid residues are an artificial chemical analogue of a corresponding naturally occurring amino acid. In some embodiments, a "peptide" can be less than or equal to 50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long. Amino acids are referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Unless otherwise indicated, amino acid sequences are written left to right in amino to carboxy orientation. “Percent (%) sequence complementarity” with respect to a reference nucleic acid sequence is defined as the percentage of nucleic acids in a candidate sequence that are complementary to the nucleic acids in the reference nucleic acid sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence complementarity. A given nucleotide is considered to be “complementary” to a reference nucleotide as described herein if the two nucleotides form canonical Watson-Crick base pairs. For the avoidance of doubt, Watson-Crick base pairs in the context of the present disclosure include adenine-thymine, adenine-uracil, and cytosine-guanine base pairs. A proper Watson-Crick base pair is referred to in this context as a “match,” while each unpaired nucleotide, and each incorrectly paired nucleotide, is referred to as a “mismatch.” Alignment for purposes of determining percent nucleic acid sequence complementarity can be achieved in various ways that are within the capabilities of one of skill in the art, for example, using publicly available computer software such as BLAST, BLAST-2, or Megalign software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal complementarity over the full length of the sequences being compared. As an illustration, the percent sequence complementarity of a given nucleic acid sequence, A, to a given nucleic acid sequence, B, (which can alternatively be phrased as a given nucleic acid sequence, A that has a certain percent complementarity to a given nucleic acid sequence, B) is calculated as follows: 100 multiplied by (the fraction X / Y) where X is the number of complementary base pairs in an alignment (e.g., as executed by computer software, such as BLAST) in that program’s alignment of A and B, and where Y is the total number of nucleic acids in B. It will be appreciated that where the length of nucleic acid sequence A is not equal to the length of nucleic acid sequence B, the percent sequence complementarity of A to B will not equal the percent sequence complementarity of B to A. As used herein, a query nucleic acid sequence is considered to be PATENT ATTORNEY DOCKET NO.50858-164WO2 “completely complementary” to a reference nucleic acid sequence if the query nucleic acid sequence has 100% sequence complementarity to the reference nucleic acid sequence. As used herein, the terms “percent (%) sequence identity,” “percent (%) identity,” and the like, with respect to a reference nucleic acid or polypeptide sequence, is defined as the percentage of nucleic acids or amino acids in a candidate sequence that are identical to the nucleic acids or amino acids in the reference nucleic acid or polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid or amino acid sequence identity can be achieved in various ways that are within the capabilities of one of skill in the art, for example, using publicly available computer software such as BLAST, BLAST-2, or Megalign software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For example, percent sequence identity values may be generated using the sequence comparison computer program BLAST. As an illustration, the percent sequence identity of a given nucleic acid or amino acid sequence, A, to, with, or against a given nucleic acid or amino acid sequence, B, (which can alternatively be phrased as a given nucleic acid or amino acid sequence, A that has a certain percent sequence identity to, with, or against a given nucleic acid or amino acid sequence, B) is calculated as follows: 100 multiplied by (the fraction X / Y) where X is the number of nucleotides or amino acids scored as identical matches by a sequence alignment program (e.g., BLAST) in that program’s alignment of A and B, and where Y is the total number of nucleic acids in B. It will be appreciated that where the length of nucleic acid or amino acid sequence A is not equal to the length of nucleic acid or amino acid sequence B, the percent sequence identity of A to B will not equal the percent sequence identity of B to A. As used herein, the term “operatively linked” in the context of a nucleic acid fragment is intended to mean that the two nucleic acid fragments are joined such that the amino acid sequences encoded by the two nucleic acid fragments remain in-frame. As used herein, the term "pharmacokinetic" refers to any one or more properties of a molecule or compound as it relates to the determination of the fate of substances administered to a living organism. Pharmacokinetics is divided into several areas including the extent and rate of absorption, distribution, metabolism and excretion. This is commonly referred to as ADME where: (A) Absorption is the process of a substance entering the blood circulation; (D) Distribution is the dispersion or dissemination of substances throughout the fluids and tissues of the body; (M) Metabolism (or Biotransformation) is the irreversible transformation of parent compounds into daughter metabolites; and (E) Excretion (or Elimination) refers to the elimination of the substances from the body. In rare cases, some drugs irreversibly accumulate in body tissue. As used herein, the term “regulatory sequence” includes promoters, enhancers, and other expression control elements (e.g., polyadenylation signals) that control the transcription or translation, e.g., of open reading frames described herein. Such regulatory sequences are described, for example, in Goeddel, Gene Expression Technology: Methods in Enzymology 185 (Academic Press, San Diego, CA, 1990); incorporated herein by reference. PATENT ATTORNEY DOCKET NO.50858-164WO2 As used herein, the phrases "signal sequence," "signal peptide," and "transit peptide" are used interchangeably and refer to a sequence that can direct the transport or localization of a protein to a certain organelle, cell compartment, or extracellular export. The term encompasses both the signal sequence polypeptide and the nucleic acid sequence encoding the signal sequence. Thus, references to a signal sequence in the context of a nucleic acid refer in fact to the nucleic acid sequence encoding the signal sequence polypeptide. As used herein, the term "similarity" refers to the overall relatedness between polymeric molecules, e.g., between nucleic acid molecules (e.g., DNA molecules and / or RNA molecules) and / or between polypeptide molecules. Calculation of percent similarity of polymeric molecules to one another can be performed in the same manner as a calculation of percent identity, except that calculation of percent similarity takes into account conservative substitutions as is understood in the art. As used herein, the phrase “specifically binds” refers to a binding reaction which is determinative of the presence of an antigen in a heterogeneous population of proteins and other biological molecules that is recognized, e.g., by a protein or nucleic acid with particularity. A protein or nucleic acid that specifically binds to an antigen will bind to the antigen with a KD of less than 100 nM. For example, a protein or nucleic acid that specifically binds to an antigen will bind to the antigen with a KD of up to 100 nM (e.g., between 1 pM and 100 nM). A protein or nucleic acid that does not exhibit specific binding to a particular antigen or epitope thereof will exhibit a KD of greater than 100 nM (e.g., greater than 500 nm, 1 µM, 100 µM, 500 µM, or 1 mM) for that particular antigen or epitope thereof. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein or carbohydrate. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein or carbohydrate. See, Harlow & Lane, Antibodies, A Laboratory Manual, Cold Spring Harbor Press, New York (1988) and Harlow & Lane, Using Antibodies, A Laboratory Manual, Cold Spring Harbor Press, New York (1999), for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity. As used herein, the terms “subject” and “patient” refer to an organism that receives treatment for a particular disease or condition. Examples of subjects and patients include mammals, such as humans, primates, pigs, goats, rabbits, hamsters, cats, dogs, guinea pigs, members of the bovidae family (such as cattle, bison, buffalo, and yaks, among others), sheep, and horses, among others. A patient that may be treated using the compositions and methods described herein may have an established disease, in which case the patient has been diagnosed as having the disease and has shown symptoms of the disease for a prolonged period of time (e.g., over the course of days, weeks, months, or years). Alternatively, a patient may be symptomatic for a particular disease, but has yet to be diagnosed with the disease by a physician. Other patients that may be treated using the compositions and methods described herein include those that have been diagnosed as having a particular disease and may or may not be showing symptoms of the disease as of yet. For example, a patient eligible for treatment with the compositions and methods described herein may be described as diagnosed but asymptomatic if the patient has received a diagnosis of a disease, even though the patient may not yet be showing symptoms thereof. As used herein, "transfection" refers to the introduction of a nucleic acid (e.g., exogenous nucleic acids) into a cell wherein a polypeptide encoded by the nucleic acid is expressed (e.g., mRNA) or the polypeptide modulates a cellular function (e.g., siRNA, miRNA). As used herein, "expression" of a nucleic PATENT ATTORNEY DOCKET NO.50858-164WO2 acid sequence refers to translation of a nucleic acid (e.g., an mRNA) into a polypeptide or protein and / or post-translational modification of a polypeptide or protein. Methods of transfection include, but are not limited to, chemical methods, physical treatments and cationic lipids or mixtures. As used herein, the terms “treat” or “treatment” refer to therapeutic treatment, in which the object is to inhibit or slow down (lessen) an undesired physiological change or disorder. Beneficial or desired clinical results of treatment include, without limitation, alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable. Those in need of treatment include those already having the condition or disorder, as well as those prone to have the condition or disorder or those in which the condition or disorder is to be inhibited. As used herein, the term "effective amount" of an agent is that amount sufficient to effect beneficial or desired results, for example, clinical results, and, as such, an "effective amount" depends upon the context in which it is being applied. For example, in the context of administering an agent that treats a protein deficiency, an effective amount of an agent is, for example, an amount of mRNA expressing sufficient the desired protein to ameliorate, reduce, eliminate, or prevent the symptoms associated with the corresponding protein deficiency, as compared to the severity of the symptom observed without administration of the agent. The term "effective amount" can be used interchangeably with "effective dose," "therapeutically effective amount," or "therapeutically effective dose." As used herein, “methods of administration” can include intravenous, intramuscular, intradermal, subcutaneous, or other methods of delivering a composition to a subject. A method of administration can be selected to target delivery (e.g., to specifically deliver) to a specific region or system of a body. The phrase "pharmaceutically acceptable" is employed herein to refer to those compounds, materials, compositions, and / or dosage forms that are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit / risk ratio. The phrase "pharmaceutically acceptable excipient," as used herein, refers any ingredient other than the compounds described herein (for example, a vehicle capable of suspending or dissolving the active compound) and having the properties of being substantially nontoxic and non-inflammatory in a patient. Excipients can include, for example: antiadherents, antioxidants, binders, coatings, compression aids, disintegrants, dyes (colors), emollients, emulsifiers, fillers (diluents), film formers or coatings, flavors, fragrances, glidants (flow enhancers), lubricants, preservatives, printing inks, sorbents, suspension or dispersing agents, sweeteners, and waters of hydration. Exemplary excipients include, but are not limited to: butylated hydroxytoluene (BHT), calcium carbonate, calcium phosphate (dibasic), calcium stearate, croscarmellose, crosslinked polyvinyl pyrrolidone, citric acid, crospovidone, cysteine, ethylcellulose, gelatin, hydroxypropyl cellulose, hydroxypropyl methylcellulose, lactose, magnesium stearate, maltitol, mannitol, methionine, methylcellulose, methyl paraben, microcrystalline cellulose, polyethylene glycol, polyvinyl pyrrolidone, povidone, pregelatinized starch, propyl paraben, retinyl palmitate, shellac, silicon dioxide, sodium carboxymethyl cellulose, sodium citrate, sodium starch glycolate, sorbitol, starch (corn), stearic acid, sucrose, talc, titanium dioxide, vitamin A, vitamin E, vitamin C, and xylitol. The present disclosure also includes pharmaceutically acceptable salts of the compounds described herein. As used herein, "pharmaceutically acceptable salts" refers to derivatives of the disclosed compounds PATENT ATTORNEY DOCKET NO.50858-164WO2 wherein the parent compound is modified by converting an existing acid or base moiety to its salt form (e.g., by reacting the free base group with a suitable organic acid). Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like. Representative acid addition salts include acetate, acetic acid, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzene sulfonic acid, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, glucoheptonate, glycerophosphate, hemisulfate, heptonate, hexanoate, hydrobromide, hydrochloride, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, toluenesulfonate, undecanoate, valerate salts, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like, as well as nontoxic ammonium, quaternary ammonium, and amine cations, including, but not limited to ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, ethylamine, and the like. The pharmaceutically acceptable salts of the present disclosure include the conventional non-toxic salts of the parent compound formed, for example, from non-toxic inorganic or organic acids. The pharmaceutically acceptable salts of the present disclosure can be synthesized from the parent compound that contains a basic or acidic moiety by conventional chemical methods. Generally, such salts can be prepared by reacting the free acid or base forms of these compounds with a stoichiometric amount of the appropriate base or acid in water or in an organic solvent, or in a mixture of the two; generally, nonaqueous media like ether, ethyl acetate, ethanol, isopropanol, or acetonitrile are used. Lists of suitable salts are found in Remington's Pharmaceutical Sciences, 17thed., Mack Publishing Company, Easton, Pa., 1985, p.1418, Pharmaceutical Salts: Properties, Selection, and Use, P.H. Stahl and C.G. Wermuth (eds.), Wiley-VCH, 2008, and Berge et al., Journal of Pharmaceutical Science, 66, 1-19 (1977), each of which is incorporated herein by reference in its entirety. The term "pharmaceutically acceptable solvate," as used herein, means a compound of the present disclosure wherein molecules of a suitable solvent are incorporated in the crystal lattice. A suitable solvent is physiologically tolerable at the dosage administered. For example, solvates can be prepared by crystallization, recrystallization, or precipitation from a solution that includes organic solvents, water, or a mixture thereof. Examples of suitable solvents are ethanol, water (for example, mono-, di-, and tri-hydrates), N-methylpyrrolidinone (NMP), dimethyl sulfoxide (DMSO), N,N'-dimethylformamide (DMF), N,N'- dimethylacetamide (DMAC), 1,3-dimethyl-2-imidazolidinone (DMEU), 1,3-dimethyl-3,4,5,6-tetrahydro-2-(1H)- pyrimidinone (DMPU), acetonitrile (ACN), propylene glycol, ethyl acetate, benzyl alcohol, 2-pyrrolidone, benzyl benzoate, and the like. When water is the solvent, the solvate is referred to as a "hydrate." As used herein, the term "alkyl", "alkyl group", or "alkylene" means a linear or branched, saturated hydrocarbon including one or more carbon atoms (e.g., one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, or more carbon atoms), which is optionally substituted. The notation "C1-14 alkyl" means an optionally substituted linear or branched, saturated hydrocarbon including 1-14 carbon atoms. Unless otherwise specified, an alkyl group described herein refers to both unsubstituted and substituted alkyl groups. PATENT ATTORNEY DOCKET NO.50858-164WO2 As used herein, the term "alkenyl", "alkenyl group", or "alkenylene" means a linear or branched hydrocarbon including two or more carbon atoms (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, or more carbon atoms) and at least one double bond, which is optionally substituted. The notation "C2-14 alkenyl" means an optionally substituted linear or branched hydrocarbon including 2-14 carbon atoms and at least one carbon- carbon double bond. An alkenyl group may include one, two, three, four, or more carbon-carbon double bonds. For example, C18 alkenyl may include one or more double bonds. A C18 alkenyl group including two double bonds may be a linoleyl group. Unless otherwise specified, an alkenyl group described herein refers to both unsubstituted and substituted alkenyl groups. As used herein, the term "alkynyl", "alkynyl group", or "alkynylene" means a linear or branched hydrocarbon including two or more carbon atoms (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, or more carbon atoms) and at least one carbon-carbon triple bond, which is optionally substituted. The notation "C2-14 alkynyl" means an optionally substituted linear or branched hydrocarbon including 2-14 carbon atoms and at least one carbon-carbon triple bond. An alkynyl group may include one, two, three, four, or more carbon- carbon triple bonds. For example, C18 alkynyl may include one or more carbon-carbon triple bonds. Unless otherwise specified, an alkynyl group described herein refers to both unsubstituted and substituted alkynyl groups. As used herein, the term "carbocycle" or "carbocyclic group" means an optionally substituted mono- or multi-cyclic system including one or more rings of carbon atoms. Rings may be three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, or twenty membered rings. The notation "C3-6 carbocycle" means a carbocycle including a single ring having 3- 6 carbon atoms. Carbocycles may include one or more carbon-carbon double or triple bonds and may be non-aromatic or aromatic (e.g., cycloalkyl or aryl groups). Examples of carbocycles include cyclopropyl, cyclopentyl, cyclohexyl, phenyl, naphthyl, and 1,2 dihydronaphthyl groups. The term "cycloalkyl" as used herein means a non-aromatic carbocycle and may or may not include any double or triple bond. Unless otherwise specified, carbocycles described herein refers to both unsubstituted and substituted carbocycle groups, i.e., optionally substituted carbocycles. As used herein, the term "heterocycle" or "heterocyclic group" means an optionally substituted mono- or multi-cyclic system including one or more rings, where at least one ring includes at least one heteroatom. Heteroatoms may be, for example, nitrogen, oxygen, or sulfur atoms. Rings may be three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen membered rings. Heterocycles may include one or more double or triple bonds and may be non-aromatic or aromatic (e.g., heterocycloalkyl or heteroaryl groups). Examples of heterocycles include imidazolyl, imidazolidinyl, oxazolyl, oxazolidinyl, thiazolyl, thiazolidinyl, pyrazolidinyl, pyrazolyl, isoxazolidinyl, isoxazolyl, isothiazolidinyl, isothiazolyl, morpholinyl, pyrrolyl, pyrrolidinyl, furyl, tetrahydrofuryl, thiophenyl, pyridinyl, piperidinyl, quinolyl, and isoquinolyl groups. The term "heterocycloalkyl" as used herein means a non-aromatic heterocycle and may or may not include any double or triple bond. Unless otherwise specified, heterocycles described herein refer to both unsubstituted and substituted heterocycle groups, i.e., optionally substituted heterocycles. As used herein, the term "heteroalkyl", "heteroalkenyl", or "heteroalkynyl", refers respectively to an alkyl, alkenyl, alkynyl group, as defined herein, which further comprises one or more (e.g., 1, 2, 3, or 4) PATENT ATTORNEY DOCKET NO.50858-164WO2 heteroatoms (e.g., oxygen, sulfur, nitrogen, boron, silicon, phosphorus) wherein the one or more heteroatoms is inserted between adjacent carbon atoms within the parent carbon chain and / or one or more heteroatoms is inserted between a carbon atom and the parent molecule, i.e., between the point of attachment. Unless otherwise specified, heteroalkyls, heteroalkenyls, or heteroalkynyls described herein refers to both unsubstituted and substituted heteroalkyls, heteroalkenyls, or heteroalkynyls, i.e., optionally substituted heteroalkyls, heteroalkenyls, or heteroalkynyls. As used herein, a "biodegradable group" is a group that may facilitate faster metabolism of a lipid in a mammalian entity. A biodegradable group may be selected from the group consisting of, but is not limited to, -C(O)O-, -OC(O)-, -C(O)N(R')-, -N(R')C(O)-, -C(O)-, -C(S)-, -C(S)S-, -SC(S)-, -CH(OH)-, - P(O)(OR')O-, -S(O)2-, an aryl group, and a heteroaryl group. As used herein, an "aryl group" is an optionally substituted carbocyclic group including one or more aromatic rings. Examples of aryl groups include phenyl and naphthyl groups. As used herein, a "heteroaryl group" is an optionally substituted heterocyclic group including one or more aromatic rings. Examples of heteroaryl groups include pyrrolyl, furyl, thiophenyl, imidazolyl, oxazolyl, and thiazolyl. Both aryl and heteroaryl groups may be optionally substituted. For example, M and M' can be selected from the non-limiting group consisting of optionally substituted phenyl, oxazole, and thiazole. In the Formulas herein, M and M' can be independently selected from the list of biodegradable groups above. Unless otherwise specified, aryl or heteroaryl groups described herein refers to both unsubstituted and substituted groups, i.e., optionally substituted aryl or heteroaryl groups. Alkyl, alkenyl, and cyclyl (e.g., carbocyclyl and heterocyclyl) groups may be optionally substituted unless otherwise specified. Optional substituents may be selected from the group consisting of, but are not limited to, a halogen atom (e.g., a chloride, bromide, fluoride, or iodide group), a carboxylic acid (e.g., C(O)OH), an alcohol (e.g., a hydroxyl, OH), an ester (e.g., C(O)OR OC(O)R), an aldehyde (e.g., C(O)H), a carbonyl (e.g., C(O)R, alternatively represented by C=O), an acyl halide (e.g., C(O)X, in which X is a halide selected from bromide, fluoride, chloride, and iodide), a carbonate (e.g., OC(O)OR), an alkoxy (e.g., OR), an acetal (e.g., C(OR)2R"", in which each OR are alkoxy groups that can be the same or different and R"" is an alkyl or alkenyl group), a phosphate (e.g., P(O)43-), a thiol (e.g., SH), a sulfoxide (e.g., S(O)R), a sulfinic acid (e.g., S(O)OH), a sulfonic acid (e.g., S(O)2OH), a thial (e.g., C(S)H), a sulfate (e.g.,S(O)42-), a sulfonyl (e.g., S(O)2 ), an amide (e.g., C(O)NR2, or N(R)C(O)R), an azido (e.g., N3), a nitro (e.g., NO2), a cyano (e.g., CN), an isocyano (e.g., NC), an acyloxy (e.g., OC(O)R), an amino (e.g., NR2, NRH, or NH2), a carbamoyl (e.g., OC(O)NR2, OC(O)NRH, or OC(O)NH2), a sulfonamide (e.g., S(O)2NR2, S(O)2NRH, S(O)2NH2, N(R)S(O)2R, N(H)S(O)2R, N(R)S(O)2H, or N(H)S(O)2H), an alkyl group, an alkenyl group, and a cyclyl (e.g., carbocyclyl or heterocyclyl) group. In any of the preceding, R is an alkyl or alkenyl group, as defined herein. In some embodiments, the substituent groups themselves may be further substituted with, for example, one, two, three, four, five, or six substituents as defined herein. For example, a C1-6 alkyl group may be further substituted with one, two, three, four, five, or six substituents as described herein. Compounds of the disclosure that contain nitrogens can be converted to N-oxides by treatment with an oxidizing agent (e.g., 3-chloroperoxybenzoic acid (mCPBA) and / or hydrogen peroxides) to afford other compounds of the disclosure. Thus, all shown and claimed nitrogen-containing compounds are considered, when allowed by valency and structure, to include both the compound as shown and its N-oxide derivative (which can be designated as N→O or N+-O-). Furthermore, in other instances, the nitrogens in the compounds of the disclosure can be converted to N-hydroxy or N-alkoxy compounds. For example, N- PATENT ATTORNEY DOCKET NO.50858-164WO2 hydroxy compounds can be prepared by oxidation of the parent amine by an oxidizing agent such as m CPBA. All shown and claimed nitrogen-containing compounds are also considered, when allowed by valency and structure, to cover both the compound as shown and its N-hydroxy (i.e., N-OH) and N-alkoxy (i.e., N- OR, wherein R is substituted or unsubstituted C1-C6 alkyl, C1-C6 alkenyl, C1-C6 alkynyl, 3-14-membered carbocycle or 3-14-membered heterocycle) derivatives. As used herein, the term “programmable nucleic acid editor” (PNE) refers to a polypeptide or polypeptides comprising at least a CRISPR nuclease which associates with or complexes with at least one guide nucleic acid. In some embodiments, the PNE is a fusion protein, and the components of the PNE are domains of the fusion protein, optionally connected by any of the linkers disclosed herein. In some embodiments, the PNE is a multi-protein complex, and the components of the PNE are provided as individual polypeptides. In some embodiments, the PNE is a multi-protein complex, and one or more components of the PNE are provided endogenously by the cell. The PNEs may be used in editing, modifying or altering a target nucleotide sequence of a nucleic acid. Exemplary PNEs include any of the PNEs provided herein, such as the PNEs in Table 2. As used herein, the terms “component” and “element” are used interchangeably and refer to a polypeptide in a PNE. In some embodiments, the PNE is a fusion protein, and the components of the PNE are domains of the fusion protein, optionally connected by any of the linkers disclosed herein. In some embodiments, the PNE is a multi-protein complex, and the components of the PNE are provided as individual polypeptides. In some embodiments, the PNE is a multi-protein complex, and one or more components of the PNE are provided endogenously by the cell. As used herein, the term CRISPR nuclease refers to any CRISPR-associated polypeptide. CRISPR nucleases are RNA-guided nucleases which allow for the targeting of specific sequences by complexing the nucleases with guide RNA that specifically hybridizes with a particular target sequence. CRISPR nucleases use RNA:DNA hybridization to target and bind to specific sequences in a DNA molecule. Each CRISPR nuclease is associated with at least one guide nucleic acid (e.g., guide RNA), which localizes the CRISPR nuclease to a DNA sequence that comprises a DNA strand (i.e., a target strand) that is complementary to the guide nucleic acid, or a portion thereof (e.g., the protospacer of a guide RNA). In other words, the guide nucleic acid “programs” the CRISPR nuclease to localize and bind to a complementary sequence. The CRISPR nuclease may include one or more nuclease activities, which then cut the DNA leaving various types of lesions. The CRISPR nuclease may be from any type of CRISPR system, such as a Cas9 or any CRISPR nuclease described herein. In some embodiments, the CRISPR nuclease is a nickase CRISPR nuclease (nCas), in which one of the two nuclease domains is inactivated. An nCas may only cleave one strand of a target DNA. In some embodiments, the CRISPR nuclease is a catalytically dead CRISPR nuclease (dCas), in which both nuclease domains are inactivated. A dCas may not cleave either strand of a target DNA. The term “PAM” or “protospacer adjacent motif” as used herein refers to a nucleotide sequence of a target DNA located in proximity to the targeted DNA sequence and recognized by the CRISPR nuclease, i.e., by the guide RNA forming a complex with the CRISPR nuclease and the target DNA. The PAM sequence may differ depending on the CRISPR nuclease identity. Commonly accepted abbreviations that are used in the art as well as herein to represent ambiguity in nucleotide bases of the PAM include the following: R=G or PATENT ATTORNEY DOCKET NO.50858-164WO2 A; Y=C or T; M=A or C; K=G or T; S=G or C; W=A or T; H=A or C or T; B=G or T or C; V=G or C or A; D=G or A or T; n=A or C or G or T. The term “Cas9” refers to any naturally occurring Cas9 from any organism, any naturally occurring Cas9 equivalent or functional fragment thereof, any Cas9 homolog, ortholog, or paralog from any organism, and any mutant or variant of a Cas9, naturally occurring or engineered. Cas9 sequences and structures are well known to those of skill in the art (see, e.g., Ferretti et al., "Complete genome sequence of an M1 strain of Streptococcus pyogenes", Proc. Natl. Acad Sci. U.S.A.98:4658-4663(2001); Deltcheva et al., "CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III", Nature 471:602- 607(2011); and Jinek et al., "A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity" Science 337:816-821(2012), the entire contents of each of which are incorporated herein by reference). The term “RuvC domain” refers to the "RuvC" or "RuvC-like" domain of a CRISPR nuclease. RuvC stands for "Resolved Holliday Junction nuclease" and is responsible for cleaving the DNA strand opposite to the DNA strand which is complementary to the RNA guide strand. Together with the HNH domain, the RuvC domain creates a double-strand break in the target DNA, allowing for gene editing or modification. The term “HNH domain” refers to HNH domain of a CRISPR nuclease. The HNH domain in CRISPR nucleases stands for "Histidine-Asparagine-Histidine." These conserved amino acid residues play a crucial role in the nuclease activity of this domain. The HNH domain is one of the two main types of nuclease domains found in CRISPR-associated (Cas) proteins. In the context of CRISPR systems, the HNH domain is responsible for cleaving the DNA strand that is complementary to the RNA guide strand, thereby creating a cut in the target DNA. This break is a key step in the CRISPR-Cas gene editing process, allowing for precise DNA modification. Together with the RuvC domain, the HNH domain creates a double-strand break in the target DNA, allowing for gene editing or modification. The term “nCas” refers to a CRISPR nuclease with one of the two nuclease domains inactivated. This enzyme is capable of cleaving only one strand of a target DNA. In some cases, the nCas can cleave the complementary strand of a guide target sequence but has reduced ability to cleave the non-complementary strand of a double stranded guide target sequence. For example, the nCas can have a mutation that reduces the function of the RuvC domain, such as a D10A mutation in Cas9 or a corresponding mutation in any CRISPR nuclease of the invention. In some cases, the nCas can cleave the non-complementary strand of a double stranded guide target sequence but has reduced ability to cleave the complementary strand of the guide target sequence. For example, an nCas can have a mutation that reduces the function of the HNH domain, such as an H840A mutation in Cas9 or a corresponding mutation in any CRISPR nuclease of the invention. As used herein, the term “dCas” refers to a nuclease-inactive CRISPR nuclease or catalytically dead CRISPR nuclease, or a functional fragment thereof, and embraces any naturally occurring dCas from any organism, any naturally-occurring dCas equivalent or functional fragment thereof, any dCas homolog, ortholog, or paralog from any organism, and any mutant or variant of a dCas, naturally-occurring or engineered. In some cases, a dCas has a reduced ability to cleave both the complementary and the non- complementary strands of a double stranded target DNA but retains the ability to bind a target DNA. As a non-limiting example, in some cases, the dCas harbors both the D10A and the H840A mutations in Cas9, or corresponding mutations in any CRISPR nuclease of the invention. Additional suitable nuclease-inactive dCas can be apparent to those of skill in the art based on this disclosure and knowledge in the field and are PATENT ATTORNEY DOCKET NO.50858-164WO2 within the scope of this disclosure. Such additional exemplary suitable dCas include, but are not limited to, D10A / H840A, D10A / D839A / H840A, and D10A / D839A / H840A / N863A mutant domains (See, e.g., Prashant et al., “CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering” Nature Biotechnology.2013; 31(9): 833-838, the entire contents of which are incorporated herein by reference). As used herein, the term "guide RNA (gRNA)" and its grammatical equivalents can refer to an RNA which can be specific for a target DNA and can form a complex with a PNE. The gRNA may form a complex with a gene editor, a base editor, or a prime editor. A gRNA is typically single-stranded and can be programmed to site-specifically bind (i.e., via complementary base pairing) to a target sequence of a nucleic acid, thereby directing a PNE that is in conjunction with the gRNA to the target sequence. As will be appreciated by one having skill in the art, in a gRNA sequence uracil (U) replaces thymine (T) in the sequence. In some embodiments, a gRNA may comprise two or more individual nucleic acids, which can interact with one another via complementary base pairing (a dual guide nucleic acid). For example, a gRNA can comprise a CRISPR RNA (“crRNA”) and a trans-activating CRISPR RNA (“tracrRNA”). The crRNA comprises a sequence that recognizes the target sequence. The tracrRNA comprises repeat sequences which form a scaffold region that stabilizes the gRNA-CRISPR protein complex. In other embodiments, a gRNA can comprise both the nucleic acid targeting portion of the nucleic acid and the scaffold portion of the nucleic acid in a single molecule (i.e., a single guide RNA (sgRNA)). Herein the term gRNA contemplates any single, dual or multi-molecule nucleic acid capable of interacting with and directing a PNE to a target nucleic acid sequence. The term “PEgRNA” refers to a gRNA for use with the prime editors of the invention. A PEgRNA is a gRNA which additionally comprises an extension arm. The extension arm is a single strand extension at the 3ʹ end or the 5ʹ end of the PEgRNA which comprises a primer binding site and a DNA synthesis template sequence that encodes via a polymerase (e.g., a reverse transcriptase) a single stranded DNA flap containing the genetic change of interest, which then integrates into the endogenous DNA by replacing the corresponding endogenous strand, thereby installing the desired genetic change. The term “homology arm” refers to a portion of the extension arm that encodes a portion of the resulting reverse transcriptase-encoded single strand DNA flap that is to be integrated into the target DNA site by replacing the endogenous strand. The portion of the single strand DNA flap encoded by the homology arm is complementary to the non-edited strand of the target DNA sequence, which facilitates the displacement of the endogenous strand and annealing of the single strand DNA flap in its place, thereby installing the edit. This component is further defined elsewhere. The homology arm is part of the DNA synthesis template since it is by definition encoded by the polymerase of the prime editors described herein. As used herein, the term “gene editor” refers to a polypeptide or polypeptides comprising at least a CRISPR nuclease described herein. In some embodiments, the gene editor is a fusion protein, and the components of the gene editor are domains of the fusion protein, optionally connected by any of the linkers disclosed herein. In some embodiments, the gene editor is a multi-protein complex, and the components of the gene editor are provided as individual polypeptides. In some embodiments, the gene editor is a multi- protein complex, and one or more components of the gene editor are provided endogenously by the cell. The gene editor may be used in editing, modifying or altering a target nucleotide sequence of a nucleic acid. The CRISPR nuclease of the gene editor may produce double-stranded breaks in the target nucleic acid, or PATENT ATTORNEY DOCKET NO.50858-164WO2 single-stranded breaks (e.g., a nCas). The gene editor may be further delivered with a repair template containing the desired edit for use in homology-directed repair. As used herein, the term “base editor” refers to a polypeptide or polypeptides comprising at least a CRISPR nuclease described herein and at least one base editing polypeptide. In some embodiments, the base editor is a fusion protein, and the components of the base editor are domains of the fusion protein, optionally connected by any of the linkers disclosed herein. In some embodiments, the base editor is a multi- protein complex, and the components of the base editor are provided as individual polypeptides. In some embodiments, the base editor is a multi-protein complex, and one or more components of the base editor are provided endogenously by the cell. The base editing polypeptide may be any polypeptide which catalyzes the conversion of one nucleobase to another nucleobase. The base editor polypeptide may be a deaminase, such as a cytidine deaminase or an adenine deaminase. The base editor may comprise one or more additional polypeptides, such as an inhibitor of base repair (IBR, e.g., a uracil glycosylase inhibitor). The base editor may be used in editing, modifying or altering a target nucleotide sequence of a nucleic acid. The term "deaminase" refers to an enzyme that catalyzes a deamination reaction (i.e., the removal of an amino group from an amino acid or other compound). The deaminase may be a cytidine deaminase, catalyzing the hydrolytic deamination of cytidine or deoxycytidine to uracil or deoxyuracil, respectively. The deaminase may be an adenine deaminase. Deamination of adenine yields inosine, which is treated as guanine by polymerases. As used herein, the term “inhibitors of base excision repair” (IBR) are proteins that are capable of inhibiting the activity of a nucleic acid repair enzyme, for example a base excision repair enzyme. In some embodiments, the base repair inhibitor is uracil glycosylase inhibitor (UGI). UGI refers to a protein that is capable of inhibiting a uracil-DNA glycosylase base-excision repair enzyme. In some embodiments, the base repair inhibitor is an inhibitor of inosine base excision repair. As used herein, the term “prime editor” refers to a polypeptide or polypeptides comprising at least a CRISPR nuclease described herein and at least one reverse transcriptase polypeptide. In some embodiments, the prime editor is a fusion protein, and the components of the prime editor are domains of the fusion protein, optionally connected by any of the linkers disclosed herein. In some embodiments, the prime editor is a multi-protein complex, and the components of the prime editor are provided as individual polypeptides. In some embodiments, the prime editor is a multi-protein complex, and one or more components of the prime editor are provided endogenously by the cell. The CRISPR nuclease associates with or complexes with at least one guide nucleic acid. The prime editor may be used in editing, modifying or altering a target nucleotide sequence of a nucleic acid. Prime editors comprising a CRISPR nuclease and at least one reverse transcriptase polypeptide write new genetic information into a specified DNA site, wherein the prime editing system is programmed with a prime editing (PE) guide RNA ("PEgRNA") that both specifies the target site and templates the synthesis of the desired edit in the form of a replacement DNA strand by way of an extension engineered onto a guide RNA. The replacement strand containing the desired edit shares the same sequence as the endogenous strand of the target site to be edited (with the exception that it includes the desired edit). Through DNA repair and / or replication machinery, the endogenous strand of the target site is replaced by the newly synthesized replacement strand containing the desired edit. The term "reverse transcriptase" describes a class of polymerases characterized as RNA-dependent DNA polymerases. All known reverse transcriptases require a primer to synthesize a DNA transcript from an PATENT ATTORNEY DOCKET NO.50858-164WO2 RNA template. Historically, reverse transcriptase has been used primarily to transcribe mRNA into cDNA which can then be cloned into a vector for further manipulation. Avian myoblastosis virus (AMV) reverse transcriptase was the first widely used RNA-dependent DNA polymerase (Verma, Biochim. Biophys. Acta 473:1 (1977)). The enzyme has 5ʹ-3ʹ RNA-directed DNA polymerase activity, 5ʹ-3ʹ DNA-directed DNA polymerase activity, and RNase H activity. RNase H is a processive 5ʹ and 3ʹ ribonuclease specific for the RNA strand for RNA-DNA hybrids (Perbal, A Practical Guide to Molecular Cloning, New York: Wiley & Sons (1984)). Errors in transcription cannot be corrected by reverse transcriptase because known viral reverse transcriptases lack the 3ʹ-5ʹ exonuclease activity necessary for proofreading (Saunders and Saunders, Microbial Genetics Applied to Biotechnology, London: Croom Helm (1987)). A detailed study of the activity of AMV reverse transcriptase and its associated RNase H activity has been presented by Berger et al., Biochemistry 22:2365-2372 (1983). Another reverse transcriptase which is used extensively in molecular biology is reverse transcriptase originating from Moloney murine leukemia virus (M-MLV). See, e.g., Gerard, G. R., DNA 5:271-279 (1986) and Kotewicz, M. L., et al., Gene 35:249-258 (1985). M-MLV reverse transcriptase substantially lacking in RNase H activity has also been described. See, e.g., U.S. Pat. No. 5,244,797. As used herein, the term “flap endonuclease” refers to an enzyme that catalyzes the removal of 5ʹ single strand DNA flaps. Flap endonucleases are naturally occurring enzymes that process the removal of 5ʹ flaps formed during cellular processes, including DNA replication. Flap endonucleases are known in the art and can be found described in Patel et al., "Flap endonucleases pass 5'-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5'-ends," Nucleic Acids Research, 2012, 40(10): 4507-4519, Tsutakawa et al., "Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily," Cell, 2011, 145(2): 198-211, and Balakrishnan et al., "Flap Endonuclease l," Annu Rev Biochem, 2013, Vol 82: 119-138 (each of which are incorporated herein by reference). As used herein, the term “fusion protein” refers to a hybrid polypeptide which comprises protein domains from at least two different proteins. One protein may be located at the amino-terminal (N-terminal) portion of the fusion protein or at the carboxy-terminal (C-terminal) protein thus forming an "amino-terminal fusion protein" or a "carboxy-terminal fusion protein," respectively. A protein may comprise different domains, for example, a nucleic acid binding domain (e.g., the gRNA binding domain of CRISPR nuclease that directs the binding of the protein to a target site) and a nucleic acid cleavage domain or a catalytic domain of a nucleic-acid editing protein. Another example includes a CRISPR nuclease to a reverse transcriptase. Any of the proteins provided herein may be produced by any method known in the art. For example, the proteins provided herein may be produced via recombinant protein expression and purification, which is especially suited for fusion proteins comprising a peptide linker. Methods for recombinant protein expression and purification are well known, and include those described by Green and Sambrook, Molecular Cloning: A 4thLaboratory Manual (ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)), the entire contents of which are incorporated herein by reference. The term “linker,” as used herein, refers to a molecule linking two other molecules or moieties. The linker can be an amino acid sequence in the case of a linker joining two fusion proteins. For example, a CRISPR nuclease can be fused to a reverse transcriptase by an amino acid linker sequence. The linker can also be a nucleotide sequence in the case of joining two nucleotide sequences together. For example, in the PATENT ATTORNEY DOCKET NO.50858-164WO2 instant case, the traditional guide RNA is linked via a spacer or linker nucleotide sequence to the RNA extension of a prime editing guide RNA which may comprise a RT template sequence and an RT primer binding site. In other embodiments, the linker is an organic molecule, group, polymer, or chemical moiety. In some embodiments, the linker is 5-100 amino acids in length, for example, 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. Longer or shorter linkers are also contemplated. Additional examples of linkers include, but are not limited to, unsaturated alkanes, polyethylene glycols (e.g., ethylene or propylene glycol monomeric units, e.g., diethylene glycol, dipropylene glycol, triethylene glycol, tripropylene glycol, tetraethylene glycol, or tetraethylene glycol), and dextran polymers and derivatives thereof., Other examples include, but are not limited to, cleavable moieties within the linker, such as, for example, a disulfide bond (-S-S-) or an azo bond (-N=N-), which can be cleaved using a reducing agent or photolysis. Non-limiting examples of a selectively cleavable bond include an amido bond can be cleaved for example by the use of tris(2-carboxyethyl)phosphine (TCEP), or other reducing agents, and / or photolysis, as well as an ester bond can be cleaved for example by acidic or basic hydrolysis. The term “nuclear localization sequence” or “NLS” refers to an amino acid sequence that promotes import of a protein into the cell nucleus, for example, by nuclear transport. Nuclear localization sequences are known in the art and would be apparent to the skilled artisan. For example, NLS sequences are described in Plank et al., international PCT application, PCT / EP2000 / 011690, filed November 23, 2000, published as WO / 2001 / 038547 on May 31, 2001, the contents of which are incorporated herein by reference for its disclosure of exemplary nuclear localization sequences. The term “host cell” " is an organism into which an expression vector, phage, virus, or other DNA construct, including a polynucleotide of the present invention has been introduced. Exemplary host strains include prokaryotic cells (e.g., bacterial cells) or eukaryotic cells (e.g., mammalian cells, yeast cells, or fungal cells) capable of expressing the CRISPR nuclease. BRIEF DESCRIPTION OF THE DRAWINGS FIG.1 shows the bioinformatic pipeline developed to identify novel CRISPR-Cas systems in genome sequences. Genome sequences from various sources are processed with three state-of-the-art sequence mining tools to identify Cas nuclease genes, CRISPR arrays, and tracrRNA sequences. The pool of potential Cas proteins is further enriched by scanning the genomes with custom HMMs and filtered for the presence of domains and residues required for endonuclease activity. The three functional elements Cas, CRISPR array, and tracrRNA are mapped to each other via there genomic locus as well as the complementarity of the CRISPR repeats and the tracrRNAs. FIG.2 shows a phylogenetic tree of the Cas nucleases of the invention. The full-length amino acid sequences were aligned using Clustal Omega and the tree was calculated with FastTree (using the Whelan- And-Goldman model). FIG.3 is a graph showing the gene editing efficiency of a Cas nuclease of the disclosure in mammalian cells, as is described in Example 2, below. Percent indel formation was performed for SpCas9 and Nuclease 49 in HEK293T cells. PATENT ATTORNEY DOCKET NO.50858-164WO2 FIG.4 is a graph showing the gene editing efficiency of a Cas nuclease of the disclosure in mammalian cells, as is described in Example 3, below. Percent indel formation was performed for SpCas9 and Nuclease 1 in HEK293T cells. FIGS.5A-5C shows PAM sequence identification results for Nucleases 53, 21, and 40, respectively. Experiments were performed using the materials and methods outlined in Example 6. FIG.6 is a graph showing percent indel formation of Nuclease 53 with various sgRNAs. Experiments were performed in HEK293T cells using plasmid guides, as outlined in Example 7. FIG.7 is a graph showing percent indel formation of Nuclease 53 with various sgRNAs. Experiments were performed in Hep3b cells using mRNA encoding the CRISPR nucleases and sgRNAs, as outlined in Example 7. FIG.8 is a graph showing percent editing of Nuclease 53 with various sgRNAs. Experiments were performed in PHH cells at an exemplary locus using mRNA encoding the CRISPR nucleases and sgRNAs, as outlined in Example 7. FIG.9 is a graph showing percent indel formation of Nuclease 1 with various sgRNAs. Experiments were performed as outlined in Example 8. FIG.10 is a graph showing percent indel formation of Nuclease 1 with various sgRNAs. Experiments were performed as outlined in Example 8. FIG.11 is a graph showing percent indel formation of Nuclease 21 with various sgRNAs. Experiments were performed as outlined in Example 9. FIG.12 is a graph showing percent indel formation of Nuclease 40 with various sgRNAs. Experiments were performed as outlined in Example 10. FIG.13 is a graph showing percent editing of Nuclease 1, 21, and 40. Experiments were performed as outlined in Example 11. FIG.14 is a graph showing percent prime editing of Nuclease 1 fused to a reverse transcriptase (RT) with various nicking sgRNAs and PEgRNA. Experiments were performed as outlined in Example 12. DETAILED DESCRIPTION Disclosed herein are novel programmable nucleobase editors (PNEs) for editing, modifying or altering a target nucleotide sequence of a nucleic acid. In particular, the novel PNEs are described in Table 2. The sections that follow describe exemplary PNEs of the disclosure in further detail. 1. PNEs PNE refers to a polypeptide or polypeptides comprising at least a CRISPR nuclease which associates with or complexes with at least one guide nucleic acid. In some embodiments, the PNE is a fusion protein, and the components of the PNE are domains of the fusion protein, optionally connected by any of the linkers disclosed herein. In some embodiments, the PNE is a multi-protein complex, and the components of the PNE are provided as individual polypeptides. In some embodiments, the PNE is a multi- protein complex, and one or more components of the PNE are provided endogenously by the cell. The PNEs may be used in editing, modifying or altering a target nucleotide sequence of a nucleic acid. PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE can be associated with or complexed with at least one guide nucleic acid (e.g., guide RNA or a PEgRNA), which localizes the PNE to a DNA strand (i.e., a target strand) that is complementary to the guide nucleic acid, or a portion thereof (e.g., the spacer of a guide RNA which anneals to the protospacer of the DNA target). In other words, the guide nucleic acid “programs” the PNE to localize and bind to complementary sequence of the protospacer in the DNA. In some embodiments, the PNEs of the disclosure are gene editors. In some embodiments, the PNEs of the disclosure are base editors. In some embodiments, the PNEs of the disclosure are prime editors. The elements of a PNE and their mechanisms are described in the sections below. a. CRISPR Nuclease In some aspects, a PNE comprises at least a CRISPR nuclease. Non-limiting, exemplary CRISPR nucleases are provided herein. Without being bound by theory, the mechanism of action of certain CRISPR nucleases herein includes the step of forming an R-loop whereby the CRISPR nuclease induces the unwinding of a double-strand DNA target, thereby separating the strands in the region bound by the CRISPR nuclease. The guide RNA spacer then hybridizes to the “target strand” at the protospacer sequence. This displaces a “non-target strand” that is complementary to the target strand, which forms the single strand region of the R-loop. In some embodiments, the CRISPR nuclease includes one or more nuclease activities, which then cut the DNA leaving various types of lesions. For example, the CRISPR nuclease may comprise a nuclease activity that cuts the non-target strand at a first location, and / or cuts the target strand at a second location. In some embodiments, a CRISPR nuclease can cut zero, one, or two strands of a target nucleic acid. In some embodiments, the CRISPR nuclease is a nickase, which cuts one strand of a target nucleic acid. In some embodiments, the CRISPR nuclease is catalytically dead, which cuts zero strands of a target nucleic acid. In some embodiments, the CRISPR nuclease comprises any one of the amino acid sequences as set forth herein. In some embodiments the CRISPR nuclease comprises an amino acid sequence that is at least 60%, at least 65%, 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%, or at least 99.5% identical to any one of the amino acid sequences set forth herein. Examples of CRISPR nucleases include, without limitation, Cas9 (e.g., dCas9 and nCas9), Cas12a / Cpf1, Cas12b / C2c1, Cas12c / C2c3, Cas12d / CasY, Cas12e / CasX, Cas12g, Cas12h, Cas12i, and Cas12j / CasΦ, Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas5d, Cas5t, Cas5h, Cas5a, Cas6, Cas7, Cas8, Cas8a, Cas8b, Cas8c, Cas9 (also known as Csn1 or Csx12), Cas10, Cas10d, Csy1 , Csy2, Csy3, Csy4, Cse1, Cse2, Cse3, Cse4, Cse5e, Csc1, Csc2, Csa5, Csn1, Csn2, Csm1, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx1S, Csx11, Csf1, Csf2, CsO, Csf4, Csd1, Csd2, Cst1, Cst2, Csh1, Csh2, Csa1, Csa2, Csa3, Csa4, Csa5, Type II Cas effector proteins, Type V Cas effector proteins, Type VI Cas effector proteins, CARF, DinG, homologues thereof, or modified or engineered versions thereof. i. CRISPR Nucleases of the Invention In some embodiments, CRISPR nucleases of the disclosure are from: Lactobacillus sp., Streptococcus equinus, Streptococcus mutans, Bacillus sp-63030, Enterococcus gilvus, Streptococcus sp., PATENT ATTORNEY DOCKET NO.50858-164WO2 Lactobacillus murinus, Lactobacillus ruminis, Lactobacillus salivarius, Lactobacillus jensenii, Lactobacillus hamsteri, Lactobacillus delbrueckii, Lactobacillus johnsonii, Lactobacillus plantarum, Lactobacillus rhamnosus, uncultured Turicibacter sp., Ureibacillus thermosphaericus, Streptococcus orisratti DSM 15617, Streptococcus salivarius, Streptococcus henryi DSM 19005, Lentihominibacter hominis, Streptococcus sp. CCH8-G7, Streptococcus pacificus, Clostridia bacterium, Streptococcus ruminantium, uncultured Ruminococcus sp, Alicyclobacillus sacchari, Lactobacillus farciminis DSM 20184, Lactobacillus farciminis, Enterococcus hermanniensis, Enterococcus asini, Companilactobacillus zhachilii, Companilactobacillus halodurans, Companilactobacillus keshanensis, Companilactobacillus suantsaicola, Companilactobacillus hulinensis, Bombilactobacillus apium, Vagococcus penaei, or Lactobacillus gallinarum. The amino acid sequence and the nucleic acid sequence encoding the amino acid sequence of exemplary CRISPR nucleases of the disclosure are provided in Table 2.

[0002] PATENT ATTORNEY DOCKET NO.50858-164WO2 Table 2. Exemplary CRISPR Nucleases of the Invention. PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET 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NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a CRISPR nuclease having at least 50% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 1-53. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a CRISPR nuclease having at least 55% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 1-53. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a CRISPR nuclease having at least 60% sequence identity (e.g., 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 1-53. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a CRISPR nuclease having at least 65% sequence identity (e.g., 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 1-53. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a CRISPR nuclease having at least 70% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 1-53. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a CRISPR nuclease having at least 75% sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 1-53. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a CRISPR nuclease having at least 80% sequence identity (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 1-53. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a CRISPR nuclease having at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 1-53. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a CRISPR nuclease having at least 90% sequence identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 1-53. PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a CRISPR nuclease having at least 95% sequence identity (e.g., 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 1-53. In some embodiments, a nucleic acid encoding a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may have at least 50% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 54-106. In some embodiments, a nucleic acid encoding a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may have at least 55% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 54-106. In some embodiments, a nucleic acid encoding a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may have at least 60% sequence identity (e.g., 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 54-106. In some embodiments, a nucleic acid encoding a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may have at least 65% sequence identity (e.g., 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 54-106. In some embodiments, a nucleic acid encoding a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may have at least 70% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 54-106. In some embodiments, a nucleic acid encoding a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may have at least 75% sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 54-106. In some embodiments, a nucleic acid encoding a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may have at least 80% sequence identity (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 54-106. In some embodiments, a nucleic acid encoding a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may have at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 54-106. PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a nucleic acid encoding a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may have at least 90% sequence identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 54-106. In some embodiments, a nucleic acid encoding a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may have at least 95% sequence identity (e.g., 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 54-106. ii. Cas9 In some embodiments, the CRISPR nuclease is a Cas9. In some embodiments, Cas9 refers to Cas9 from Streptococcus pyogenes (NCBI Reference Sequence: NC_017053.1). In some embodiments, wild type Cas9 corresponds to Cas9 from Streptococcus pyogenes (NCBI Reference Sequence: NC_002737.2). In some embodiments, Cas9 refers to Cas9 from: Corynebacterium ulcerans (NCBI Refs: NC_015683.1, NC_017317.1); Corynebacterium diphtheria (NCBI Refs: NC_016782.1, NC_016786.1); Spiroplasma syrphidicola (NCBI Ref: NC_021284.1); Prevotella intermedia (NCBI Ref: NC_ 017861.1 ); Spiroplasma taiwanense (NCBI Ref: NC_021846.1); Streptococcus iniae (NCBI Ref: NC_021314.1); Belliella baltica (NCBI Ref: NC_018010.1); Psychroflexus torquis (NCBI Ref: NC_018721.1); Streptococcus thermophilus (NCBI Ref: YP_820832.1), Listeria innocua (NCBI Ref: NP_ 472073.1), Campylobacter jejuni (NCBI Ref: YP_ 002344900.1) or Neisseria meningitidis (NCBI Ref:YP_002342100.1) or to a Cas9 from any other organism. In some embodiments, Cas9 refers to a Cas9 from archaea or nanoarchaea, which constitute a domain and kingdom of single-celled prokaryotic microbes. In some embodiments, the programmable nucleotide binding protein may be a CasX or CasY protein, which have been described in, for example, Burstein et al., "New CRISPR-Cas systems from uncultivated microbes." Cell Res.2017 Feb 21. doi: 10.1038 / cr.2017.21, the entire contents of which is hereby incorporated by reference. Using genome- resolved metagenomics, a number of CRISPR-Cas systems were identified, including the first reported Cas9 in the archaeal domain of life. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, two previously unknown systems were discovered, CRISPR- CasX and CRISPR-CasY, which are among the most compact systems yet discovered. The Cas9 domain may be a nuclease active Cas9 domain, a nuclease inactive Cas9 domain (dCas9), or a Cas9 nickase (nCas9). Cas9 generates double-strand breaks (DSBs) through the combined activity of two nuclease domains, RuvC and HNH. The HNH subdomain cleaves the strand complementary to the gRNA, whereas the RuvC subdomain cleaves the non-complementary strand. iii. nCas In some embodiments, the CRISPR nuclease is a nickase CRISPR nuclease (nCas). In some cases, the nCas can cleave the complementary strand of a guide target sequence but has reduced ability to cleave the non-complementary strand of a double stranded guide target sequence. In this way, nCas enzymes that exhibit single-stranded break (SSB) activity are functionally distinguished from Cas enzymes that exhibit double-stranded break (DSB) activity. As used herein, the terms “single-stranded break activity” and “SSB activity” refer to the ability of a Cas enzyme to catalyze the cleavage of only one strand of a target PATENT ATTORNEY DOCKET NO.50858-164WO2 polynucleotide, whereas “double-stranded break activity” and “DSB activity” refer to the ability of a Cas enzyme to catalyze the cleavage of both strands of a (double-stranded) target polynucleotide. For example, the nCas can have a mutation that reduces the function of the RuvC domain. As a non-limiting example, in some embodiments, an nCas may comprise a D10A mutation (aspartate to alanine at amino acid position 10) in Cas9 or a corresponding mutation in any CRISPR nuclease of the invention. Such an nCas can therefore cleave the complementary strand of a double stranded guide target sequence but has reduced ability to cleave the non-complementary strand of a double stranded guide target sequence (thus resulting in a single strand break (SSB) instead of a double strand break (DSB)) (see, for example, Jinek et al., Science.2012 Aug.17; 337(6096):816-21). In some embodiments, nickase mutations may include D10X, H983X, D986X, or E762X mutations in Cas9, wherein X is any amino acid other than the wild type amino acid or a corresponding mutation in any CRISPR nuclease of the invention. In certain embodiments, the nickase could be DI0A, or H983A, or D986A, or E762A mutation, or a combination thereof, in Cas9 or corresponding mutation(s) in any CRISPR nuclease of the invention. Exemplary RuvC domains of the disclosure are provided in Table 3. Table 3. Exemplary RuvC domains of the disclosure. PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a RuvC domain having at least 50% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a RuvC domain having at least 55% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a RuvC domain having at least 60% sequence identity (e.g., 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, PATENT ATTORNEY DOCKET NO.50858-164WO2 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a RuvC domain having at least 65% sequence identity (e.g., 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a RuvC domain having at least 70% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a RuvC domain having at least 75% sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a RuvC domain having at least 80% sequence identity (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a RuvC domain having at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a RuvC domain having at least 90% sequence identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a RuvC domain having at least 95% sequence identity (e.g., 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 107-148 and 503-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a combination of RuvC domains having at least 50% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to a combination of amino acid sequences selected from SEQ ID NOs: 107-109; SEQ ID NOs: 110-112; SEQ ID NOs: 113-115; SEQ ID NOs: 116-118; SEQ ID NOs: 119-121; SEQ ID NOs: 122-124; SEQ ID NOs: 125- 127; SEQ ID NOs: 128-130; SEQ ID NOs: 131-133; SEQ ID NOs: 134-136; SEQ ID NOs: 137-139; SEQ ID NOs: 140-142; SEQ ID NOs: 143-145; SEQ ID NOs: 146-148; SEQ ID NOs: 503-505; and SEQ ID NOs: 506-508. PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a combination of RuvC domains having at least 55% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to a combination of amino acid sequences selected from SEQ ID NOs: 107-109; SEQ ID NOs: 110-112; SEQ ID NOs: 113-115; SEQ ID NOs: 116-118; SEQ ID NOs: 119-121; SEQ ID NOs: 122-124; SEQ ID NOs: 125-127; SEQ ID NOs: 128- 130; SEQ ID NOs: 131-133; SEQ ID NOs: 134-136; SEQ ID NOs: 137-139; SEQ ID NOs: 140-142; SEQ ID NOs: 143-145; SEQ ID NOs: 146-148; SEQ ID NOs: 503-505; and SEQ ID NOs: 506-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a combination of RuvC domains having at least 60% sequence identity (e.g., 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to a combination of amino acid sequences selected from SEQ ID NOs: 107-109; SEQ ID NOs: 110-112; SEQ ID NOs: 113-115; SEQ ID NOs: 116-118; SEQ ID NOs: 119- 121; SEQ ID NOs: 122-124; SEQ ID NOs: 125-127; SEQ ID NOs: 128-130; SEQ ID NOs: 131-133; SEQ ID NOs: 134-136; SEQ ID NOs: 137-139; SEQ ID NOs: 140-142; SEQ ID NOs: 143-145; SEQ ID NOs: 146- 148; SEQ ID NOs: 503-505; and SEQ ID NOs: 506-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a combination of RuvC domains having at least 65% sequence identity (e.g., 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to a combination of amino acid sequences selected from SEQ ID NOs: 107-109; SEQ ID NOs: 110- 112; SEQ ID NOs: 113-115; SEQ ID NOs: 116-118; SEQ ID NOs: 119-121; SEQ ID NOs: 122-124; SEQ ID NOs: 125-127; SEQ ID NOs: 128-130; SEQ ID NOs: 131-133; SEQ ID NOs: 134-136; SEQ ID NOs: 137- 139; SEQ ID NOs: 140-142; SEQ ID NOs: 143-145; SEQ ID NOs: 146-148; SEQ ID NOs: 503-505; and SEQ ID NOs: 506-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a combination of RuvC domains having at least 70% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to a combination of amino acid sequences selected from SEQ ID NOs: 107-109; SEQ ID NOs: 110-112; SEQ ID NOs: 113-115; SEQ ID NOs: 116-118; SEQ ID NOs: 119-121; SEQ ID NOs: 122-124; SEQ ID NOs: 125-127; SEQ ID NOs: 128-130; SEQ ID NOs: 131-133; SEQ ID NOs: 134-136; SEQ ID NOs: 137-139; SEQ ID NOs: 140-142; SEQ ID NOs: 143-145; SEQ ID NOs: 146-148; SEQ ID NOs: 503-505; and SEQ ID NOs: 506-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a combination of RuvC domains having at least 75% sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to a combination of amino acid sequences selected from SEQ ID NOs: 107-109; SEQ ID NOs: 110-112; SEQ ID NOs: 113-115; SEQ ID NOs: 116-118; SEQ ID NOs: 119-121; SEQ ID NOs: 122-124; SEQ ID NOs: 125-127; SEQ ID NOs: 128-130; SEQ ID NOs: 131- PATENT ATTORNEY DOCKET NO.50858-164WO2 133; SEQ ID NOs: 134-136; SEQ ID NOs: 137-139; SEQ ID NOs: 140-142; SEQ ID NOs: 143-145; SEQ ID NOs: 146-148; SEQ ID NOs: 503-505; and SEQ ID NOs: 506-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a combination of RuvC domains having at least 80% sequence identity (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to a combination of amino acid sequences selected from SEQ ID NOs: 107-109; SEQ ID NOs: 110-112; SEQ ID NOs: 113-115; SEQ ID NOs: 116-118; SEQ ID NOs: 119-121; SEQ ID NOs: 122-124; SEQ ID NOs: 125-127; SEQ ID NOs: 128-130; SEQ ID NOs: 131-133; SEQ ID NOs: 134-136; SEQ ID NOs: 137-139; SEQ ID NOs: 140-142; SEQ ID NOs: 143-145; SEQ ID NOs: 146-148; SEQ ID NOs: 503- 505; and SEQ ID NOs: 506-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a combination of RuvC domains having at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to a combination of amino acid sequences selected from SEQ ID NOs: 107-109; SEQ ID NOs: 110-112; SEQ ID NOs: 113-115; SEQ ID NOs: 116-118; SEQ ID NOs: 119-121; SEQ ID NOs: 122-124; SEQ ID NOs: 125- 127; SEQ ID NOs: 128-130; SEQ ID NOs: 131-133; SEQ ID NOs: 134-136; SEQ ID NOs: 137-139; SEQ ID NOs: 140-142; SEQ ID NOs: 143-145; SEQ ID NOs: 146-148; SEQ ID NOs: 503-505; and SEQ ID NOs: 506-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a combination of RuvC domains having at least 90% sequence identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to a combination of amino acid sequences selected from SEQ ID NOs: 107-109; SEQ ID NOs: 110-112; SEQ ID NOs: 113-115; SEQ ID NOs: 116-118; SEQ ID NOs: 119-121; SEQ ID NOs: 122-124; SEQ ID NOs: 125-127; SEQ ID NOs: 128- 130; SEQ ID NOs: 131-133; SEQ ID NOs: 134-136; SEQ ID NOs: 137-139; SEQ ID NOs: 140-142; SEQ ID NOs: 143-145; SEQ ID NOs: 146-148; SEQ ID NOs: 503-505; and SEQ ID NOs: 506-508. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain a combination of RuvC domains having at least 95% sequence identity (e.g., 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to a combination of amino acid sequences selected from SEQ ID NOs: 107-109; SEQ ID NOs: 110-112; SEQ ID NOs: 113-115; SEQ ID NOs: 116-118; SEQ ID NOs: 119- 121; SEQ ID NOs: 122-124; SEQ ID NOs: 125-127; SEQ ID NOs: 128-130; SEQ ID NOs: 131-133; SEQ ID NOs: 134-136; SEQ ID NOs: 137-139; SEQ ID NOs: 140-142; SEQ ID NOs: 143-145; SEQ ID NOs: 146- 148; SEQ ID NOs: 503-505; and SEQ ID NOs: 506-508. Amino acid positions that are suggested for mutation to inactivate one or more RuvC domains of the disclosure are given in Table 4 (amino acid position numbering is relative to the nuclease SEQ ID NO. given in column 2 of Table 4). PATENT ATTORNEY DOCKET NO.50858-164WO2 Table 4. Amino acid position(s) suggested for mutation to inactivate one or more RuvC domains. In some cases, the nCas can cleave the non-complementary strand of a double stranded guide target sequence but has reduced ability to cleave the complementary strand of the guide target sequence. For example, an nCas can have a mutation that reduces the function of the HNH domain. As a non-limiting example, in some embodiments, the nCas may comprise an H840A mutation (histidine to alanine at amino acid position 840) in Cas9 or a corresponding mutation in any CRISPR nuclease of the invention. Such an nCas can therefore cleave the non-complementary strand of the guide target sequence but has reduced ability to cleave the complementary strand of the guide target sequence (thus resulting in a SSB instead of a DSB). In some embodiments, nickase mutations may include H840X and R863X in Cas9, wherein X is any amino acid other than the wild type amino acid, or a corresponding mutation in any CRISPR nuclease of the invention. In certain embodiments, the nickase could be H840A or R863A or a combination thereof in Cas9 or corresponding mutation(s) in any CRISPR nuclease of the invention. Exemplary HNH domains of the disclosure are provided in Table 5. PATENT ATTORNEY DOCKET NO.50858-164WO2 Table 5. Exemplary HNH domains of the disclosure. PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain an HNH domain having at least 50% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 149-162, 509, and 510. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain an HNH domain having at least 55% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 149-162, 509, and 510. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain an HNH domain having at least 60% sequence identity (e.g., 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 149-162, 509, and 510. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain an HNH domain having at least 65% sequence identity (e.g., 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 149-162, 509, and 510. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain an HNH domain having at least 70% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 149-162, 509, and 510. PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain an HNH domain having at least 75% sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 149-162, 509, and 510. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain an HNH domain having at least 80% sequence identity (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 149-162, 509, and 510. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain an HNH domain having at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 149-162, 509, and 510. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain an HNH domain having at least 90% sequence identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 149-162, 509, and 510. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may contain an HNH domain having at least 95% sequence identity (e.g., 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 149-162, 509, and 510. Amino acid positions that are suggested for mutation to inactivate an HNH domain of the disclosure are given in Table 6 (amino acid position numbering is relative to the nuclease SEQ ID NO. given in column 2 of Table 6). Table 6. Amino acid position(s) suggested for mutation to inactivate the HNH domain. PATENT ATTORNEY DOCKET NO.50858-164WO2 iv. dCas In some embodiments, the CRISPR nuclease is a catalytically dead CRISPR nuclease (dCas). In some cases, a dCas has a reduced ability to cleave both the complementary and the non-complementary strands of a double stranded target DNA. As a non-limiting example, in some cases, the dCas harbors both the D10A and the H840A mutations in Cas9, or corresponding mutations in any CRISPR nuclease of the invention, such that the dCas has a reduced ability to cleave both the complementary and the non- complementary strands of a double stranded target DNA. Such a dCas has a reduced ability to cleave a target DNA but retains the ability to bind a target DNA. In other embodiments, a dCas can comprise one or more deletions of all or a portion of a catalytic domain (e.g., RuvC and / or HNH domains). In further embodiments, a dCas comprises a point mutation (e.g., D10A or H840A in Cas9, or corresponding mutation(s) in any CRISPR nuclease of the invention) as well as a deletion of all or a portion of a catalytic domain. Also contemplated herein are mutations capable of generating a dCas from a previously functional version of the Cas. For example, dCas variants having mutations other than D10A and H840A (or corresponding mutation(s) in any CRISPR nuclease of the invention) are provided, which result in nuclease inactivated Cas. Such mutations, by way of example, include other amino acid substitutions at D10 and H840 (or corresponding mutation(s) in any CRISPR nuclease of the invention), or other substitutions within the catalytic domains of CRISPR nuclease (e.g., substitutions in the HNH nuclease subdomain and / or the RuvC subdomain). Additional suitable nuclease-inactive dCas can be apparent to those of skill in the art based on this disclosure and knowledge in the field and are within the scope of this disclosure. Such additional exemplary suitable dCas include, but are not limited to, D10A / H840A, D10A / D839A / H840A, and D10A / D839A / H840A / N863A mutant domains (See, e.g., Prashant et al., CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nature Biotechnology. 2013; 31(9): 833-838, the entire contents of which are incorporated herein by reference). v. PAM Sequences Some aspects of the disclosure provide CRISPR nuclease that have different PAM specificities. Typically, CRISPR nucleases, such as Cas9 from S. pyogenes (spCas9), require a canonical NGG PAM sequence to bind a particular nucleic acid region. This may limit the ability to target desired bases within a genome. In some embodiments, the PNEs provided herein may need to be placed at a precise location, for example where a target base is placed within a 4 base region (e.g., a “editing window”), which is approximately 15 bases upstream of the PAM. See Komor, A.C., et al., “Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage” Nature 533, 420-424 (2016), the entire contents of which are hereby incorporated by reference. Accordingly, in some embodiments, any of the PNEs provided herein may contain a CRISPR nucleases that is capable of binding a nucleotide sequence that does not contain a canonical (e.g., NGG) PAM sequence. PATENT ATTORNEY DOCKET NO.50858-164WO2 Exemplary PAM sequences of the CRISPR nucleases of the disclosure are provided in Table 7. PAM sequences were determined using a PAM identification assay (see Examples 1 and 2) with timepoints at 4 hours and after overnight incubation. Commonly accepted abbreviations that are used in the art as well as herein to represent ambiguity in nucleotide bases of the PAM include the following: R=G or A; Y=C or T; M=A or C; K=G or T; S=G or C; W=A or T; H=A or C or T; B=G or T or C; V=G or C or A; D=G or A or T; n=A or C or G or T. Table 7. Exemplary PAM sequences of the CRISPR nucleases of the disclosure. PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a CRISPR nuclease of the disclosure may exhibit specificity for a PAM sequence having at least 50% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of the PAM sequences disclosed in Table 7. In some embodiments, a CRISPR nuclease of the disclosure may exhibit specificity for a PAM sequence having at least 55% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of the PAM sequences disclosed in Table 7. In some embodiments, a CRISPR nuclease of the disclosure may exhibit specificity for a PAM sequence having at least 60% sequence identity (e.g., 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of the PAM sequences disclosed in Table 7. In some embodiments, a CRISPR nuclease of the disclosure may exhibit specificity for a PAM sequence having at least 65% sequence identity (e.g., 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of the PAM sequences disclosed in Table 7. In some embodiments, a CRISPR nuclease of the disclosure may exhibit specificity for a PAM sequence having at least 70% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of the PAM sequences disclosed in Table 7. PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a CRISPR nuclease of the disclosure may exhibit specificity for a PAM sequence having at least 75% sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of the PAM sequences disclosed in Table 7. In some embodiments, a CRISPR nuclease of the disclosure may exhibit specificity for a PAM sequence having at least 80% sequence identity (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of the PAM sequences disclosed in Table 7. In some embodiments, a CRISPR nuclease of the disclosure may exhibit specificity for a PAM sequence having at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of the PAM sequences disclosed in Table 7. In some embodiments, a CRISPR nuclease of the disclosure may exhibit specificity for a PAM sequence having at least 90% sequence identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of the PAM sequences disclosed in Table 7. In some embodiments, a CRISPR nuclease of the disclosure may exhibit specificity for a PAM sequence having at least 95% sequence identity (e.g., 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of the PAM sequences disclosed in Table 7. vi. AlphaFold Structure Prediction AlphaFold is a computational method for predicting the three-dimensional structure of a polypeptide from its amino acid sequence (Jumper et al., Highly accurate protein structure prediction with AlphaFold. Nature, 2021). Predicted structures for millions of polypeptides deposited in the UniProt database have been deposited in the AlphaFold Protein Structure Database, using the AlphaFold Monomer v2.0 model (Varadi et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Research, 2021). In the AlphaFold Protein Structure Database, the three-dimensional structure of a polypeptide can be obtained by searching for the UniProt accession number of the polypeptide. In addition to the many three-dimensional structures that are already publicly available, code is available for reproducing and predicting structures of new polypeptides at source code repositories such as Github.com under deepmind / alphafold / , using notebooks / AlphaFold.ipynb, which uses Alphafold v2.3.1 or newer. Additionally, it can be found in Github.com under sokrypton / ColabFold using v1.5.2 or newer, using AlphaFold2.ipynb. For technical details, please see Jumper et al. (vide supra). AlphaFold produces a per-residue estimate of its confidence on a scale from 0 to 100. This confidence measure is called pLDDT and corresponds to the model’s predicted score on the lDDT-Cα metric. It is stored in the B-factor fields of the mmCIF and PDB files available for download (although unlike a B-factor, higher pLDDT is better). Regions with pLDDT score of more than 90 are expected to be modelled to high accuracy. These should be suitable for any application that benefits from high accuracy (e.g., characterization of binding sites). Regions with a pLDDT score between 70 and 90 are expected to be modelled well, corresponding to a generally good backbone prediction. PATENT ATTORNEY DOCKET NO.50858-164WO2 Structural Similarity The relatedness between two amino acid sequences has conventionally been described by the parameter “sequence identity”. However, since the biological function of a polypeptide is defined by its three- dimensional structure rather than its amino acid sequence, a better way of assessing a functional relationship between polypeptides is by comparing their three-dimensional structures. Thus, for the purposes of the present invention, the relatedness between the three-dimensional structure of two polypeptides is described by the parameter “structural similarity”. A three-dimensional structure of any polypeptide may be obtained experimentally via, e.g., X-ray crystallography or using in silico methods such as AlphaFold (vide supra). The structural similarity between three-dimensional structures may then be determined by the TM-score, which is calculated using the following general formula (Zhang & Skolnick, Proteins 57:702–710, 2004): TM − score where LN is the length of the native structure, LT is the length of the aligned residues to the template structure, diis the distance between the ith pair of aligned residues and d0 is a scale to normalize the match difference. ‘Max’ denotes the maximum value after optimal spatial superposition. For the purposes of the present invention, LN is always the length of the reference protein, indicating the use of a fixed reference length L to prevent artificially large TM-scores from alignment of substructures: TM − score A structural alignment of the three-dimensional structure of two polypeptides is necessary before the TM-score can be calculated. This is achieved via algorithms that optimize the structural overlap, and several methods are available, such as CEalign (Shindyalov and Bourne, Protein Eng., 11, 739-747, 1998), DALI (Holm and Sander, Trends Biochem. Sci., 20, 478-480, 1995), or TM-align (Nucleic Acids Res.33:2302- 2309, 2005). For the purposes of the present invention, TM-align is applied. For convenience, TM-score is integrated in the TM-align software, which is available from the author’s website. The version of TM-align is preferably updated 2019-08-22 or later, and the TM-score between a reference and query protein is determined by running this command: TMalign <query.pdb> <reference.pdb> -L <length of reference> Where <query.pdb> is the name of the PDB file containing coordinates of the query polypeptide, <reference.pdb> is the name of the PDB file containing coordinates of the reference polypeptide. The TM- score is calculated and reported in the output, along with several other parameters from the alignment. b. gRNAs As used herein, the term "guide RNA (gRNA)" and its grammatical equivalents can refer to an RNA which can be specific for a target DNA and can form a complex with a PNE. The gRNA may form a complex with a gene editor, a base editor, or a prime editor. A gRNA is typically single-stranded and can be programmed to site-specifically bind (i.e., via complementary base pairing) to a target sequence of a nucleic PATENT ATTORNEY DOCKET NO.50858-164WO2 acid, thereby directing a PNE that is in conjunction with the gRNA to the target sequence. As will be appreciated by one having skill in the art, in a gRNA sequence uracil (U) replaces thymine (T) in the sequence. In some embodiments, a gRNA comprises two or more individual nucleic acids, which can interact with one another via complementary base pairing (a dual guide nucleic acid). For example, a gRNA can comprise a CRISPR RNA (crRNA) and a trans-activating CRISPR RNA (tracrRNA). Such dual gRNA systems can be employed as a guide nucleic acid to direct the PNEs disclosed herein to a target nucleic acid sequence. i. tracrRNA A gRNA can comprise one or more trans-activating CRISPR RNAs (tracrRNA). TracrRNAs comprises repeat sequences which forms a scaffold region that stabilizes the gRNA-CRISPR protein complex. Exemplary tracrRNAs of the disclosure for use with nucleases of the disclosure are provided in Table 8, with tracrRNA sequences shown as corresponding DNA (containing T in place of U). Table 8. Exemplary tracrRNAs of the disclosure PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a tracrRNA having at least 50% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 163-215 and 270-291. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a tracrRNA having at least 55% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 163-215 and 270- 291. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a tracrRNA having at least 60% sequence identity (e.g., 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 163-215 and 270-291. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a tracrRNA having at least 65% sequence identity (e.g., 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 163-215 and 270-291. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a tracrRNA having at least 70% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 163-215 and 270-291. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a tracrRNA having at least 75% sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 163-215 and 270-291. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a tracrRNA having at least 80% sequence identity (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 163-215 and 270-291. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a tracrRNA having at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 163-215 and 270-291. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a tracrRNA having at least 90% sequence identity (e.g., 90%, 91%, 92%, 93%, PATENT ATTORNEY DOCKET NO.50858-164WO2 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 163-215 and 270-291. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a tracrRNA having at least 95% sequence identity (e.g., 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 163-215 and 270-291. ii. crRNA A gRNA can comprise a crRNA, which is a sequence that recognizes the target sequence. Exemplary crRNAs of the disclosure for use with nucleases of the disclosure are provided in Table 9, with crRNA sequences shown as corresponding DNA (containing T in place of U). Table 9. Exemplary crRNAs of the disclosure PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a crRNA having at least 50% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 216 and 292-319. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a crRNA having at least 55% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 216 and 292-319. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a crRNA having at least 60% sequence identity (e.g., 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 216 and 292-319. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a crRNA having at least 65% sequence identity (e.g., 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 216 and 292-319. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a crRNA having at least 70% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 216 and 292-319. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a crRNA having at least 75% sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 216 and 292-319. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a crRNA having at least 80% sequence identity (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 216 and 292-319. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a crRNA having at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, PATENT ATTORNEY DOCKET NO.50858-164WO2 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 216 and 292-319. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a crRNA having at least 90% sequence identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 216 and 292-319. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a crRNA having at least 95% sequence identity (e.g., 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 216 and 292-319. iii. sgRNA In other embodiments, a gRNA can comprise both the nucleic acid targeting portion of the nucleic acid and the scaffold portion of the nucleic acid in a single molecule (i.e., a single-guide RNA). For example, a single-molecule gRNA can be a single guide RNA (sgRNA or gRNA). Typically, a sgRNA comprises a "nucleic acid-targeting segment" that includes a sequence capable of recognizing and binding to a target nucleic acid sequence, and a “scaffold" that stabilizes the sgRNA within a PNE. In some embodiments, the nucleic acid targeting segment of the sgRNA recognizes and binds to a DNA nucleic acid, thereby facilitating the editing of a base in DNA. In other cases, the nucleic acid targeting segment of the sgRNA recognizes and binds to an RNA nucleic acid. A sgRNA can comprise three regions: a first region at the 5' end that can be complementary to a target site in a chromosomal sequence, a second internal region that can form a stem loop structure, and a third 3' region that can be single stranded. A first region of each sgRNA can also be different such that each sgRNA guides a PNE to a specific target site. Further, second and third regions of each sgRNA can be identical in all sgRNAs. A first region of a sgRNA can be complementary to sequence at a target site in a chromosomal sequence such that the first region of the sgRNA can base pair with the target site. In some cases, a first region of a sgRNA can comprise from or from about 10 nucleotides to 25 nucleotides (i.e., from 10 nucleotides to nucleotides; or from about 10 nucleotides to about 25 nucleotides; or from 10 nucleotides to about 25 nucleotides; or from about 10 nucleotides to 25 nucleotides) or more. For example, a region of base pairing between a first region of a gRNA and a target site in a chromosomal sequence can be or can be about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, or more nucleotides in length. In some embodiments, a first region of a gRNA can be or can be about 19, 20, or 21 nucleotides in length. A sgRNA can also comprise a second region that forms a secondary structure. For example, a secondary structure formed by a sgRNA can comprise a stem (or hairpin) and a loop. A length of a loop and a stem can vary. For example, a loop can range from or from about 3 to 10 nucleotides in length, and a stem can range from or from about 6 to 20 base pairs in length. A stem can comprise one or more bulges of 1 to 10 or about 10 nucleotides. The overall length of a second region can range from or from about 16 to 60 nucleotides in length. For example, a loop can be or can be about 4 nucleotides in length and a stem can be or can be about 12 base pairs. A sgRNA can also comprise a third region at the 3' end that can be essentially single-stranded. For example, a third region is sometimes not complementarity to any chromosomal sequence in a cell of interest and is sometimes not complementarity to the rest of a sgRNA. Further, the length of a third region can vary. PATENT ATTORNEY DOCKET NO.50858-164WO2 A third region can be more than or more than about 4 nucleotides in length. For example, the length of a third region can range from or from about 5 to 60 nucleotides in length. Exemplary sgRNAs of the disclosure for use with nucleases of the disclosure are provided in Table 10, with sgRNA sequences shown as corresponding DNA (containing T in place of U). Table 10. Exemplary sgRNAs of the disclosure PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a sgRNA having at least 50% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 217-269 and 320-371. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a sgRNA having at least 55% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 217-269 and 320-371. PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a sgRNA having at least 60% sequence identity (e.g., 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 217-269 and 320-371. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a sgRNA having at least 65% sequence identity (e.g., 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 217-269 and 320-371. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a sgRNA having at least 70% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 217- 269 and 320-371. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a sgRNA having at least 75% sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 217-269 and 320-371. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a sgRNA having at least 80% sequence identity (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 217-269 and 320-371. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a sgRNA having at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 217-269 and 320-371. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a sgRNA having at least 90% sequence identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 217-269 and 320- 371. In some embodiments, a PNE (e.g., a gene editor, a base editor, or a prime editor) of the disclosure may form a complex with a sgRNA having at least 95% sequence identity (e.g., 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to any one of SEQ ID NOs: 217-269 and 320-371. In some embodiments, the gRNA is a chemically modified gRNA that comprises any nucleotide other than the four canonical ribonucleotides, namely A, C, G, and U, whether unnatural or natural (e.g., a pseudouridine, inosine or a deoxynucleotide). Likewise, a guide RNA that comprises any backbone or internucleoside linkage other than a natural phosphodiester internucleoside linkage possesses a chemical modification and therefore is a chemically modified guide RNA. In certain embodiments, the retained functionality includes binding a CRISPR nuclease. In certain embodiments, the retained functionality includes binding a target nucleic acid. In certain embodiments, the retained functionality includes targeting a PATENT ATTORNEY DOCKET NO.50858-164WO2 CRISPR nuclease or a gRNA:CRISPR nuclease complex to a target nucleic acid. In certain embodiments, the retained functionality includes nicking a target nucleic acid by a gRNA:CRISPR nuclease complex. In certain embodiments, the retained functionality includes cleaving a target nucleic acid by a gRNA:CRISPR nuclease complex. In certain embodiments, the retained functionality is any other known function of a guide RNA in a CRISPR-Cas system with a CRISPR nuclease, including an artificial CRISPR-Cas system with an engineered CRISPR nuclease. In certain embodiments, the retained functionality is any other function of a natural guide RNA. In certain embodiments, a nucleotide sugar modification incorporated into the guide RNA is selected from the group consisting of 2′-O—C1-4alkyl such as 2′-O-methyl (2′-OMe), 2′-deoxy (2-H), 2′-O—C1-3alkyl- O—C1-3alkyl such as 2′-methoxyethyl (“2′-MOE”), 2′-fluoro (“2-F”),2′-amino (“2′-NH2”), 2′-arabinosyl (“2′- arabino”) nucleotide, 2′-F-arabinosyl (“2′-F-arabino”) nucleotide, 2′-locked nucleic acid (“LNA”) nucleotide, 2′- unlocked nucleic acid (“ULNA”) nucleotide, a sugar in L form (“L-sugar”), and 4′-thioribosyl nucleotide. In certain embodiments, an internucleoside linkage modification incorporated into the guide RNA is selected from the group consisting of: phosphorothioate “P(S)” (P(S)), phosphonocarboxylate (P(CH2)nCOOR) such as phosphonoacetate “PACE” (P(CH2COO—)), thiophosphonocarboxylate ((S)P(CH2)nCOOR) such as thiophosphonoacetate “thioPACE” ((S)P(CH2COO—)), alkylphosphonate (P(C1-3alkyl) such as methylphosphonate —P(CH3), boranophosphonate (P(BH3)), and phosphorodithioate (P(S)2). In certain embodiments, a nucleobase (“base”) modification incorporated into the guide RNA is selected from the group consisting of: 2-thiouracil (“2-thioU”), 2-thiocytosine (“2-thioC”), 4-thiouracil (“4- thioU”), 6-thioguanine (“6-thioG”), 2-aminoadenine (“2-aminoA”), 2-aminopurine, pseudouracil, hypoxanthine, 7-deazaguanine, 7-deaza-8-azaguanine, 7-deazaadenine, 7-deaza-8-azaadenine, 5-methylcytosine (“5- methylC”), 5-methyluracil (“5-methylU”), 5-hydroxymethylcytosine, 5-hydroxymethyluracil, 5,6-dehydrouracil, 5-propynylcytosine, 5-propynyluracil, 5-ethynylcytosine, 5-ethynyluracil, 5-allyluracil (“5-allylU”), 5- allylcytosine (“5-allylC”), 5-aminoallyluracil (“5-aminoallylU”), 5-aminoallyl-cytosine (“5-aminoallylC”), an abasic nucleotide, Z base, P base, Unstructured Nucleic Acid (“UNA”), isoguanine (“isoG”), isocytosine (“isoC”) [as described in “Enzymatic Incorporation of a New Base pair into DNA and RNA Extends the Genetic Alphabet.” Piccirilli, J. A.; Krauch, T.; Moroney, S. E.; Benner, S. A. (1990) Nature, 343, 33], 5- methyl-2-pyrimidine [as described in Rappaport, H. P. (1993) Biochemistry, 32, 3047], x(A,G,C,T) and y(A,G,C,T). In certain embodiments, one or more isotopic modifications are introduced on the nucleotide sugar, the nucleobase, the phosphodiester linkage and / or the nucleotide phosphates. Such modifications include nucleotides comprising one or more 15N, 13C, 14C, Deuterium, 3H, 32P, 125I, 131I atoms or other atoms or elements used as tracers. In certain embodiments, a 5’ modification incorporated into the guide RNA is selected from the group consisting of: PEG (polyethyleneglycol), hydrocarbon linkers (including: heteroatom (O,S,N)-substituted hydrocarbon spacers; halo-substituted hydrocarbon spacers; keto-, carboxyl-, amido-, thionyl-, carbamoyl-, thionocarbamaoyl-containing hydrocarbon spacers), spermine linkers, dyes including fluorescent dyes (for example fluoresceins, rhodamines, cyanines) attached to linkers such as for example 6-fluorescein-hexyl, quenchers (for example dabcyl, BHQ) and other labels (for example biotin, digoxigenin, acridine, streptavidin, avidin, peptides and / or proteins). In certain embodiments, a 5’ modification comprises a conjugation (or ligation) of the guide RNA to another molecule comprising an oligonucleotide (comprising PATENT ATTORNEY DOCKET NO.50858-164WO2 deoxynucleotides and / or ribonucleotides), a peptide, a protein, a sugar, an oligosaccharide, a steroid, a lipid, a folic acid, a vitamin and / or other molecule. In certain embodiments, a 5’ modification incorporated into the guide RNA is located internally in the guide RNA sequence via a linker such as for example 2-(4- butylamidofluorescein)propane-1,3-diol bis(phosphodiester) linker (depicted below), which is incorporated as a phosphodiester linkage and can be incorporated anywhere between two nucleotides in the guide RNA. In certain embodiments, the 5’ modification comprises a terminal functional group such as an amine, a thiol (or sulfhydryl), a hydroxyl, a carboxyl, carbonyl, thionyl, thiocarbonyl, a carbamoyl, a thiocarbamoyl, a phoshoryl, an alkene, an alkyne, an halogen or a functional group-terminated linker, either of which can be subsequently conjugated to a desired moiety, for example a fluorescent dye or a non-fluorescent label or tag or any other molecule such as for example an oligonucleotide (comprising deoxynucleotides and / or ribonucleotides, including an aptamer), an amino acid, a peptide, a protein, a sugar, an oligosaccharide, a steroid, a lipid, a folic acid, a vitamin. The conjugation employs standard chemistry well-known in the art, including but not limited to coupling via N-hydroxysuccinimide, isothiocyanate, DCC (or DCI), and / or any other standard method as described in “Bioconjugate Techniques” by Greg T. Hermanson, Publisher Elsevier Science, 3rd ed. (2013), the contents of which are incorporated herein by reference in their entireties. In certain embodiments, the label or dye is attached or conjugated to a modified nucleotide in the gRNA. The conjugation of a fluorescent dye or other moiety such as a non-fluorescent label or tag (for example biotin, avidin, streptavidin, or moiety containing an isotopic label such as 15N, 13C, 14C, Deuterium, 3H, 32P, 125I and the like) or any other molecule such as for example an oligonucleotide (comprising deoxynucleotides and / or ribonucleotides including an aptamer), an amino acid, a peptide, a protein, a sugar, an oligosaccharide, a steroid, a lipid, a folic acid, a vitamin or other molecule can be effectuated using the so-called “click” chemistry or the so-called “squarate” conjugation chemistry. A target nucleotide sequence can comprise DNA, RNA, or a combination of both and can be single- stranded or double-stranded. A target nucleotide sequence can be genomic DNA (i.e., chromosomal DNA), plasmid DNA, or an RNA molecule (e.g., messenger RNA, ribosomal RNA, transfer RNA, microRNA, small interfering RNA). The target nucleotide sequence can be bound (and in some embodiments, cleaved) by an RNA-guided, nucleic acid-binding protein in vitro or in a cell. The chromosomal sequence targeted by the PNE can be a nuclear, plastid or mitochondrial chromosomal sequence. In some embodiments, the target nucleotide sequence is unique in the target genome. A gRNA can target any exon or intron of a gene target. In some cases, a guide can target exon 1 or 2 of a gene, in other cases; a guide can target exon 3 or 4 of a gene. A composition can comprise multiple gRNAs that all target the same exon or in some cases, multiple gRNAs that can target different exons. An exon and an intron of a gene can be targeted. A gRNA can target a nucleic acid sequence of or of about 20 nucleotides. A target nucleic acid can be less than or less than about 20 nucleotides. A target nucleic acid can be at least or at least about 5, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, or anywhere between 1-100 nucleotides in length. A target nucleic acid can be at most or at most about 5, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40, 50, or anywhere between 1-100 nucleotides in length. A target nucleic acid sequence can be or can be about 20 bases immediately 5' of the first nucleotide of the PAM. A gRNA can target a nucleic acid sequence. A target PATENT ATTORNEY DOCKET NO.50858-164WO2 nucleic acid can be at least or at least about 1-10, 1-20, 1-30, 1-40, 1-50, 1-60, 1-70, 1-80, 1-90, or 1-100 nucleotides. In certain embodiments, the gRNA can be introduced into a target cell, organelle, or embryo as an RNA molecule. The gRNA can be transcribed in vitro or chemically synthesized. In some embodiments, a nucleotide sequence encoding the gRNA is introduced into the cell, organelle, or embryo. In some of these embodiments, the nucleotide sequence encoding the guide RNA is operably linked to a promoter (e.g., an RNA polymerase III promoter). The promoter can be a native promoter or heterologous to the gRNA-encoding nucleotide sequence. In various embodiments, the gRNA can be introduced into a target cell, organelle, or embryo as a ribonucleoprotein complex, as described herein, wherein the gRNA is bound to PNE. The gRNA directs an associated PNE to a particular target nucleotide sequence of interest through hybridization of the gRNA to the target nucleotide sequence. c. Gene Editors In some embodiments, the PNE of the disclosure is a gene editor. In some embodiments, the gene editor of the disclosure comprises a CRISPR nuclease. The CRISPR nuclease of the gene editor may be any CRISPR nuclease provided herein, such as a CRISPR nuclease of the invention. In some embodiments, the CRISPR nuclease of the gene editor is a nCas. The nCas of the gene editor may be any nCas provided herein, such as an nCas of the invention. In some embodiments, the CRISPR nuclease of the base editor is a dCas, such as any dCas provided herein. The dCas of the gene editor may be any dCas provided herein, such as an dCas of the invention. In some embodiments, the gene editor of the disclosure further comprises an NLS domain. In some embodiments, the gene editor is a fusion protein, and the components of the gene editor are domains of the fusion protein, optionally connected by any of the linkers disclosed herein. In some embodiments, the gene editor is a multi-protein complex, and the components of the gene editor are provided as individual polypeptides. In some embodiments, the gene editor is a multi-protein complex, and one or more components of the gene editor are provided endogenously by the cell. CRISPR nucleases have two functional endonuclease domains: RuvC and HNH. The CRISPR nuclease undergoes a conformational change upon target binding that positions the nuclease domains to cleave opposite strands of the target DNA. The end result of CRISPR nuclease-mediated DNA cleavage is a double-strand break (DSB) within the target DNA (~3-4 nucleotides upstream of the PAM sequence). The resulting DSB is then repaired by one of two general repair pathways: (1) the efficient but error-prone non- homologous end joining (NHEJ) pathway; or (2) the less efficient but high-fidelity homology directed repair (HDR) pathway. The modifications of the target DNA due to NHEJ and / or homology-directed repair lead to, for example, gene correction, gene replacement, gene tagging, transgene insertion, nucleotide deletion, gene disruption, gene mutation, etc. The NHEJ repair pathway is the most active repair mechanism, and it frequently causes small nucleotide insertions or deletions (indels) at the DSB site. The randomness of NHEJ-mediated DSB repair has important practical implications because a population of cells expressing a CRISPR nuclease and a gRNA or a guide nucleic acid can result in a diverse array of mutations. In most cases, NHEJ gives rise to small indels in the target DNA that result in amino acid deletions, insertions, or frameshift mutations leading PATENT ATTORNEY DOCKET NO.50858-164WO2 to premature stop codons within the open reading frame (ORF) of the targeted gene. The ideal end result is a loss-of function mutation within the targeted gene. While NHEJ-mediated DSB repair often disrupts the open reading frame of the gene, homology directed repair (HDR) can be used to generate specific nucleotide changes ranging from a single nucleotide change to large insertions like the addition of a fluorophore or tag. In homology-directed repair, a donor nucleic acid with homology to the cleaved target DNA sequence is used as a template for repair of the cleaved target DNA sequence, resulting in the transfer of genetic information from the donor nucleic acid to the target DNA. In order to utilize HDR for gene editing, a DNA repair template containing the desired sequence can be delivered into the cell type of interest with the gRNA(s) and CRISPR nuclease or nCas. The repair template can contain the desired edit as well as additional homologous sequence immediately upstream and downstream of the target (termed left & right homology arms). The length of each homology arm can be dependent on the size of the change being introduced, with larger insertions requiring longer homology arms. The repair template can be a single-stranded oligonucleotide, double-stranded oligonucleotide, or a double-stranded DNA plasmid. The efficiency of HDR is generally low (<10% of modified alleles) even in cells that express Cas, gRNA and an exogenous repair template. The efficiency of HDR can be enhanced by synchronizing the cells, since HDR takes place during the S and G2 phases of the cell cycle. Chemically or genetically inhibiting genes involved in NHEJ can also increase HDR frequency. nCas retains one nuclease domain and generates a DNA nick rather than a DSB. The nickase system can also be combined with HDR-mediated gene editing for specific gene edits. d. Base Editors In some embodiments, the PNE of the disclosure is a base editor. In some embodiments, base editors of the disclosure include a CRISPR nuclease and at least one base editing protein. In some embodiments, base editors of the disclosure include a CRISPR nuclease, at least one base editing protein, and at least one IBR domain. The CRISPR nuclease of the base editor may be any CRISPR nuclease provided herein, such as a CRISPR nuclease of the invention. In some embodiments, the CRISPR nuclease of the base editor is a nCas. The nCas of the base editor may be any nCas provided herein, such as an nCas of the invention. In some embodiments, the CRISPR nuclease of the base editor is a dCas, such as any dCas provided herein. The dCas of the base editor may be any dCas provided herein, such as an dCas of the invention. In some embodiments, the base editing polypeptide is a deaminase. In some embodiments, the deaminase is a cytosine deaminase domain. In some embodiments, the deaminase is an adenine deaminase domain. In some embodiments, the base editors provided herein further comprise one or more NLS domains. In some embodiments, the NLS comprises an amino acid sequence of any one of the NLS sequences provided or referenced herein. In some embodiments, the base editor is a fusion protein, and the components of the base editor are domains of the fusion protein, optionally connected by any of the linkers disclosed herein. In some embodiments, the base editor is a multi-protein complex, and the components of the base editor are provided as individual polypeptides. In some embodiments, the base editor is a multi-protein complex, and one or more components of the base editor are provided endogenously by the cell. The CRISPR nuclease directs the enzymatic activity of the base editing polypeptide to a specific site in genomic DNA. The advantages of using a CRISPR nuclease as the recognition agent are twofold: (1) the PATENT ATTORNEY DOCKET NO.50858-164WO2 sequence specificity of the PNE can be easily altered by simply changing the sgRNA sequence; and (2) CRISPR nucleases bind their target sequence by denaturing the dsDNA, resulting in a stretch of DNA that is single-stranded and therefore a viable substrate for the base editor. In some embodiments, a base editor comprising a dCas or nCas and a deaminase can be targeted to particular genomic locations to alter the expression of a desired sequence. The binding of this base editor to a target sequence results in deamination of a nucleotide base, resulting in conversion from one nucleotide base to another. In some embodiments, a base editor which has nickase activity on the target strand nicks the target strand, while the complementary, non-target strand is modified by the deaminase. Cellular DNA- repair machinery may repair the nicked, target strand using the modified non-target strand as a template, thereby introducing a mutation in the DNA. The base editors described herein can deaminate a target base in any nucleic acid, including DNA, RNA and DNA-RNA hybrids. Typically, a base editing polypeptide acts on a base that is positioned in the context of a single-stranded portion of a nucleic acid. In some embodiments, the entire nucleic acid comprising a target base can be single-stranded. For example, a base editing polypeptide incorporated into the base editor can deaminate a target base in a single-stranded RNA nucleic acid. In other embodiments, a base editor comprising a base editing polypeptide can act on a double stranded nucleic acid, but the target base can be positioned in a portion of the nucleic acid which at the time of the deamination reaction is in a single-stranded state. For example, in embodiments where the base editor comprises a CRISPR nuclease, several nucleotides can be left unpaired during formation of the Cas-gRNA-target DNA complex, resulting in formation of a CRISPR nuclease "R-loop complex". These unpaired nucleotides can form a bubble of single- stranded DNA that can serve as a substrate for a single-strand specific base editing polypeptide. In some embodiments, the base editor system provided herein comprises the steps of: (a) contacting a target nucleotide sequence of a nucleic acid (e.g., a double-stranded DNA or RNA, a single- stranded DNA or RNA) of a subject with a base editor comprising an nCas and a deaminase, which is capable of inducing changes at one or more bases within a nucleic acid molecule as described herein and at least one gRNA, wherein the target nucleotide sequence comprises a targeted nucleobase pair; (b) inducing strand separation of the target region; (c) converting a first nucleobase of the target nucleobase pair in a single strand of the target region to a second nucleobase; and (d) cutting no more than one strand of the target region, where a third nucleobase complementary to the first nucleobase base is replaced by a fourth nucleobase complementary to the second nucleobase. It should be appreciated that in some embodiments, step (b) is omitted. In some embodiments, the targeted nucleobase pair is a plurality of nucleobase pairs in one or more genes. In some embodiments, the base editor system provided herein is capable of multiplex editing of a plurality of nucleobase pairs in one or more genes. In some embodiments, the plurality of nucleobase pairs is located in the same gene. In some embodiments, the plurality of nucleobase pairs is located in one or more genes, wherein at least one gene is located in a different locus. In some embodiments, the cut single strand (nicked strand) is hybridized to the guide nucleic acid. In some embodiments, the cut single strand is opposite to the strand comprising the first nucleobase. In some embodiments, the first base is adenine, and the second base is not a G, C, A, or T. In some embodiments, the second base is inosine. In some embodiments, the first base is cytidine, and the second base is not a G, C, or A. In some embodiments, the second base is uridine. PATENT ATTORNEY DOCKET NO.50858-164WO2 i. C to T Editing In some embodiments, the base editor comprises a CRISPR nuclease, at least one cytidine deaminase, and at least one IBR. In some cases, the CRISPR nuclease is an nCas. In some embodiments, the IBR domain is a uracil glycosylase inhibitor (UGI) domain. A cytidine deaminase is capable of deaminating a target cytidine (C) base of a nucleic acid to produce uridine (U), which has the base pairing properties of thymine. Details of C to T nucleobase editing proteins are described in International PCT Application No. PCT / US2016 / 058344 (WO2017 / 070632) and Komor, AC., et al., "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage" Nature 533, 420-424 (2016), the entire contents of which are hereby incorporated by reference. In some embodiments, for example where the nucleic acid is double-stranded (e.g., DNA), the uridine base can then be substituted with a thymidine base (e.g., by cellular repair machinery) to give rise to a C:G to a T:A transition. In other embodiments, deamination of a C to U in a nucleic acid by a base editor cannot be accompanied by substitution of the U to a T. In some embodiments, the cytidine deaminase includes, without limitation: APOBEC family members, including but not limited to: APOBEC1, APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D ("APOBEC3E" now refers to this), APOBEC3F, APOBEC3G, APOBEC3H, APOBEC4, Activation-induced (cytidine) deaminase (AID), hAPOBEC1, which is derived from Homo sapiens, rAPOBEC1, which is derived from Rattus norvegicus, ppAPOBEC1l, which is derived from Pongo pygmaeus, AmAPOBEC1 (BEM3.31), derived from Alligator mississippiensis, ocAPOBEC1, which is derived from Oryctolagus cuniculus, SsAPOBEC2 (BEM3.39), which is derived from Sus scrofa, hAPOBEC3A, which is derived from Homo sapiens, maAPOBEC1, which is derived from Mesocricetus auratus, mdAPOBEC1, which is derived from Monodelphis domestica; cytidine deaminase 1 (CDA1), hA3A, which is APOBEC3A derived from Homo sapiens, RrA3F (BEM3.14), which is APOBEC3F derived from Rhinopithecus roxellana; PmCDA1, which is derived from Petromyzon marinus (Petromyzon marinus cytosine deaminase 1, "PmCDA1"); AID (Activation-induced cytidine deaminase; AICDA), which is derived from a mammal (e.g., human, swine, bovine, horse, monkey etc.); hAID, which is derived from Homo sapiens; and FENRY. In some embodiments, the nucleic acid editing domain is at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%), or at least 99.5% identical to the deaminase domain of any deaminase described herein. In some cases, a suitable cytidine deaminase is an AID and comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MDSLLMNRRKFLYQFKNVRWAKGRRETYLCYVVKRRDSATSFSLDFGYLRNKNGCHVELLFLRYISDWDLD PGRCYRVTWFTSWSPCYDCARHVADFLRGNPNLSLRIFTARLYFCEDRKAEPEGLRRLHRAGVQIAIMTFKE NHERTFKAWEGLHENSVRLSRQLRRILLPLYEVDDLRDAFRTLGL (SEQ ID NO: 374). In some cases, a suitable cytidine deaminase is an AID and comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MDSLLMNRRKFLYQFKNVRWAKGRRETYLCYVVKRRDSATSFSLDFGYLRNKNGCHVELLFLRYISDWDLD PGRCYRVTWFTSWSPCYDCARHVADFLRGNPNLSLRIFTARLYFCEDRKAEPEGLRRLHRAGVQIAIMTFK DYFYCWNTFVENHERTFKAWEGLHENSVRLSRQLRRILLPLYEVDDLRDAFRTLGL (SEQ ID NO: 375). PATENT ATTORNEY DOCKET NO.50858-164WO2 In some embodiments, a suitable cytidine deaminase may be any cytidine deaminase described in WO2021041885, US20200172885, US20200208138, US20200010856, US20180312825, US20170073670, WO2020160517, WO2020028823, US20200010835, PCT / US2019 / 055705, US20200208138, US20200172931, WO2019241649, and WO2020160517, the contents of each of which are incorporated herein by reference in their entirety. In some embodiments, the IBR is a uracil glycosylase inhibitor (UGI). UGI refers to a protein that is capable of inhibiting a uracil-DNA glycosylase base-excision repair enzyme, i.e., that binds a host uracil-DNA glycosylase and prevents removal of uracil residues from DNA. A UGI domain can for example improve the efficiency of base editors comprising a cytidine deaminase domain by inhibiting the conversion of a U formed by deamination of a C back to the C nucleobase. In some cases, cellular DNA repair response to the presence of U:G heteroduplex DNA can be responsible for a decrease in nucleobase editing efficiency in cells. In such cases, uracil DNA glycosylase (UDG) can catalyze removal of U from DNA in cells, which can initiate base excision repair (BER), mostly resulting in reversion of the U:G pair to a C:G pair. In such cases, BER can be inhibited in base editors comprising one or more domains that bind the single strand, block the edited base, inhibit UGI, inhibit BER, protect the edited base, and / or promote repairing of the non-edited strand. Thus, this disclosure contemplates a base editor comprising a UGI domain. UGI refers to a protein that is capable of inhibiting a uracil-DNA glycosylase base-excision repair enzyme, i.e., that binds a host uracil-DNA glycosylase and prevents removal of uracil residues from DNA. A UGI domain can improve the efficiency of base editors comprising a cytidine deaminase domain by inhibiting the conversion of a U formed by deamination of a C back to the C nucleobase. In some cases, cellular DNA repair response to the presence of U:G heteroduplex DNA can be responsible for a decrease in nucleobase editing efficiency in cells. In such cases, uracil DNA glycosylase (UDG) can catalyze removal of U from DNA in cells, which can initiate base excision repair (BER), mostly resulting in reversion of the U:G pair to a C:G pair. In such cases, BER can be inhibited in base editors comprising one or more domains that bind the single strand, block the edited base, inhibit UGI, inhibit BER, protect the edited base, and / or promote repairing of the non-edited strand. It should be understood that the use of a UGI domain may increase the editing efficiency of a nucleic acid editing domain that is capable of catalyzing a C to U change. For example, base editors comprising a UGI domain may be more efficient in deaminating C residues. Suitable UGI protein and nucleotide sequences are provided herein and additional suitable UGI sequences are known to those in the art, and include, for example, those published in Wang et al., 1989. J. Biol. Chem.264: 1163-1171; Lundquist et al., 1997. J. Biol. Chem.272:21408-21419; Ravishankar et al., 1998. Nucleic Acids Res.26:4880-4887; and Putnametal., 1999. J. Mol. Biol.287:331-346(1999), the entire contents of each are incorporated herein by reference. In some embodiments, the UGI comprises the following amino acid sequence: MTNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDS NGENKIKML (SEQ ID NO: 376). In some embodiments, a suitable UGI may be any UGI described in US20200172885, US20180312825, and PCT / US2019 / 055705, the contents of each of which are incorporated herein by reference in their entirety. PATENT ATTORNEY DOCKET NO.50858-164WO2 ii. A to G Editing In some embodiments, a base editor disclosed herein comprises a CRISPR nuclease and at least one adenosine deaminase. Such a base editor can facilitate the editing of an adenine (A) nucleobase to a guanine (G) nucleobase by deaminating the A to form inosine (I), which exhibits base pairing properties of G. Adenosine deaminase is capable of deaminating (i.e., removing an amine group) adenine of a deoxyadenosine residue in deoxyribonucleic acid (DNA). In some embodiments, the CRISPR nuclease is a nuclease inactive CRISPR nuclease (e.g., dCas) or a nickase CRISPR nuclease (e.g., nCas). In some embodiments, the base editor further comprises a NLS. An adenosine deaminase can facilitate the editing of an adenine (A) nucleobase to a guanine (G) nucleobase by deaminating the A to form inosine (I), which exhibits base pairing properties of G. Adenosine deaminase is capable of deaminating (i.e., removing an amine group) adenine of a deoxyadenosine residue in deoxyribonucleic acid (DNA). The adenosine deaminase can be derived from any suitable organism (e.g., E. coli). In some embodiments, the adenosine deaminase is from a prokaryote. In some embodiments, the adenosine deaminase is from a bacterium. In some embodiments, the adenosine deaminase is from Escherichia coli, Staphylococcus aureus, Salmonella typhi, Shewanella putrefaciens, Haemophilus influenzae, Caulobacter crescentus, or Bacillus subtilis. In some embodiments, the adenosine deaminase is from E. coli. In some embodiments, the adenine deaminase is a naturally occurring adenosine deaminase that includes one or more mutations corresponding to any of the mutations provided herein (e.g., mutations in ecTadA). The corresponding residue in any homologous protein can be identified by e.g., sequence alignment and determination of homologous residues. The mutations in any naturally-occurring adenosine deaminase (e.g., having homology to ecTadA) that corresponds to any of the mutations described herein (e.g., any of the mutations identified in ecTadA) can be generated accordingly. In some embodiments, the adenosine deaminase comprises an amino acid sequence that is at least 60%, at least 65%, 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%, or at least 99.5% identical to any one of the amino acid sequences set forth in any of the adenosine deaminases provided herein. It should be appreciated that adenosine deaminases provided herein may include one or more mutations (e.g., any of the mutations provided herein). In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MSEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVM QNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHPGMNHRVEITEGILADECA ALLSDFFRMRRQEIKAQKKAQSSTD (SEQ ID NO: 377). In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MRRAFITGVFFLSEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEI MALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHPGMNHRV EITEGILADECAALLSDFFRMRRQEIKAQKKAQSSTD (SEQ ID NO: 378). PATENT ATTORNEY DOCKET NO.50858-164WO2 In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Staphylococcus aureus TadA amino acid sequence: MGSHMTNDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWR LEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFNHRAIVDKGVLKEACSTLLT TFFK NLRANKKSTN (SEQ ID NO: 379). In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Bacillus subtilis TadA amino acid sequence: MTQDELYMKEAIKEAKKAEEKGEVPIGAVLVINGEIIARAHNLRETEQRSIAHAEMLVIDEACKALGTWRLEGA TLYVTLEPCPMCAGAVVLSRVEKVVFGAFDPKGGCSGTLMNLLQEERFNHQAEVVSGVLEEECGGMLSAF FRELRKKKKAARKNLSE (SEQ ID NO: 380). In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Salmonella typhimurium TadA: MPPAFITGVTSLSDVELDHEYWMRHALTLAKRAWDEREVPVGAVLVHNHRVIGEGWNRPIGRHDPTAHAEI MALRQGGLVLQNYRLLDTTLYVTLEPCVMCAGAMVHSRIGRVVFGARDAKTGAAGSLIDVLHHPGMNHRVE IIEGVLRDECATLLSDFFRMRRQEIKALKKADRAEGAGPAV (SEQ ID NO: 381). In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Shewanella putrefaciens TadA amino acid sequence: MDEYWMQVAMQMAEKAEAAGEVPVGAVLVKDGQQIATGYNLSISQHDPTAHAEILCLRSAGKKLENYRLLD ATLYITLEPCAMCAGAMVHSRIARVVYGARDEKTGAAGTVVNLLQHPAFNHQVEVTSGVLAEACSAQLSRFF KRRRDEKKALKLAQRAQQGIE (SEQ ID NO: 382). In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Haemophilus influenzae F3031 TadA amino acid sequence: MDAAKVRSEFDEKMMRYALELADKAEALGEIPVGAVLVDDARNIIGEGWNLSIVQSDPTAHAEIIALRNGAKNI QNYRLLNSTLYVTLEPCTMCAGAILHSRIKRLVFGASDYKTGAIGSRFHFFDDYKMNHTLEITSGVLAEECSQ KLS TFFQKRREEKKIEKALLKSLSDK (SEQ ID NO: 383). In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Caulobacter crescentus TadA amino acid sequence: MRTDESEDQDHRMMRLALDAARAAAEAGETPVGAVILDPSTGEVIATAGNGPIAAHDPTAHAEIAAMRAAAA KLGNYRLTDLTLVVTLEPCAMCAGAISHARIGRVVFGADDPKGGAVVHGPKFFAQPTCHWRPEVTGGVLAD ESADLLRGFFRARRKAKI (SEQ ID NO: 384). In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Geobacter sulfurreducens TadA amino acid sequence: MSSLKKTPIRDDAYWMGKAIREAAKAAARDEVPIGAVIVRDGAVIGRGHNLREGSNDPSAHAEMIAIRQAAR PATENT ATTORNEY DOCKET NO.50858-164WO2 RSANWRLTGATLYVTLEPCLMCMGAIILARLERVVFGCYDPKGGAAGSLYDLSADPRLNHQVRLSPGVCQE ECGTMLSDFFRDLRRRKKAKATPALFIDERKVPPEP (SEQ ID NO: 385). In some embodiments, a suitable adenosine deaminase may be any adenosine deaminase described in WO2021041885, US20200208138, US20200010856, US20170073670, WO2020028823, WO 2021 / 050571, WO2020168132, WO2021050571, US20200308571, US10113163, and US10947530, the contents of each of which are incorporated herein by reference in their entirety. iii. Abasic Editor In some embodiments, virtually any base editor known in the art can used. In one embodiment, the invention features a multi-effector base editor comprising an abasic nucleobase editor domain. Abasic nucleobase editors are known in the art and described, for example, by Kavli et al., EMBO J.15:3442-3447, 1996, which is incorporated herein by reference. e. Prime Editors In some embodiments, the PNE is a prime editor. In some embodiments, the prime editor comprises a CRISPR nuclease and a reverse transcriptase (RT) polypeptide. In some embodiments, the gRNA for use with the prime editor is a prime editing gRNA (PEgRNA). The CRISPR nuclease of the prime editor may be any CRISPR nuclease provided herein, such as a CRISPR nuclease of the invention. In some embodiments, the CRISPR nuclease of the prime editor is a nCas. The nCas of the prime editor may be any nCas provided herein, such as an nCas of the invention. In some embodiments, the CRISPR nuclease of the prime editor is a dCas, such as any dCas provided herein. The dCas of the prime editor may be any dCas provided herein, such as an dCas of the invention. In some embodiments, the prime editors further comprise a flap endonuclease polypeptide. In some embodiments, the flap endonuclease polypeptide of the prime editor is a FEN1 domain. In some embodiments, the prime editors further comprise an NLS sequence. In some embodiments, the prime editor is a fusion protein, and the components of the prime editor are domains of the fusion protein, optionally connected by any of the linkers disclosed herein. In some embodiments, the prime editor is a multi-protein complex, and the components of the prime editor are provided as individual polypeptides. In some embodiments, the prime editor is a multi-protein complex, and one or more components of the prime editor are provided endogenously by the cell. i. Mechanism In various embodiments, prime editing operates by contacting a target DNA molecule (for which a change in the nucleotide sequence is desired to be introduced) with a PNE complexed with a PEgRNA. The extended guide RNA comprises an extension at the 3' or 5' end of the gRNA, or at an intramolecular location in the gRNA and encodes the desired nucleotide change (e.g., single nucleotide change, insertion, or deletion). In step (a), the PNE / PEgRNA complex contacts the DNA molecule and the PEgRNA guides the PNE to bind to a target locus. In step (b), a nick in one of the strands of DNA of the target locus is introduced (e.g., by a nuclease or chemical agent), thereby creating an available 3' end in one of the strands of the target locus. In certain embodiments, the nick is created in the strand of DNA that corresponds to the R-loop strand, i.e., the strand that is not hybridized to the guide RNA sequence, i.e., the “non-target strand.” The nick, however, could be introduced in either of the strands. That is, the nick could be introduced into the R- PATENT ATTORNEY DOCKET NO.50858-164WO2 loop “target strand” (i.e., the strand hybridized to the protospacer sequence of the PEgRNA) or the “non- target strand” (i.e, the strand forming the single-stranded portion of the R-loop and which is complementary to the target strand). In step (c), the 3' end of the DNA strand (formed by the nick) interacts with the extended portion of the guide RNA in order to prime reverse transcription (i.e, “target-primed RT”). In certain embodiments, the 3' end DNA strand hybridizes to a specific RT priming sequence on the PEgRNA, i.e, the “reverse transcriptase priming sequence.” In step (d), a reverse transcriptase is introduced (as a fusion protein with the prime editor or in trans) which synthesizes a single strand of DNA from the 3' end of the primed site towards the 5' end of the PEgRNA. This forms a single-strand DNA flap comprising the desired nucleotide change (e.g., the single base change, insertion, or deletion, or a combination thereof) and which is otherwise homologous to the endogenous DNA at or adjacent to the nick site. In step (e), the PNE and PEgRNA are released. Steps (f) and (g) relate to the resolution of the single strand DNA flap such that the desired nucleotide change becomes incorporated into the target locus. This process can be driven towards the desired product formation by removing the corresponding 5' endogenous DNA flap (e.g., by a FEN1 domain or similar enzyme that is provide in trans, as a fusion with the prime editor, or endogenously provided) that forms once the 3' single strand DNA flap invades and hybridizes to the endogenous DNA sequence. Without being bound by theory, cellular endogenous DNA repair and replication processes resolves the mismatched DNA to incorporate the nucleotide change(s) to form the desired altered product. The process can also be driven towards product formation with “second strand nicking” or “temporal second strand nicking”. The process of prime editing may introduce at least one or more of the following genetic changes: transversions, transitions, deletions, and insertions. In addition, prime editing may be implemented for specific applications. For example, and as exemplified and discussed herein, prime editing can be used to (a) install mutation-correcting changes to a nucleotide sequence, (b) install protein and RNA tags, (c) installation of immunoepitopes on proteins of interest, (d) install inducible dimerization domains in proteins, (e) install or remove sequences to alter that activity of a biomolecule, (f) install recombinase target sites to direct specific genetic changes, and (g) mutagenesis of a target sequence by using an error- prone RT. In addition to these methods which, in general, insert, change, or delete nucleotide sequences at target sites of interest, prime editors can also be used to construct highly programmable libraries, as well as to conduct cell data recording and lineage tracing studies. The inventors have also contemplated additional design features of PEgRNAs that are aimed to improve the efficacy of prime editing. Still further, the inventors have conceived of methods for successfully delivering prime editors using vector delivery systems and which involve splitting the PNE using intein domains. ii. PEgRNA In some embodiments, the gRNA for use with the prime editor is a PEgRNA. In some embodiments, the PEgRNA usable in the prime editing system disclosed herein comprises a ~20 nt protospacer sequence and a gRNA core region, which binds with the PNE. In this embodiment, the PEgRNA includes an extended RNA segment at the 5' end, i.e., a 5’ extension. In this embodiment, the 5' extension includes a reverse transcription template sequence, a reverse transcription primer binding site, and an optional 5-20 nucleotide linker sequence. The RT primer binding site hybridizes to the free 3ʹ end that is formed after a nick is formed PATENT ATTORNEY DOCKET NO.50858-164WO2 in the non-target strand of the R-loop, thereby priming reverse transcriptase for DNA polymerization in the 5'- 3' direction. In some embodiments, the PEgRNA usable in the prime editing system disclosed herein includes a ~20 nt protospacer sequence and a gRNA core, which binds with the CRISPR nuclease of the PNE. In this embodiment, the PEgRNA includes an extended RNA segment at the 3' end, i.e., a 3' extension. In this embodiment, the 3' extension includes an RT template sequence, and a reverse transcription primer binding site. The RT primer binding site hybridizes to the free 3' end that is formed after a nick is formed in the non- target strand of the R-loop, thereby priming the RT domain for DNA polymerization in the 5'-3' direction. In some embodiments, the PEgRNA usable in the prime editing system disclosed herein includes a ~20 nt protospacer sequence and a gRNA core, which binds with the PNE. In this embodiment, the guide RNA includes an extended RNA segment at an intermolecular position within the gRNA core, i.e., an intramolecular extension. In this embodiment, the intramolecular extension includes a RT template sequence, and a RT primer binding site. The RT primer binding site hybridizes to the free 3' end that is formed after a nick is formed in the non-target strand of the R-loop, thereby priming the RT domain for DNA polymerization in the 5'-3' direction. In some embodiments, the position of the intermolecular RNA extension is not in the protospacer sequence of the PEgRNA. In another embodiment, the position of the intermolecular RNA extension in the gRNA core. In still another embodiment, the position of the intermolecular RNA extension is any within the PEgRNA molecule except within the protospacer sequence, or at a position which disrupts the protospacer sequence. In one embodiment, the intermolecular RNA extension is inserted downstream from the 3' end of the protospacer sequence. In another embodiment, the intermolecular RNA extension is inserted at least 1 nucleotide, at least 2 nucleotides, at least 3 nucleotides, at least 4 nucleotides, 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, at least 20 nucleotides, at least 21 nucleotides, at least 22 nucleotides, at least 23 nucleotides, at least 24 nucleotides, at least 25 nucleotides downstream of the 3' end of the protospacer sequence. In other embodiments, the intermolecular RNA extension is inserted into the gRNA core, which refers to the portion of the guide RNA corresponding or comprising the tracrRNA, which binds and / or interacts with the CRISPR nuclease or equivalent thereof. Preferably the insertion of the intermolecular RNA extension does not disrupt or minimally disrupts the interaction between the tracrRNA portion and the PNE. The length of the RNA extension can be any useful length. In various embodiments, the RNA extension is 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, at least 20 nucleotides, at least 21 nucleotides, at least 22 nucleotides, at least 23 nucleotides, at least 24 nucleotides, at least 25 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides, at least 100 nucleotides, at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, or at least 500 nucleotides in length. PATENT ATTORNEY DOCKET NO.50858-164WO2 The RT template sequence can also be any suitable length. For example, the RT template sequence can be at least 3 nucleotides, at least 4 nucleotides, 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, at least 20 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides, at least 100 nucleotides, at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, or at least 500 nucleotides in length. In still other embodiments, wherein the RT primer binding site sequence is at least 3 nucleotides, at least 4 nucleotides, 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, at least 20 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides, at least 100 nucleotides, at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, or at least 500 nucleotides in length. In other embodiments, the optional linker or spacer sequence is at least 3 nucleotides, at least 4 nucleotides, 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, at least 20 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides, at least 100 nucleotides, at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, or at least 500 nucleotides in length. The RT template sequence, in certain embodiments, encodes a single-stranded DNA molecule which is homologous to the non-target strand (and thus, complementary to the corresponding site of the target strand) but includes one or more nucleotide changes. The least one nucleotide change may include one or more single-base nucleotide changes, one or more deletions, and one or more insertions. The synthesized single-stranded DNA product of the RT template sequence is homologous to the non-target strand and contains one or more nucleotide changes. The single-stranded DNA product of the RT template sequence hybridizes in equilibrium with the complementary target strand sequence, thereby displacing the homologous endogenous target strand sequence. The displaced endogenous strand may be referred to in some embodiments as a 5' endogenous DNA flap species. This 5' endogenous DNA flap species can be removed by a 5' flap endonuclease (e.g., FEN1) and the single-stranded DNA product, now hybridized to the endogenous target strand, may be ligated, thereby creating a mismatch between the endogenous sequence and the newly synthesized strand. The mismatch may be resolved by the cell’s innate DNA repair and / or replication processes. In various embodiments, the nucleotide sequence of the RT template sequence corresponds to the nucleotide sequence of the non-target strand which becomes displaced as the 5' flap species and which overlaps with the site to be edited. PATENT ATTORNEY DOCKET NO.50858-164WO2 In various embodiments of the extended guide RNAs, the RT template sequence may encode a single-strand DNA flap that is complementary to an endogenous DNA sequence adjacent to a nick site, wherein the single-strand DNA flap comprises a desired nucleotide change. The single-stranded DNA flap may displace an endogenous single-strand DNA at the nick site. The displaced endogenous single-strand DNA at the nick site can have a 5’ end and form an endogenous flap, which can be excised by the cell. In various embodiments, excision of the 5’ end endogenous flap can help drive product formation since removing the 5’ end endogenous flap encourages hybridization of the single-strand 3’ DNA flap to the corresponding complementary DNA strand, and the incorporation or assimilation of the desired nucleotide change carried by the single-strand 3’ DNA flap into the target DNA. In various embodiments of the extended guide RNAs, the cellular repair of the single- strand DNA flap results in installation of the desired nucleotide change, thereby forming a desired product. In still other embodiments, the desired nucleotide change is installed in an editing window that is between about -5 to +5 of the nick site, or between about -10 to +10 of the nick site, or between about -20 to +20 of the nick site, or between about -30 to +30 of the nick site, or between about -40 to + 40 of the nick site, or between about -50 to +50 of the nick site, or between about -60 to +60 of the nick site, or between about -70 to +70 of the nick site, or between about -80 to +80 of the nick site, or between about -90 to +90 of the nick site, or between about -100 to +100 of the nick site, or between about -200 to +200 of the nick site. In other embodiments, the desired nucleotide change is installed in an editing window that is between about +1 to +2 from the nick site, or about +1 to +3, +1 to +4, +1 to +5, +1 to +6, +1 to +7, +1 to +8, +1 to +9, +1 to +10, +1 to +11, +1 to +12, +1 to +13, +1 to +14, +1 to +15, +1 to +16, +1 to +17, +1 to +18, +1 to +19, +1 to +20, +1 to +21, +1 to +22, +1 to +23, +1 to +24, +1 to +25, +1 to +26, +1 to +27, +1 to +28, +1 to +29, +1 to +30, +1 to +31, +1 to +32, +1 to +33, +1 to +34, +1 to +35, +1 to +36, +1 to +37, +1 to +38, +1 to +39, +1 to +40, +1 to +41, +1 to +42, +1 to +43, +1 to +44, +1 to +45, +1 to +46, +1 to +47, +1 to +48, +1 to +49, +1 to +50, +1 to +51, +1 to +52, +1 to +53, +1 to +54, +1 to +55, +1 to +56, +1 to +57, +1 to +58, +1 to +59, +1 to +60, +1 to +61, +1 to +62, +1 to +63, +1 to +64, +1 to +65, +1 to +66, +1 to +67, +1 to +68, +1 to +69, +1 to +70, +1 to +71, +1 to +72, +1 to +73, +1 to +74, +1 to +75, +1 to +76, +1 to +77, +1 to +78, +1 to +79, +1 to +80, +1 to +81, +1 to +82, +1 to +83, +1 to +84, +1 to +85, +1 to +86, +1 to +87, +1 to +88, +1 to +89, +1 to +90, +1 to +90, +1 to +91, +1 to +92, +1 to +93, +1 to +94, +1 to +95, +1 to +96, +1 to +97, +1 to +98, +1 to +99, +1 to +100, +1 to +101, +1 to +102, +1 to +103, +1 to +104, +1 to +105, +1 to +106, +1 to +107, +1 to +108, +1 to +109, +1 to +110, +1 to +111, +1 to +112, +1 to +113, +1 to +114, +1 to +115, +1 to +116, +1 to +117, +1 to +118, +1 to +119, +1 to +120, +1 to +121, +1 to +122, +1 to +123, +1 to +124, +1 to +125, +1 to +130, +1 to +135, +1 to +140, +1 to +145, +1 to +150, +1 to +155, +1 to +160, +1 to +165, +1 to +170, +1 to +175, +1 to +180, +1 to +185, +1 to +190, +1 to +195, or +1 to +200, from the nick site. In some embodiments, the PEgRNA comprises three main component elements ordered in the 5ʹ to 3ʹ direction, namely: a spacer, a gRNA core, and an extension arm at the 3ʹ end. The extension arm may further be divided into the following structural elements in the 5ʹ to 3ʹ direction, namely: a primer binding site (A), an edit template (B), and a homology arm (C). In addition, the PEgRNA may comprise an optional 3ʹ end modifier region (e1) and an optional 5ʹ end modifier region (e2). Still further, the PEgRNA may comprise a transcriptional termination signal at the 3ʹ end of the PEgRNA. These structural elements are further defined herein. The depiction of the structure of the PEgRNA is not meant to be limiting and embraces variations in the arrangement of the elements. For example, the optional sequence modifiers (e1) and (e2) could be PATENT ATTORNEY DOCKET NO.50858-164WO2 positioned within or between any of the other regions shown, and not limited to being located at the 3ʹ and 5ʹ ends. In some embodiments, the PEgRNA comprises three main component elements ordered in the 5ʹ to 3ʹ direction, namely: a spacer, a gRNA core, and an extension arm at the 3ʹ end. The extension arm may further be divided into the following structural elements in the 5ʹ to 3ʹ direction, namely: a primer binding site (A), an edit template (B), and a homology arm (C). In addition, the PEgRNA may comprise an optional 3ʹ end modifier region (e1) and an optional 5ʹ end modifier region (e2). Still further, the PEgRNA may comprise a transcriptional termination signal on the 3ʹ end of the PEgRNA. These structural elements are further defined herein. The depiction of the structure of the PEgRNA is not meant to be limiting and embraces variations in the arrangement of the elements. For example, the optional sequence modifiers (e1) and (e2) could be positioned within or between any of the other regions shown, and not limited to being located at the 3ʹ and 5ʹ ends. Exemplary PEgRNAs of the disclosure for use with nucleases of the disclosure are provided in Table 11. Table 11. Exemplary PEgRNAs of the disclosure In some embodiments, a prime editor of the disclosure (e.g., a prime editor including a Cas nuclease of the disclosure) may form a complex with a PEgRNA having at least 50% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to SEQ ID NO: 372. In some embodiments, a PNE (e.g., a prime editor including a Cas nuclease of the disclosure) of the disclosure may form a complex with a PEgRNA having at least 55% sequence identity (e.g., 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%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to SEQ ID NO: 372. In some embodiments, a PNE (e.g., a prime editor including a Cas nuclease of the disclosure) of the disclosure may form a complex with a PEgRNA having at least 60% sequence identity (e.g., 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to SEQ ID NO: 372. In some embodiments, a PNE (e.g., a prime editor including a Cas nuclease of the disclosure) of the disclosure may form a complex with a PEgRNA having at least 65% sequence identity (e.g., 65%, 66%, PATENT ATTORNEY DOCKET NO.50858-164WO2 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to SEQ ID NO: 372. In some embodiments, a PNE (e.g., a prime editor including a Cas nuclease of the disclosure) of the disclosure may form a complex with a PEgRNA having at least 70% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to SEQ ID NO: 372. In some embodiments, a PNE (e.g., a prime editor including a Cas nuclease of the disclosure) of the disclosure may form a complex with a PEgRNA having at least 75% sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to SEQ ID NO: 372. In some embodiments, a PNE (e.g., a prime editor including a Cas nuclease of the disclosure) of the disclosure may form a complex with a PEgRNA having at least 80% sequence identity (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to SEQ ID NO: 372. In some embodiments, a PNE (e.g., a prime editor including a Cas nuclease of the disclosure) of the disclosure may form a complex with a PEgRNA having at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to SEQ ID NO: 372. In some embodiments, a PNE (e.g., a prime editor including a Cas nuclease of the disclosure) of the disclosure may form a complex with a PEgRNA having at least 90% sequence identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to SEQ ID NO: 372. In some embodiments, a PNE (e.g., a prime editor including a Cas nuclease of the disclosure) of the disclosure may form a complex with a PEgRNA having at least 95% sequence identity (e.g., 95%, 96%, 97%, 98%, 99%, 99%, or 100% sequence identity) to SEQ ID NO: 372. iii. Reverse Transcriptases The disclosure contemplates any wild-type RT obtained from any naturally occurring organism or virus, or obtained from a commercial or non-commercial source. In addition, the reverse transcriptases usable in the prime editors of the disclosure can include any naturally occurring mutant RT, engineered mutant RT, or other variant RT, including truncated variants that retain function. The RTs may also be engineered to contain specific amino acid substitutions, such as those specifically disclosed herein. RTs are multi-functional enzymes typically with three enzymatic activities including RNA- and DNA- dependent DNA polymerization activity, and an RNaseH activity that catalyzes the cleavage of RNA in RNA- DNA hybrids. Some mutants of RTs have disabled the RNaseH moiety to prevent unintended damage to the mRNA. These enzymes that synthesize complementary DNA (cDNA) using mRNA as a template were first identified in RNA viruses. Exemplary enzymes for use with the herein disclosed prime editor can include, but are not limited to, M-MLV reverse transcriptase and RSV reverse transcriptase. Enzymes having RT activity are commercially PATENT ATTORNEY DOCKET NO.50858-164WO2 available. Some exemplary reverse transcriptases that can be fused to CRISPR nucleases or provided as individual proteins according to various embodiments of this disclosure are provided below. A person of ordinary skill in the art will recognize that wild-type RTs, including but not limited to, Moloney Murine Leukemia Virus (M-MLV); Human Immunodeficiency Virus (HIV) reverse transcriptase and avian Sarcoma-Leukosis Virus (ASLV) reverse transcriptase, which includes but is not limited to Rous Sarcoma Virus (RSV) reverse transcriptase, Avian Myeloblastosis Virus (AMV) reverse transcriptase, Avian Erythroblastosis Virus (AEV) Helper Virus MCAV reverse transcriptase, Avian Myelocytomatosis Virus MC29 Helper Virus MCAV reverse transcriptase, Avian Reticuloendotheliosis Virus (REV-T) Helper Virus REV-A reverse transcriptase, Avian Sarcoma Virus UR2 Helper Virus UR2AV reverse transcriptase, Avian Sarcoma Virus Y73 Helper Virus YAV reverse transcriptase, Rous Associated Virus (RAV) reverse transcriptase, and Myeloblastosis Associated Virus (MAV) reverse transcriptase may be suitably used in the subject methods and composition described herein. In some embodiments, the RT may be any RT described in WO 2020 / 191248, the contents of which is herein incorporated by reference. RTs used herein may also include RTs having 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 any reference RT protein, including any wild type RT, or mutant RT, or fragment RT, or other variant of RT disclosed or contemplated herein or known in the art. Exemplary reverse transcriptases include variants with at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to the following wild-type enzymes or partial enzymes: AFPLERPDWDYTTQAGRNHLVHYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTP YDPEDPGQETNVSMSFIWQSAPDIGRKLGRLEDLKSKTLGDLVREAEKIFNKRETPEEREERIRRETEEKEE RRRTVDEQKEKERDRRRHREMSKLLATVVIGQEQDRQEGERKRPQLDKDQCAYCKEKGHWAKDCPKKPR GPRGPRPQTSLLTLGDXGGQGQDPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGAT GGKRYRWTTDRKVHLATGKVTHSFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPLQVLTLNI EDEYRLHETSKEPDVSLGFTWLSDFPQAWAESGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKP HIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTV LDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPTLFDEALHRDLADFR (SEQ ID NO: 386, wherein X is any amino acid) TLQLEEEYRLFEPESTQKQEMDIWLKNFPQAWAETGGMGTAHCQAPVLIQLKATATPISIRQYPMPHEAYQG IKPHIRRMLDQGILKPCQSPWNTPLLPVKKPGTEDYRPVQDLREVNKRVEDIHPTVPNPYNLLSTLPPSHPW YTVLDLKDAFFCLRLHSESQLLFAFEWRDPEIGLSGQLTWTRLPQGFKNSPTLFDEALHSDLADFRVRYPAL VLLQYVDDLLLAAATRTECLEGTKALLETLGNKGYRASAKKAQICLQEVTYLGYSLKDGQRWLTKARKEAILSI PVPKNSRQVREFLGTAGYCRLWIPGFAELAAPLYPLTRPGTLFQWGTEQQLAFEDIKKALLSSPALGLPDITK PFELFIDENSGFAKGVLVQKLGPWKRPVAYLSKKLDTVASGWPPCLRMVAAIAILVKDAGKLTLGQPLTILTS HPVEALVRQPPNKWLSNARMTHYQAMLLDAERVHFGPTVSLNPATLLPLPSGGNHHDCLQILAETHGTRPD LTDQPLPDADLTWYTDGSSFIRNGEREAGAAVTTESEVIWAAPLPPGTSAQRAELIALTQALKMAEGKKLTV YTDSRYAFATTHVHGEIYRRRGLLTSEGKEIKNKNEILALLEALFLPKRLSIIHCPGHQKGDSPQAKGNRLADD TAKKAATETHSSLTVL (SEQ ID NO: 387) PATENT ATTORNEY DOCKET NO.50858-164WO2 PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKL VDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYN VLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKK HQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLXKLLRGTKALTEV IPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDV KQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGA ETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQP DQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKV (SEQ ID NO: 388, wherein X is any amino acid) PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKL VDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYN VLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKK HQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEV IPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDV KQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGA ETF (SEQ ID NO: 389) TVALHLAIPLKWKPNHTPVWIDQWPLPEGKLVALTQLVEKELQLGHIEPSLSCWNTPVFVIRKASGSYRLLHD LRAVNAKLVPFGAVQQGAPVLSALPRGWPLMVLDLKDCFFSIPLAEQDREAFAFTLPSVNNQAPARRFQWK VLPQGMTCSPTICQLIVGQILEPLRLKHPSLRMLHYMDDLLLAASSHDGLEAAGEEVISTLERAGFTISPDKVQ KEPGVQYLGYKLGSTYAAPVGLVAEPRIATLWDVQKLVGSLQWLRPALGIPPRLRGPFYEQLRGSDPNEAR EWNLDMKMAWREIVQLSTTAALERWDPALPLEGAVARCEQGAIGVLGQGLSTHPRPCLWLFSTQPTKAFTA WLEVLTLLITKLRASAVRTFGKEVDILLLPACFRDELPLPEGILLALRGFAGKIRSSDTPSIFDIARPLHVSLKVR VTDHPVPGPTVFTDASSSTHKGVVVWREGPRWEIKEIADLGASVQQLEARAVAMALLLWPTTPTNVVTDSA FVAKMLLKMGQEGVPSTAAAFILEDALSQRSAMAAVLHVRSHSEVPGFFTEGNDVADSQATFQAYPLREAK DLHTALHIGPRALSKACNISMQQAREVVQTCPHCNSAPALEAGVNPRGLGPLQIWQTDFTLEPRMAPRSWL AVTVDTASSAIVVTQHGRVTSVAAQHHWATVIAVLGRPKAIKTDNGSCFTSKSTREWLARWGIAHTTGIPGN SQGQAMVERANRLLKDKIRVLAEGDGFMKRIPTSKQGELLAKAMYALNHFERGENTKTPIQKHWRPTVLTE GPPVKIRIETGEWEKGWNVLVWGRGYAAVKNRDTDKVIWVPSRKVKPDIAQKDEVTKKDEASPLFA (SEQ ID NO: 390) MMDHLLQKTQIQNQTEQVMNITNPNSIYIKGRLYFKGYKKIELHCFVDTGASLCIASKFVIPEEHWINAERPIM VKIADGSSITINKVCRDIDLIIAGEIFHIPTVYQQESGIDFIIGNNFCQLYEPFIQFTDRVIFTKDRTYPVHIAKLTRA VRVGTEGFLESMKKRSKTQQPEPVNISTNKIAILSEGRRLSEEKLFITQQRMQKIEELLEKVCSENPLDPNKTK QWMKASIKLSDPSKAIKVKPMKYSPMDREEFDKQIKELLDLKVIKPSKSPHMAPAFLVNNEAEKRRGKKRMV VNYKAMNKATVGDAYNLPNKDELLTLIRGKKIFSSFDCKSGFWQVLLDQDSRPLTAFTCPQGHYEWNVVPF GLKQAPSIFQRHMDEAFRVFRKFCCVYVDDILVFSNNEEDHLLHVAMILQKCNQHGIILSKKKAQLFKKKINFL GLEIDEGTHKPQGHILEHINKFPDTLEDKKQLQRFLGILTYASDYIPKLAQIRKPLQAKLKENVPWKWTKEDTL YMQKVKKNLQGFPPLHHPLPEEKLIIETDASDDYWGGMLKAIKINEGTNTELICRYASGSFKAAEKNYHSNDK PATENT ATTORNEY DOCKET NO.50858-164WO2 ETLAVINTIKKFSIYLTPVHFLIRTDNTHFKSFVNLNYKGDSKLGRNIRWQAWLSHYSFDVEHIKGTDNHFADF LSREFNRVNS (SEQ ID NO: 391) MKEKISKIDKNFYTDIFIKTSFQNEFEAGGVIPPIAKNQVSTISNKNKTFYSLAHSSPHYSIQTRIEKFLLKNIPLS ASSFAFRKERSYLHYLEPHTQNVKYCHLDIVSFFHSIDVNIVRDTFSVYFSDEFLVKEKQSLLDAFMASVTLTA ELDGVEKTFIPMGFKSSPSISNIIFRKIDILIQKFCDKNKITYTRYADDLLFSTKKENNILSSTFFINEISSILSINKF KLNKSKYLYKEGTISLGGYVIENILKDNSSGNIRLSSSKLNPLYKALYEIKKGSSSKHICIKVFNLKLKRFIYKKN KEKFEAKFYSSQLKNKLLGYRSYLLSFVIFHKKYKCINPIFLEKCVFLISEIESIMNRKF (SEQ ID NO: 392) MKITSNNVTAVINGKGWHSINWKKCHQHVKTIQTRIAKAACNQQWRTVGRLQRLLVRSFSARALAVKRVTEN SGRKTPGVDGQIWSTPESKWEAIFKLRRKGYKPLPLKRVFIPKSNGKKRPLGIPVMLDRAMQALHLLGLEPV SETNADHNSYGFRPARCTADAIQQVCNMYSSRNASKWVLEGDIKGCFEHISHEWLLENIPMDKQILRNWLK AGIIEKSIFSKTLSGTPQGGIISPV LANMALDGLERLLQNRFGRNRLI (SEQ ID NO: 393) MSKIKINYEKYHIKPFPHFDQRIKVNKKVKENLQNPFYIAAHSFYPFIHYKKISYKFKNGTLSSPKERDIFYSGH MDGYIYKHYGEILNHKYNNTCIGKGIDHVSLAYRNNKMGKSNIHFAAEVINFISEQQQAFIFVSDFSSYFDSLD HAILKEKLIEVLEEQDKLSKDWWNVFKHITRYNWVEKEEVISDLECTKEKIARDKKSRERYYTPAEFREFRKR VNIKSNDTGVGIPQGTAISAVLANVYAIDLDQKLNQYALKYGGIYRRYSDDIIMVLPMTSDGQDPSNDHVSFIK SVVKRNKVTMGDSKTSVLYYANNNIYEDYQRKRESKMDYLGFSFDGMTVKIREKSLFKYYHRTYKKINSINW ASVKKEKKVGRKKLYLLYSHLGRNYKGHGNFISYCKKAHAVFEGNKKIESLINQQIKRHWKKIQKRLVDV (SEQ ID NO: 394) DTSNLMEQILSSDNLNRAYLQVVRNKGAEGVDGMKYTELKEHLAKNGETIKGQLRTRKYKPQPARRVEIPKP DGGVRNLGVPTVTDRFIQQAIAQVLTPIYEEQFHDHSYGFRPNRCAQQAILTALNIMNDGNDWIVDIDLEKFF DTVNHDKLMTLIGRTIKDGDVISIVRKYLVSGIMIDDEYEDSIVGTPQGGNLSPLLANIMLNELDKEMEKRGLNF VRYADDCIIMVGSEMSANRVMRNISRFIEEKLGLKVNMTKSKVDRPSGLKYLGFGFYFDPRAHQFKAKPHAK SVAKFKKRMKELTCRSWGVSNSYKVEKLNQLIRGWINYFKIGSMKTLCKELDSRIRYRLRMCIWKQWKTPQ NQEKNLVKLGIDRNTARRVAYTGKRIAYVCNKGAVNVAISNKRLASFGLISMLDYYIEKCVTC (SEQ ID NO: 395) ALLERILARDNLITALKRVEANQGAPGIDGVSTDQLRDYIRAHWSTIHAQLLAGTYRPAPVRRVEIPKPGGGT RQLGIPTVVDRLIQQAILQELTPIFDPDFSSSSFGFRPGRNAHDAVRQAQGYIQEGYRYVVDMDLEKFFDRV NHDILMSRVARKVKDKRVLKLIRAYLQAGVMIEGVKVQTEEGTPQGGPLSPLLANILLDDLDKELEKRGLKFC RYADDCNIYVKSLRAGQRVKQSIQRFLEKTLKLKVNEEKSAVDRPWKRAFLGFSFTPERKARIRLAPRSIQRL KQRIRQLTNPNWSISMPERIHRVNQYVMGWIGYFRLVETPSVLQTIEGWIRRRLRLCQWLQWKRVRTRIREL RALGLKETAVMEIANTRKGAWRTTKTPQLHQALGKTYWTAQGLKSLTQR (SEQ ID NO: 396) In some embodiments, a suitable reverse transcriptase may be any reverse transcriptase described in WO2020191233, WO2020191233, WO2020191243, WO2020191246, WO2020191245, WO2020191234, WO2020191233, WO2020191241, US20200085066, US20200109398, US20200109398, WO2020191239, PATENT ATTORNEY DOCKET NO.50858-164WO2 WO2020191245, and WO 2020191248, the contents of each of which are incorporated herein by reference in their entirety. iv. Flap Endonucleases Flap endonucleases (e.g., FEN1) refers to an enzyme that catalyzes the removal of 5ʹ single strand DNA flaps. These are naturally occurring enzymes that process the removal of 5ʹ flaps formed during cellular processes, including DNA replication. The methods herein described may utilize endogenously supplied flap endonucleases or those provided in trans to remove the 5ʹ flap of endogenous DNA formed at the target site. Flap endonucleases are known in the art and can be found described in Patel et al., “Flap endonucleases pass 5ʹ-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5ʹ- ends,” Nucleic Acids Research, 2012, 40(10): 4507-4519 and Tsutakawa et al., “Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily,” Cell, 2011, 145(2): 198-211 (each of which are incorporated herein by reference). An exemplary flap endonuclease is FEN1. The flap endonucleases may also include any FEN1 variant, mutant, or other flap endonuclease ortholog, homolog, or variant. Non-limiting flap endonuclease examples are as follows: MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRM MENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLL SLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGL NQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPE SVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGSLSSAKRKEPEPKGS TKKKAKTGAAGKFKRGK (SEQ ID NO: 397) MGVNDLWQILEPVKQHIPLRNLGGKTIAVDLSLWVCEAQTVKKMMGSVMKPHLRNLFFRISYLTQMDVKLVF VMEGEPPKLKADVISKRNQSRYGSSGKSWSQKTGRSHFKSVLRECLHMLECLGIPWVQAAGEAEAMCAYL NAGGHVDGCLTNDGDTFLYGAQTVYRNFTMNTKDPHVDCYTMSSIKSKLGLDRDALVGLAILLGCDYLPKG VPGVGKEQALKLIQILKGQSLLQRFNRWNETSCNSSPQLLVTKKLAHCSVCSHPGSPKDHERNGCRLCKSD KYCEPHDYEYCCPCEWHRTEHDRQLSEVENNIKKKACCCEGFPFHEVIQEFLLNKDKLVKVIRYQRPDLLLF QRFTLEKMEWPNHYACEKLLVLLTHYDMIERKLGSRNSNQLQPIRIVKTRIRNGVHCFEIEWEKPEHYAMED KQHGEFALLTIEEESLFEAAYPEIVAVYQKQKLEIKGKKQKRIKPKENNLPEPDEVMSFQSHMTLKPTCEIFHK QNSKLNSGISPDPTLPQESISASLNSLLLPKNTPCLNAQEQFMSSLRPLAIQQIKAVSKSLISESSQPNTSSHNI SVIADLHLSTIDWEGTSFSNSPAIQRNTFSHDLKSEVESELSAIPDGFENIPEQLSCESERYTANIKKVLDEDS DGISPEEHLLSGITDLCLQDLPLKERIFTKLSYPQDNLQPDVNLKTLSILSVKESCIANSGSDCTSHLSKDLPGI PLQNESRDSKILKGDQLLQEDYKVNTSVPYSVSNTVVKTCNVRPPNTALDHSRKVDMQTTRKILMKKSVCLD RHSSDEQSAPVFGKAKYTTQRMKHSSQKHNSSHFKESGHNKLSSPKIHIKETEQCVRSYETAENEESCFPD STKSSLSSLQCHKKENNSGTCLDSPLPLRQRLKLRFQST (SEQ ID NO: 398) MGVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRIRPIF VFDGDAPLLKKQTLVKRRQRKDLASSDSRKTTEKLLKTFLKRQAIKTAFRSKRDEALPSLTQVRRENDLYVLP PLQEEEKHSSEEEDEKEWQERMNQKQALQEEFFHNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLF EAMPEESDDFSQYQLKGLLKKNYLNQHIEHVQKEMNQQHSGHIRRQYEDEGGFLKEVESRRVVSEDTSHYI PATENT ATTORNEY DOCKET NO.50858-164WO2 LIKGIQAKTVAEVDSESLPSSSKMHGMSFDVKSSPCEKLKTEKEPDATPPSPRTLLAMQAALLGSSSEEELES ENRRQARGRNAPAAVDEGSISPRTLSAIKRALDDDEDVKVCAGDDVQTGGPGAEEMRINSSTENSDEGLKV RDGKGIPFTATLASSSVNSAEEHVASTNEGREPTDSVPKEQMSLVHVGTEAFPISDESMIKDRKDRLPLESA VVRHSDAPGLPNGRELTPASPTCTNSVSKNETHAEVLEQQNELCPYESKFDSSLLSSDDETKCKPNSASEVI GPVSLQETSSIVSVPSEAVDNVENVVSFNAKEHENFLETIQEQQTTESAGQDLISIPKAVEPMEIDSEESESD GSFIEVQSVISDEELQAEFPETSKPPSEQGEEELVGTREGEAPAESESLLRDNSERDDVDGEPQEAEKDAE DSLHEWQDINLEELETLESNLLAQQNSLKAQKQQQERIAATVTGQMFLESQELLRLFGIPYIQAPMEAEAQC AILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKNKFVEYYQYVDFHNQLGLDRNKLINLAYLLGSDYTEGIPT VGCVTAMEILNEFPGHGLEPLLKFSEWWHEAQKNPKIRPNPHDTKVKKKLRTLQLTPGFPNPAVAEAYLKPV VDDSKGSFLWGKPDLDKIREFCQRYFGWNRTKTDESLFPVLKQLDAQQTQLRIDSFFRLAQQEKEDAKRIKS QRLNRAVTCMLRKEKEAAASEIEAVSVAMEKEFELLDKAKRKTQKRGITNTLEESSSLKRKRLSDSKRKNTC GGFLGETCLSESSDGSSSEDAESSSLMNVQRRTAAKEPKTSASDSQNSVKEAPVKNGGATTSSSSDSDDD GGKEKMVLVTARSVFGKKRRKLRRARGRKRKT (SEQ ID NO: 399) In various embodiments, the prime editors contemplated herein may include any flap endonuclease variant of the above-disclosed sequences having 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 any of the above sequences. In some embodiments, a suitable flap endonuclease may be any flap endonuclease described in WO2020191233, WO2020191233, WO2020191243, WO2020191246, WO2020191245, WO2020191234, WO2020191233, WO2020191241, US20200085066, US20200109398, US20200109398, WO2020191239, WO2020191245, and WO 2020191248, the contents of each of which are incorporated herein by reference in their entirety. f. Linkers and Other Domains The PNEs of the disclosure may comprise various other elements. Non-limiting examples of additional elements are described below. i. Localization Sequence The PNE may also comprise one or more localization sequences. The localization sequence may be any signal sequence known in the art that localizes polypeptides to particular subcellular location(s) including, but not limited to, plastid localization sequences, mitochondrial localization sequences, and dual- targeting signal sequences that target to both the plastid and mitochondria (see, e.g., Nassoury and Morse (2005) Biochim Biophys Acta 1743:5-19; Kunze and Berger (2015) Front Physiol dx.doi.org / 10.3389 / fphys.2015.00259; Herrmann and Neupert (2003) IUBMB Life 55:219-225; Soll (2002) Curr Opin Plant Biol 5:529-535; Carrie and Small (2013) Biochim Bio phys Acta 1833 :253-259; Carrie et al. (2009) FEES J 276: 1187-1195; Silva-Filho (2003) Curr Opin Plant Biol 6:589-595; Peeters and Small (2001) Biochim Biophys Acta 1541:54-63; Murcha et al. (2014) J Exp Bot 65:6301-6335; Mackenzie (2005) Trends Cell Biol 15:548-554; Glaser et al. (1998) Plant Mol Biol 38:311-338). PATENT ATTORNEY DOCKET NO.50858-164WO2 The PNEs of the disclosure can comprise at least one nuclear localization sequence (NLS) to enhance transport of the polypeptide to the nucleus of a cell. Nuclear localization signals are known in the art and generally comprise a stretch of basic amino acids (see, e.g., Lange et al., J Biol. Chem. (2007, 282:5101-5105). Non-limiting examples of NLSs useful for the presently disclosed PNEs are SV40m, Large T-antigen, nucleoplasmin, and c-Myc (see, e.g., Ray et al. (2015) Bioconjug Chem 26(6): 1004-7. In various embodiments, the PNEs disclosed herein further comprise one or more, preferably, at least two NLSs. In certain embodiments, the PNEs comprise at least two NLSs. In embodiments with at least two NLSs, the NLSs can be the same or they can be different. In addition, the NLSs may be expressed as part of a fusion protein with the remaining portions of the prime editors. In some embodiments, one or more of the NLSs are bipartite NLSs (“bpNLS”). In certain embodiments, the disclosed PNEs comprise two bipartite NLSs. In some embodiments, the disclosed PNEs comprise more than two bipartite NLSs. The disclosure contemplates the use of any NLS known in the art at the time of the disclosure, or any NLS that is identified or otherwise made available in the state of the art after the time of the instant filing. A representative NLS is a peptide sequence that directs the protein to the nucleus of the cell in which the sequence is expressed. A NLS is predominantly basic, can be positioned almost anywhere in a protein's amino acid sequence, generally comprises a short sequence of four amino acids (Autieri & Agrawal, (1998) J. Biol. Chem.273: 14731-37, incorporated herein by reference) to eight amino acids, and is typically rich in lysine and arginine residues (Magin et al., (2000) Virology 274: 11-16, incorporated herein by reference). NLSs often comprise proline residues. A variety of NLSs have been identified and have been used to effect transport of biological molecules from the cytoplasm to the nucleus of a cell. See, e.g., Tinland et al., (1992) Proc. Natl. Acad. Sci. U.S.A.89:7442-46; Moede et al., (1999) FEBS Lett.461:229-34, which is incorporated by reference. Translocation is currently thought to involve nuclear pore proteins. Most NLSs can be classified in three general groups: (i) a monopartite NLS exemplified by the SV40 large T antigen NLS (PKKKRKV (SEQ ID NO: 400)); (ii) a bipartite motif consisting of two basic domains separated by a variable number of spacer amino acids and exemplified by the Xenopus nucleoplasmin NLS (KRXXXXXXXXXXKKKL (SEQ ID NO: 401), wherein X is any amino acid); and (iii) noncanonical sequences such as M9 of the hnRNP Al protein, the influenza virus nucleoprotein NLS, and the yeast Gal4 protein NLS (Dingwall and Laskey 1991). In some embodiments, an NLS comprises the amino acid sequence PKKKRKV (SEQ ID NO: 349), MDSLLMNRRKFLYQFKNVRWAKGRRETYLC (SEQ ID NO: 402), KRTADGSEFESPKKKRKV (SEQ ID NO: 403), or KRTADGSEFEPKKKRKV (SEQ ID NO: 404). In other embodiments, NLS comprises the amino acid sequences NLSKRPAAIKKAGQAKKKK (SEQ ID NO: 405), PAAKRVKLD (SEQ ID NO: 406), RQRRNELKRSF (SEQ ID NO: 407), or NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 408). In certain embodiments, the presently disclosed PNE comprises at least one cell penetrating domain that facilitates cellular uptake of the polypeptide. Cell-penetrating domains are known in the art and generally comprise stretches of positively charged amino acid residues (i.e., polycationic cell penetrating domains), alternating polar amino acid residues and non-polar amino acid residues (i.e., amphipathic cell-penetrating domains), or hydrophobic amino acid residues (i.e., hydrophobic cell penetrating domains) (see, e.g., Milletti F. (2012) Drug Discov Today 17:850-860). A non-limiting example of a cell-penetrating domain is the trans- activating transcriptional activator (TAT) from the human immunodeficiency virus 1. PATENT ATTORNEY DOCKET NO.50858-164WO2 ii. Additional PNE Elements In some embodiments, the PNE described herein may comprise one or more heterologous protein domains (e.g., about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more domains). A PNE may comprise any additional domains. Other exemplary domains that may be present are localization sequences, such as cytoplasmic localization sequences, export sequences, such as nuclear export sequences, or other localization sequences, as well as sequence tags that are useful for solubilization, purification, or detection of the fusion proteins. iii. Linkers The term "linker," as used herein, refers to a chemical group or a molecule linking two domains in the PNE. In certain embodiments, linkers may be used to link any of the peptides or peptide domains or moieties of the invention (e.g., a CRISPR nuclease linked or fused to a reverse transcriptase) in a fusion protein. Typically, the linker is positioned between, or flanked by, two groups, molecules, or other moieties and connected to each one via a covalent bond, thus connecting the two. In some embodiments, the linker is an amino acid or a plurality of amino acids (e.g., a peptide or protein). In some embodiments, the linker is an organic molecule, group, polymer, or chemical moiety. In some embodiments, the linker is 5-100 amino acids in length, for example, 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. Longer or shorter linkers are also contemplated. The linker may be as simple as a covalent bond, or it may be a polymeric linker many atoms in length. In certain embodiments, the linker is a polypeptide or based on amino acids. In other embodiments, the linker is not peptide-like. In certain embodiments, the linker is a covalent bond (e.g., a carbon-carbon bond, disulfide bond, carbon-heteroatom bond, etc.). In certain 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 other embodiments, the linker comprises amino acids. In certain embodiments, the linker comprises a peptide. In certain embodiments, the linker comprises an aryl or heteroaryl 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. In some other embodiments, the linker comprises the amino acid sequence (GGGGS)n (SEQ ID NO: 409), (G)n, (EAAAK)n (SEQ ID NO: 410), (GGS)n, (SGGS)n (SEQ ID NO: 411), (XP)n, or any combination PATENT ATTORNEY DOCKET NO.50858-164WO2 thereof, wherein n is independently an integer between 1 and 30, and wherein X is any amino acid. In some embodiments, the linker comprises the amino acid sequence (GGS)n, wherein n is 1, 3, or 7. In some embodiments, the linker comprises the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 412). In some embodiments, the linker comprises the amino acid sequence SGGSSGGSSGSETPGTSESATPESSGGSSGGS (SEQ ID NO: 413). In some embodiments, the linker comprises the amino acid sequence SGGSGGSGGS (SEQ ID NO: 414). In some embodiments, the linker comprises the amino acid sequence SGGS (SEQ ID NO: 415). In other embodiments, the linker comprises the amino acid sequence SGGSSGGSSGSETPGTSESATPESAGSYPYDVPDYAGSAAPAAKKKKLDGSGSGGSSGGS (SEQ ID NO: 416). 2. Delivery of the PNEs In some embodiments, PNEs of the invention may be delivered as ribonucleoproteins. In some embodiments, PNEs of the invention may be delivered as nucleic acids, such as an mRNA. The PNEs of the invention may be delivered by any suitable methodology, such as by vector-based transfection (in which one or more vectors comprising DNA encoding the gRNA and the PNE and which are expressed within a cell upon transfection with the vectors), direct delivery of the PNE complexed with the gRNA (e.g., RNP delivery) in a delivery format (e.g., lipid particles, nanoparticles), or by a mRNA-based delivery system. Such methods are described herein in the present disclosure and any known method may be utilized. Table 12 summarizes delivery methods for a PNE or a nucleic acid encoding a PNE. Table 12. Delivery Methods for PNEs PATENT ATTORNEY DOCKET NO.50858-164WO2 a. mRNA Delivery In some embodiments, the PNE is delivered as an mRNA. The mRNA may be provided according to any of the sections 3-24 below. b. Ribonucleoprotein Delivery In one aspect, the PNE complexed with the gRNA may be delivered as a ribonucleoprotein (RNP) to cells. The RNP comprises the nucleic acid binding protein, e.g., Cas9, in complex with the targeting gRNA. RNPs may be delivered to cells using known methods, such as electroporation, lipofection, nucleofection, or cationic lipid-mediated methods, for example, as reported by Zuris, J.A. et al., 2015, Nat. Biotechnology, 33(1):73-80. RNPs are advantageous for use in CRISPR systems, particularly for cells that are difficult to transfect, such as primary cells. In addition, RNPs can also alleviate difficulties that may occur with protein expression in cells, especially when eukaryotic promoters, e.g., CMV or EF1A, which may be used in CRISPR plasmids, are not well expressed. Advantageously, the use of RNPs does not require the delivery of foreign DNA into cells. Moreover, because an RNP comprising a PNE and gRNA complex is degraded over time, the use of RNPs has the potential to limit off-target effects. Electroporation can be used to permeabilize mammalian cells (e.g., human cells) by the application of an electrostatic potential to the cell of interest. Mammalian cells, such as human cells, subjected to an external electric field in this manner are subsequently predisposed to the uptake of exogenous nucleic acids and proteins. Electroporation of mammalian cells is described in detail, e.g., in Chu et al., Nucleic Acids Research 15:1311 (1987), the disclosure of which is incorporated herein by reference. A similar technique, Nucleofection™, utilizes an applied electric field in order to stimulate the uptake of exogenous RNPs into the nucleus of a eukaryotic cell. Nucleofection™ and protocols useful for performing this technique are described in detail, e.g., in Seki et al., J Exp Med 215:3 (2018), the disclosures of each of which are incorporated herein by reference. c. Viral Vectors for Nucleic Acid Delivery Recombinant viral genomes provide a rich source of vectors that can be used for the efficient delivery of a nucleic acid encoding a PNE of the invention into the genome of a target cell (e.g., a mammalian cell, such as a human cell). Recombinant viral genomes are particularly useful vectors for gene delivery because they deliver the gene of interest to the nucleus of the target cells. For select viruses, nucleic acids contained within such genomes may be incorporated into the genome of a target cell by generalized or specialized transduction. These processes occur as part of the natural viral replication cycle, and do not require added proteins or reagents. Examples of recombinant viral vectors used to deliver genes of interest include AAV, adenovirus (e.g., Ad5, Ad26, Ad34, Ad35, and Ad48), parvovirus (e.g., adeno- associated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g., measles and Sendai), positive PATENT ATTORNEY DOCKET NO.50858-164WO2 strand RNA viruses, such as picornavirus and alphavirus, and double stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, modified vaccinia Ankara (MVA), fowlpox and canarypox). Other viruses useful for delivering nucleic acids encoding antibody light and heavy chains or antibody fragments of the invention include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus, for example. Examples of retroviruses include: avian leukosis- sarcoma, mammalian C-type, B-type viruses, D- type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields, et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996). Other examples include murine leukemia viruses, murine sarcoma viruses, mouse mammary tumor virus, bovine leukemia virus, feline leukemia virus, feline sarcoma virus, avian leukemia virus, human T-cell leukemia virus, baboon endogenous virus, Gibbon ape leukemia virus, Mason Pfizer monkey virus, simian immunodeficiency virus, simian sarcoma virus, Rous sarcoma virus and lentiviruses. Other examples of vectors are described, for example, in US Patent No.5,801,030, the disclosure of which is incorporated herein by reference as it pertains to viral vectors for use in gene therapy. 3. Nucleic Acids Encoding PNEs of the Invention Provided herein are nucleic acids encoding any PNE of the invention described herein (e.g., a nucleic acid encoding any one or combination of a CRISPR nuclease, a base editing polypeptide, an IBR, a reverse transcriptase, and flap endonuclease polypeptide). The nucleic acid may be DNA or RNA, such as mRNA. The nucleic acid may be circular or linear. 4. Chemically Modified Nucleic Acids The nucleic acids encoding PNEs of the disclosure may have one or more chemical modifications. According to Aduri et al., (Aduri, R. et al., AMBER force field parameters for the naturally occurring modified nucleosides in RNA. Journal of Chemical Theory and Computation.2006.3(4):1464-75), there are 107 naturally occurring nucleosides, including 1-methyladenosine, 2-methylthio-N6-hydroxynorvalyl carbamoyladenosine, 2-methyladenosine, 2-O-ribosylphosphate adenosine, N6-methyl-N6- threonylcarbamoyladenosine, N6-acetyladenosine, N6-glycinylcarbamoyladenosine, N6- isopentenyladenosine, N6-methyladenosine, N6-threonylcarbamoyladenosine, N6,N6-dimethyladenosine, N6-(cis-hydroxyisopentenyl)adenosine, N6-hydroxynorvalylcarbamoyladenosine, 1,2-O-dimethyladenosine, N6,2-O-dimethyladenosine, 2-O-methyladenosine, N6,N6,O-2-trimethyladenosine, 2-methylthio-N6-(cis- hydroxyisopentenyl) adenosine, 2-methylthio-N6-methyladenosine, 2-methylthio-N6-isopentenyladenosine, 2-methylthio-N6-threonyl carbamoyladenosine, 2-thiocytidine, 3-methylcytidine , N4-acetylcytidine, 5- formylcytidine, N4-methylcytidine, 5-methylcytidine, 5-hydroxymethylcytidine, lysidine, N4-acetyl-2-O- methylcytidine, 5-formyl-2-O-methylcytidine, 5,2-O-dimethylcytidine, 2-O-methylcytidine, N4,2-O- dimethylcytidine, N4,N4,2-O-trimethylcytidine, 1-methylguanosine, N2,7-dimethylguanosine, N2- methylguanosine, 2-O-ribosylphosphate guanosine, 7-methylguanosine, under modified hydroxywybutosine, 7-aminomethyl-7-deazaguanosine, 7-cyano-7-deazaguanosine, N2,N2-dimethylguanosine, 4- demethylwyosine, epoxyqueuosine, hydroxywybutosine, isowyosine, N2,7,2-O-trimethylguanosine, N2,2-O- dimethylguanosine, 1,2-O-dimethylguanosine, 2-O-methylguanosine, N2,N2,2-O-trimethylguanosine, N2,N2,7-trimethylguanosine, peroxywybutosine, galactosyl-queuosine, mannosyl-queuosine, queuosine, PATENT ATTORNEY DOCKET NO.50858-164WO2 archaeosine, wybutosine, methylwyosine, wyosine, 2-thiouridine, 3-(3-amino-3-carboxypropyl)uridine, 3- methyluridine, 4-thiouridine, 5-methyl-2-thiouridine, 5-methylaminomethyluridine, 5-carboxymethyluridine, 5- carboxymethylaminomethyluridine, 5-hydroxyuridine, 5-methyluridine, 5-taurinomethyluridine, 5- carbamoylmethyluridine, 5-(carboxyhydroxymethyl)uridine methyl ester, dihydrouridine, 5- methyldihydrouridine, 5-methylaminomethyl-2-thiouridine, 5-(carboxyhydroxymethyl)uridine, 5- (isopentenylaminomethyl)uridine, 5-(isopentenylaminomethyl)-2-thiouridine, 3,2-O-dimethyluridine, 5- carboxymethylaminomethyl-2-O-methyluridine, 5-carbamoylmethyl-2-O-methyluridine, 5- methoxycarbonylmethyl-2-O-methyluridine, 5-(isopentenylaminomethyl)-2-O-methyluridine, 5,2-O- dimethyluridine, 2-O-methyluridine, 2-thio-2-O-methyluridine, uridine 5-oxyacetic acid, 5- methoxycarbonylmethyluridine, uridine 5-oxyacetic acid methyl ester, 5-methoxyuridine, 5-aminomethyl-2- thiouridine, 5-carboxymethylaminomethyl-2-thiouridine, 5-methylaminomethyl-2-selenouridine, 5- methoxycarbonylmethyl-2-thiouridine, 5-taurinomethyl-2-thiouridine, pseudouridine, 1-methyl-3-(3-amino-3- carboxypropyl)pseudouridine, 1-methylpseudouridine, 3-methylpseudouridine, 2-O-methylpseudouridine, inosine, 1-methylinosine, 1,2-O-dimethylinosine, and 2-O-methylinosine. Each of these may be components of nucleic acids of the present invention. a. Nucleosides Containing Modified Sugars The alternative nucleosides and nucleotides (e.g., building block molecules), which may be incorporated into a nucleic acid (e.g., RNA or mRNA, as described herein), can be altered on the sugar of the ribonucleic acid. For example, the 2′ hydroxyl group (OH) can be modified or replaced with a number of different substituents. Exemplary substitutions at the 2′-position include, but are not limited to, H, halo, optionally substituted C1-6 alkyl; optionally substituted C1-6 alkoxy; optionally substituted C6-10 aryloxy; optionally substituted C3-8 cycloalkyl; optionally substituted C3-8 cycloalkoxy; optionally substituted C6-10 aryloxy; optionally substituted C6-10 aryl-C1-6 alkoxy, optionally substituted C1-12 (heterocyclyl)oxy; a sugar (e.g., ribose, pentose, or any described herein); a polyethyleneglycol (PEG), -O(CH2CH2O)nCH2CH2OR, where R is H or optionally substituted alkyl, and n is an integer from 0 to 20 (e.g., from 0 to 4, from 0 to 8, from 0 to 10, from 0 to 16, from 1 to 4, from 1 to 8, from 1 to 10, from 1 to 16, from 1 to 20, from 2 to 4, from 2 to 8, from 2 to 10, from 2 to 16, from 2 to 20, from 4 to 8, from 4 to 10, from 4 to 16, and from 4 to 20); “locked” nucleic acids (LNA) in which the 2′-hydroxyl is connected by a C1-6 alkylene or C1-6 heteroalkylene bridge to the 4’-carbon of the same ribose sugar, where exemplary bridges included methylene, propylene, ether, or amino bridges; aminoalkyl, as defined herein; aminoalkoxy, as defined herein; amino as defined herein; and amino acid, as defined herein Generally, RNA includes the sugar group ribose, which is a 5-membered ring having an oxygen. Exemplary, non-limiting alternative nucleotides include replacement of the oxygen in ribose (e.g., with S, Se, or alkylene, such as methylene or ethylene); addition of a double bond (e.g., to replace ribose with cyclopentenyl or cyclohexenyl); ring contraction of ribose (e.g., to form a 4-membered ring of cyclobutane or oxetane); ring expansion of ribose (e.g., to form a 6- or 7-membered ring having an additional carbon or heteroatom, such as for anhydrohexitol, altritol, mannitol, cyclohexanyl, cyclohexenyl, and morpholino that also has a phosphoramidate backbone); multicyclic forms (e.g., tricyclo; and “unlocked” forms, such as glycol nucleic acid (GNA) (e.g., R-GNA or S-GNA, where ribose is replaced by glycol units attached to phosphodiester bonds), threose nucleic acid (TNA, where ribose is replace with α-L-threofuranosyl-(3′→2′)), PATENT ATTORNEY DOCKET NO.50858-164WO2 and peptide nucleic acid (PNA, where 2-amino-ethyl-glycine linkages replace the ribose and phosphodiester backbone). The sugar group can also contain one or more carbons that possess the opposite stereochemical configuration than that of the corresponding carbon in ribose. Thus, a nucleic acid molecule can include nucleotides containing, e.g., arabinose, as the sugar. b. Alterations on the nucleobase The present disclosure provides for alternative nucleosides and nucleotides. As described herein “nucleoside” is defined as a compound containing a sugar molecule (e.g., a pentose or ribose) or derivative thereof in combination with an organic base (e.g., a purine or pyrimidine) or a derivative thereof (also referred to herein as “nucleobase”). As described herein, “nucleotide” is defined as a nucleoside including a phosphate group. Exemplary non-limiting alterations include an amino group, a thiol group, an alkyl group, a halo group, or any described herein. The alternative nucleotides may by synthesized by any useful method, as described herein (e.g., chemically, enzymatically, or recombinantly to include one or more alternative or alternative nucleosides). In some embodiments, a nucleic acid of the invention (e.g., an mRNA or an oligonucleotide) includes one or more 2’-OMe nucleotides, 2’-methoxyethyl nucleotides (2’-MOE nucleotides), 2’-F nucleotide, 2’-NH2 nucleotide, 2’fluoroarabino nucleotides (FANA nucleotides), locked nucleic acid nucleotides (LNA nucleotides), or 4’-S nucleotides. The alternative nucleotide base pairing encompasses not only the standard adenosine-thymine, adenosine-uracil, and guanosine-cytosine base pairs, but also base pairs formed between nucleotides and / or alternative nucleotides including non-standard or alternative bases, wherein the arrangement of hydrogen bond donors and hydrogen bond acceptors permits hydrogen bonding between a non-standard base and a standard base or between two complementary non-standard base structures. One example of such non-standard base pairing is the base pairing between the alternative nucleotide inosine and adenine, cytosine, or uracil. The alternative nucleosides and nucleotides can include an alternative nucleobase. Examples of nucleobases found in RNA include, but are not limited to, adenine, guanine, cytosine, and uracil. Examples of nucleobase found in DNA include, but are not limited to, adenine, guanine, cytosine, and thymine. These nucleobases can be altered or wholly replaced to provide nucleic acid molecules having enhanced properties (e.g., resistance to nucleases and stability), and these properties may manifest through disruption of the binding of a major groove binding partner. In some embodiments, the alternative nucleobase is an alternative uracil. Exemplary nucleobases and nucleosides having an alternative uracil include pseudouridine (ψ), pyridin-4-one ribonucleoside, 5-aza- uridine, 6-aza-uridine, 2-thio-5-aza-uridine, 2-thio-uridine (s2U), 4-thio-uridine (s4U), 4-thio-pseudouridine, 2- thio-pseudouridine, 5-hydroxy-uridine (ho5U), 5-aminoallyl-uridine, 5-halo-uridine (e.g., 5-iodo-uridineor 5- bromo-uridine), 3-methyl-uridine (m3U), 5-methoxy-uridine (mo5U), uridine 5-oxyacetic acid (cmo5U), uridine 5-oxyacetic acid methyl ester (mcmo5U), 5-carboxymethyl-uridine (cm5U), 1-carboxymethyl-pseudouridine, 5-carboxyhydroxymethyl-uridine (chm5U), 5-carboxyhydroxymethyl-uridine methyl ester (mchm5U), 5- methoxycarbonylmethyl-uridine (mcm5U), 5-methoxycarbonylmethyl-2-thio-uridine (mcm5s2U), 5- aminomethyl-2-thio-uridine (nm5s2U), 5-methylaminomethyl-uridine (mnm5U), 5-methylaminomethyl-2-thio- PATENT ATTORNEY DOCKET NO.50858-164WO2 uridine (mnm5s2U), 5-methylaminomethyl-2-seleno-uridine (mnm5se2U), 5-carbamoylmethyl-uridine (ncm5U), 5-carboxymethylaminomethyl-uridine (cmnm5U), 5-carboxymethylaminomethyl-2-thio-uridine (cmnm5s2U), 5- propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyl-uridine (τm5U), 1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio-uridine(τm5s2U), 1-taurinomethyl-4-thio-pseudouridine, 5-methyl-uridine (m5U, i.e., having the nucleobase deoxythymine), 1-methyl-pseudouridine (m1ψ), 5-methyl-2-thio-uridine (m5s2U), 1- methyl-4-thio-pseudouridine (m1s4ψ), 4-thio-1-methyl-pseudouridine, 3-methyl-pseudouridine (m3ψ), 2-thio-1- methyl-pseudouridine, 1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine (D), dihydropseudouridine, 5,6-dihydrouridine, 5-methyl-dihydrouridine (m5D), 2-thio- dihydrouridine, 2-thio-dihydropseudouridine, 2-methoxy-uridine, 2-methoxy-4-thio-uridine, 4-methoxy- pseudouridine, 4-methoxy-2-thio-pseudouridine, N1-methyl-pseudouridine, 3-(3-amino-3- carboxypropyl)uridine (acp3U), 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine (acp3ψ), 5- (isopentenylaminomethyl)uridine (inm5U), 5-(isopentenylaminomethyl)-2-thio-uridine (inm5s2U), α-thio- uridine, 2′-O-methyl-uridine (Um), 5,2′-O-dimethyl-uridine (m5Um), 2′-O-methyl-pseudouridine (ψm), 2-thio-2′- O-methyl-uridine (s2Um), 5-methoxycarbonylmethyl-2′-O-methyl-uridine (mcm5Um), 5-carbamoylmethyl-2′-O- methyl-uridine (ncm5Um), 5-carboxymethylaminomethyl-2′-O-methyl-uridine (cmnm5Um), 3,2′-O-dimethyl- uridine (m3Um), and 5-(isopentenylaminomethyl)-2′-O-methyl-uridine (inm5Um), 1-thio-uridine, deoxythymidine, 2’‐F‐ara‐uridine, 2’‐F‐uridine, 2’‐OH‐ara‐uridine, 5‐(2‐carbomethoxyvinyl) uridine, and 5‐[3‐ (1‐E‐propenylamino)uridine. In preferred embodiments, the nucleic acid is modified to contain 1-methylpseudouridine (m1ψ) in lieu of uridine at each instance. In some embodiments, the alternative nucleobase is an alternative cytosine. Exemplary nucleobases and nucleosides having an alternative cytosine include 5-aza-cytidine, 6-aza-cytidine, pseudoisocytidine, 3- methyl-cytidine (m3C), N4-acetyl-cytidine (ac4C), 5-formyl-cytidine (f5C), N4-methyl-cytidine (m4C), 5-methyl- cytidine (m5C), 5-halo-cytidine (e.g., 5-iodo-cytidine), 5-hydroxymethyl-cytidine (hm5C), 1-methyl- pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine, 2-thio-cytidine (s2C), 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine, 4-thio-1-methyl-pseudoisocytidine, 4-thio-1-methyl-1-deaza-pseudoisocytidine, 1- methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5-methyl-zebularine, 5-aza-2-thio- zebularine, 2-thio-zebularine, 2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine, 4-methoxy- pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine, lysidine (k2C), α-thio-cytidine, 2′-O-methyl- cytidine (Cm), 5,2′-O-dimethyl-cytidine (m5Cm), N4-acetyl-2′-O-methyl-cytidine (ac4Cm), N4,2′-O-dimethyl- cytidine (m4Cm), 5-formyl-2′-O-methyl-cytidine (f5Cm), N4,N4,2′-O-trimethyl-cytidine (m42Cm), 1-thio-cytidine, 2’‐F‐ara‐cytidine, 2’‐F‐cytidine, and 2’‐OH‐ara‐cytidine. In some embodiments, the alternative nucleobase is an alternative adenine. Exemplary nucleobases and nucleosides having an alternative adenine include 2-amino-purine, 2, 6-diaminopurine, 2-amino-6-halo- purine (e.g., 2-amino-6-chloro-purine), 6-halo-purine (e.g., 6-chloro-purine), 2-amino-6-methyl-purine, 8- azido-adenosine, 7-deaza-adenine, 7-deaza-8-aza-adenine, 7-deaza-2-amino-purine, 7-deaza-8-aza-2- amino-purine, 7-deaza-2,6-diaminopurine, 7-deaza-8-aza-2,6-diaminopurine, 1-methyl-adenosine (m1A), 2- methyl-adenine (m2A), N6-methyl-adenosine (m6A), 2-methylthio-N6-methyl-adenosine (ms2m6A), N6- isopentenyl-adenosine (i6A), 2-methylthio-N6-isopentenyl-adenosine (ms2i6A), N6-(cis- hydroxyisopentenyl)adenosine (io6A), 2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine (ms2io6A), N6- glycinylcarbamoyl-adenosine (g6A), N6-threonylcarbamoyl-adenosine (t6A), N6-methyl-N6- PATENT ATTORNEY DOCKET NO.50858-164WO2 threonylcarbamoyl-adenosine (m6t6A), 2-methylthio-N6-threonylcarbamoyl-adenosine (ms2g6A), N6,N6- dimethyl-adenosine (m62A), N6-hydroxynorvalylcarbamoyl-adenosine (hn6A), 2-methylthio-N6- hydroxynorvalylcarbamoyl-adenosine (ms2hn6A), N6-acetyl-adenosine (ac6A), 7-methyl-adenine, 2- methylthio-adenine, 2-methoxy-adenine, α-thio-adenosine, 2′-O-methyl-adenosine (Am), N6,2′-O-dimethyl- adenosine (m6Am), N6,N6,2′-O-trimethyl-adenosine (m62Am), 1,2′-O-dimethyl-adenosine (m1Am), 2′-O- ribosyladenosine (phosphate) (Ar(p)), 2-amino-N6-methyl-purine, 1-thio-adenosine, 8-azido-adenosine, 2’‐F‐ ara‐adenosine, 2’‐F‐adenosine, 2’‐OH‐ara‐adenosine, and N6‐(19‐amino‐pentaoxanonadecyl)-adenosine. In some embodiments, the alternative nucleobase is an alternative guanine. Exemplary nucleobases and nucleosides having an alternative guanine include inosine (I), 1-methyl-inosine (m1I), wyosine (imG), methylwyosine (mimG), 4-demethyl-wyosine (imG-14), isowyosine (imG2), wybutosine (yW), peroxywybutosine (o2yW), hydroxywybutosine (OhyW), undermodified hydroxywybutosine (OhyW*), 7- deaza-guanosine, queuosine (Q), epoxyqueuosine (oQ), galactosyl-queuosine (galQ), mannosyl-queuosine (manQ), 7-cyano-7-deaza-guanosine (preQ0), 7-aminomethyl-7-deaza-guanosine (preQ1), archaeosine (G+), 7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine, 6-thio-7-deaza-8-aza-guanosine, 7- methyl-guanosine (m7G), 6-thio-7-methyl-guanosine, 7-methyl-inosine, 6-methoxy-guanosine, 1-methyl- guanosine (m1G), N2-methyl-guanosine (m2G), N2,N2-dimethyl-guanosine (m22G), N2,7-dimethyl-guanosine (m2,7G), N2, N2,7-dimethyl-guanosine (m2,2,7G), 8-oxo-guanosine, 7-methyl-8-oxo-guanosine, 1-methyl-6- thio-guanosine, N2-methyl-6-thio-guanosine, N2,N2-dimethyl-6-thio-guanosine, α-thio-guanosine, 2′-O- methyl-guanosine (Gm), N2-methyl-2′-O-methyl-guanosine (m2Gm), N2,N2-dimethyl-2′-O-methyl-guanosine (m22Gm), 1-methyl-2′-O-methyl-guanosine (m1Gm), N2,7-dimethyl-2′-O-methyl-guanosine (m2,7Gm), 2′-O- methyl-inosine (Im), 1,2′-O-dimethyl-inosine (m1Im), 2′-O-ribosylguanosine (phosphate) (Gr(p)) , 1-thio- guanosine, O6-methyl-guanosine, 2’‐F‐ara‐guanosine, and 2’‐F‐guanosine. The nucleobase of the nucleotide can be independently selected from a purine, a pyrimidine, a purine, or pyrimidine analog. For example, the nucleobase can each be independently selected from the group consisting of adenine, cytosine, guanine, uracil, and hypoxanthine. In some embodiments, the nucleobase can also include, for example, naturally-occurring and synthetic derivatives of a base, including pyrazolo[3,4-d]pyrimidines, 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2- aminoadenine, 6-methyl, and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo (e.g., 8-bromo), 8- amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5- bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7- methyladenine, 8-azaguanine and 8-azaadenine, deazaguanine, 7-deazaguanine, 3-deazaguanine, deazaadenine, 7-deazaadenine, 3-deazaadenine, pyrazolo[3,4-d]pyrimidine, imidazo[1,5-a]1,3,5 triazinones, 9-deazapurines, imidazo[4,5-d]pyrazines, thiazolo[4,5-d]pyrimidines, pyrazin-2-ones, 1,2,4-triazine, pyridazine; and 1,3,5 triazine. When the nucleotides are depicted using the shorthand A, G, C, T or U, each letter refers to the representative base and / or derivatives thereof (e.g., A includes adenine or adenine analogs (e.g., 7-deaza adenine)). In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5-methyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5-trifluoromethyl-cytosine, and PATENT ATTORNEY DOCKET NO.50858-164WO2 cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5-hydroxymethyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy- uracil, uracil, 5-bromo-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5-iodo-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5-methoxy-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5-ethyl- cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5-phenyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy- uracil, uracil, 5-ethnyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, N4-methyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5-fluoro-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, N4-acetyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, pseudoisocytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5-formyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5- aminoallyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uracil, uracil, 5-carboxy-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl- pseudouracil, uracil, 5-methyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, 5- trifluoromethyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, 5-hydroxymethyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, 5-bromo-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl- pseudouracil, uracil, 5-iodo-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, 5-methoxy- cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, 5-ethyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1- methyl-pseudouracil, uracil, 5-phenyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, 5- ethnyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, N4-methyl-cytosine, and cytosine as PATENT ATTORNEY DOCKET NO.50858-164WO2 the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, 5-fluoro-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, N4-acetyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, pseudoisocytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, 5-formyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl- pseudouracil, uracil, 5-aminoallyl-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 1-methyl-pseudouracil, uracil, 5- carboxy-cytosine, and cytosine as the only uracils and cytosines. In some embodiments, the nucleic acids encoding PNEs of the disclosure of the invention contain 5- methoxy-uridine, uridine, 5-methyl-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, 5- trifluoromethyl-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, 5-hydroxymethyl-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, 5-bromo-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy- uridine, uridine, 5-iodo-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, 5-methoxy-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, 5-ethyl-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy- uridine, uridine, 5-phenyl-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, 5-ethnyl-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, N4-methyl-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy- uridine, uridine, 5-fluoro-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, N4-acetyl-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, pseudoisocytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy- uridine, uridine, 5-formyl-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, 5-aminoallyl-cytidine, and cytidine as the only uridines and cytidines. In some embodiments, the nucleic acids encoding PNEs of the disclosure contain 5-methoxy-uridine, uridine, 5-carboxy-cytidine, and cytidine as the only uridines and cytidines. In some embodim...

Claims

PATENT ATTORNEY DOCKET NO.50858-164WO2 CLAIMS 1. A CRISPR-associated (Cas) nuclease comprising a polypeptide having an amino acid sequence that is at least 85% identical to the amino acid sequence of any one of SEQ ID NOs: 1-53.

2. The Cas nuclease of claim 1, wherein the amino acid sequence of the polypeptide is 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 the amino acid sequence of any one of SEQ ID NOs: 1-53.

3. The Cas nuclease of claim 1 or 2, wherein the amino acid sequence of the polypeptide differs from the amino acid sequence of any one of SEQ ID NOs: 1-53 by way of 100 or fewer amino acids, resulting from insertions, deletions, or substitutions.

4. The Cas nuclease of claim 1 or 2, wherein the amino acid sequence of the polypeptide differs from the amino acid sequence of any one of SEQ ID NOs: 1-53 by way of 90 or fewer, 85 or fewer, 80 or fewer, 75 or fewer, 70 or fewer, 65 or fewer, 60 or fewer, 55 or fewer, 50 or fewer, 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from insertions, deletions, or substitutions.

5. The Cas nuclease of claim 3 or 4, wherein the amino acid sequence of the polypeptide differs from the amino acid sequence of any one of SEQ ID NOs: 1-53 only by way of 100 or fewer amino acids, resulting from substitutions.

6. The Cas nuclease of claim 5, wherein the amino acid sequence of the polypeptide differs from the amino acid sequence of any one of SEQ ID NOs: 1-53 only by way of 90 or fewer, 85 or fewer, 80 or fewer, 75 or fewer, 70 or fewer, 65 or fewer, 60 or fewer, 55 or fewer, 50 or fewer, 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from substitutions.

7. The Cas nuclease of any one of claims 3-6, wherein the amino acid substitutions are conservative amino acid substitutions.

8. The Cas nuclease of any one of claims 1-7, wherein the Cas nuclease comprises a RuvC domain.

9. The Cas nuclease of any one of claims 1-8, wherein the Cas nuclease comprises a RuvC domain having an amino acid sequence that is at least 60% identical to the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508.

10. The Cas nuclease of claim 8 or 9, wherein the amino acid sequence of the RuvC domain is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508.PATENT ATTORNEY DOCKET NO.50858-164WO2 11. The Cas nuclease of any one of claims 8-10, wherein the amino acid sequence of the RuvC domain differs from the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508 by way of 50 or fewer amino acids, resulting from insertions, deletions, or substitutions.

12. The Cas nuclease of any one of claims 8-10, wherein the amino acid sequence of the RuvC domain differs from the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508 by way of 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from insertions, deletions, or substitutions.

13. The Cas nuclease of claim 11 or 12, wherein the amino acid sequence of the RuvC domain differs from the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508 only by way of 50 or fewer amino acids, resulting from substitutions.

14. The Cas nuclease of claim 13, wherein the amino acid sequence of the RuvC domain differs from the amino acid sequence of any one of SEQ ID NOs: 107-148 and 503-508 only by way of 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from substitutions.

15. The Cas nuclease of any one of claims 11-14, wherein the amino acid substitutions are conservative amino acid substitutions.

16. The Cas nuclease of any one of claims 1-15, wherein the Cas nuclease comprises an HNH domain.

17. The Cas nuclease of any one of claims 1-16, wherein the Cas nuclease comprises an HNH domain having an amino acid sequence that is at least 60% identical to the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510.

18. The Cas nuclease of claim 16 or 17, wherein the amino acid sequence of the HNH domain is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510.

19. The Cas nuclease of any one of claims 16-18, wherein the amino acid sequence of the HNH domain differs from the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510 by way of 50 or fewer amino acids, resulting from insertions, deletions, or substitutions.

20. The Cas nuclease of any one of claims 16-18, wherein the amino acid sequence of the HNH domain differs from the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510 by way of 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from insertions, deletions, or substitutions.PATENT ATTORNEY DOCKET NO.50858-164WO2 21. The Cas nuclease of claim 19 or 20, wherein the amino acid sequence of the HNH domain differs from the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510 only by way of 50 or fewer amino acids, resulting from substitutions.

22. The Cas nuclease of claim 21, wherein the amino acid sequence of the HNH domain differs from the amino acid sequence of any one of SEQ ID NOs: 149-162, 509, and 510 only by way of 45 or fewer, 40 or fewer, 35 or fewer, 30 or fewer, 25 or fewer, 20 or fewer, 15 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids, resulting from substitutions.

23. The Cas nuclease of any one of claims 19-22, wherein the amino acid substitutions are conservative amino acid substitutions.

24. The Cas nuclease of any one of claims 1-23, wherein the Cas nuclease has double-strand break activity toward a target DNA polynucleotide.

25. The Cas nuclease of any one of claims 1-7 and 9-24, wherein the Cas nuclease comprises one or more mutations in a RuvC domain that render the RuvC domain inactive.

26. The Cas nuclease of any one of claims 1-15 and 17-25, wherein the Cas nuclease comprises one or more mutations in an HNH domain that render the HNH domain inactive.

27. The Cas nuclease of claim 25 or 26, wherein the Cas nuclease has single-stranded break activity toward a target DNA polynucleotide.

28. The Cas nuclease of any one of claims 1-27, wherein the Cas nuclease is a fusion protein comprising the polypeptide bound to one or more additional protein domains.

29. The Cas nuclease of claim 28, wherein the one or more additional protein domains comprise a peptide that localizes to one or more subcellular organelles.

30. The Cas nuclease of claim 29, wherein the one or more additional protein domains comprise a nuclear localization sequence (NLS).

31. The Cas nuclease of any one of claims 28-30, wherein the one or more additional protein domains comprises a base editor domain.

32. The Cas nuclease of claim 31, wherein the base editor domain is an adenosine deaminase domain or a cytidine deaminase domain.

33. The Cas nuclease of any one of claims 28-32, wherein the one or more additional protein domains comprises a reverse transcriptase domain.

34. The Cas nuclease of any one of claims 1-33, wherein the Cas nuclease specifically binds a target DNA polynucleotide having a protospacer-adjacent motif (PAM) sequence set forth in Table 7.PATENT ATTORNEY DOCKET NO.50858-164WO2 35. A Cas nuclease having a TM-score of at least 0.80 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, wherein the three-dimensional structure is calculated using Alphafold.

36. The Cas nuclease of claim 35, wherein the Cas nuclease has a TM-score of at least 0.85 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, optionally wherein the Cas nuclease has a TM-score of at least 0.90 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, optionally wherein the Cas nuclease has a TM-score of at least 0.95 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1- 53, optionally wherein the Cas nuclease has a TM-score of at least 1.0 compared to the three-dimensional structure of the Cas nuclease of any one of SEQ ID NOs: 1-53, wherein the three-dimensional structure is calculated using Alphafold.

37. A nucleic acid encoding the Cas nuclease of any one of claims 1-36, optionally wherein the nucleic acid is a chemically modified nucleic acid.

38. The nucleic acid of claim 37, wherein the nucleic acid is DNA.

39. The nucleic acid of claim 37, wherein the nucleic acid is RNA.

40. The nucleic acid of any one of claims 37-39, wherein the nucleic acid is linear.

41. The nucleic acid of any one of claims 37-39, wherein the nucleic acid is circular.

42. The nucleic acid of any one of claims 39-41, wherein the RNA is an mRNA comprising one or more, or all, of: (e) a 5’ untranslated region (UTR); (f) an open reading frame (ORF) encoding the Cas nuclease; (g) a 3’ UTR; and (h) a poly-adenylyl (polyA) tail.

43. The nucleic acid of claim 42, further comprising a 5’ cap located 5’ relative to the 5’ UTR.

44. The nucleic acid of claim 42 or 43, wherein the open reading frame consists of nucleosides selected from the group consisting of adenosine, a modified adenosine, uridine, a modified uridine, guanosine, a modified guanosine, cytidine, and a modified cytidine.

45. The nucleic acid of claim 44, wherein the open reading frame consists of nucleosides selected from the group consisting of adenosine, uridine, a modified uridine, guanosine, and cytidine.

46. The nucleic acid of claim 44 or 45, wherein the modified uridine of the open reading frame is selected from the group consisting of 1-methylpseudouridine, pseudouridine, pyridin-4-one ribonucleoside, 5- aza-uridine, 6-aza-uridine, 2-thio-5-aza-uridine, 2-thio-uridine, 4-thio-uridine, 4-thio-pseudouridine, 2-thio- pseudouridine, 5-hydroxy-uridine, 5-aminoallyl-uridine, 5-halo-uridine, 3-methyl-uridine, 5-methoxy-uridine, uridine 5-oxyacetic acid, uridine 5-oxyacetic acid methyl ester, 5-carboxymethyl-uridine, 1-carboxymethyl- pseudouridine, 5-carboxyhydroxymethyl-uridine, 5-carboxyhydroxymethyl-uridine methyl ester, 5-PATENT ATTORNEY DOCKET NO.50858-164WO2 methoxycarbonylmethyl-uridine, 5-methoxycarbonylmethyl-2-thio-uridine, 5-aminomethyl-2-thio-uridine, 5- methylaminomethyl-uridine, 5-methylaminomethyl-2-thio-uridine, 5-methylaminomethyl-2-seleno-uridine, 5- carbamoylmethyl-uridine, 5-carboxymethylaminomethyl-uridine, 5-carboxymethylaminomethyl-2-thio-uridine, 5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyl-uridine, 1-taurinomethyl-pseudouridine, 5- taurinomethyl-2-thio-uridine, 1-taurinomethyl-4-thio-pseudouridine, 5-methyl-uridine, 5-methyl-2-thio-uridine, 1-methyl-4-thio-pseudouridine, 4-thio-1-methyl-pseudouridine, 3-methylpseudouridine, 2-thio-1-methyl- pseudouridine, 1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine, dihydropseudouridine, 5,6-dihydrouridine, 5-methyl-dihydrouridine, 2-thio-dihydrouridine, 2-thio- dihydropseudouridine, 2-methoxy-uridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine, 4-methoxy-2- thio-pseudouridine, N1-methyl-pseudouridine, 3-(3-amino-3-carboxypropyl)uridine, 1-methyl-3-(3-amino-3- carboxypropyl)pseudouridine, 5-(isopentenylaminomethyl)uridine, 5-(isopentenylaminomethyl)-2-thio-uridine, α-thio-uridine, 2′-O-methyl-uridine, 5,2′-O-dimethyl-uridine, 2′-O-methyl-pseudouridine, 2-thio-2′-O-methyl- uridine, 5-methoxycarbonylmethyl-2′-O-methyl-uridine, 5-carbamoylmethyl-2′-O-methyl-uridine, 5- carboxymethylaminomethyl-2′-O-methyl-uridine, 3,2′-O-dimethyl-uridine, 5-(isopentenylaminomethyl)-2′-O- methyl-uridine, 1-thio-uridine, deoxythymidine, 2’‐F‐ara‐uridine, 2’‐F‐uridine, 2’‐OH‐ara‐uridine, 5‐(2‐ carbomethoxyvinyl) uridine, and 5‐[3‐(1‐E‐propenylamino)uridine.

47. The nucleic acid of claim 46, wherein the modified uridine of the open reading frame is 1- methylpseudouridine.

48. The nucleic acid of any one of claims 44, 46, and 47, wherein the modified cytidine of the open reading frame is selected from the group consisting of 5-aza-cytidine, 6-aza-cytidine, pseudoisocytidine, 3- methyl-cytidine, N4-acetyl-cytidine, 5-formyl-cytidine, N4-methyl-cytidine, 5-methyl-cytidine, 5-halo-cytidine, 5-hydroxymethyl-cytidine, 1-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine, 2-thio- cytidine, 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine, 4-thio-1-methyl-pseudoisocytidine, 4-thio-1- methyl-1-deaza-pseudoisocytidine, 1-methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5- methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine, 2-methoxy-cytidine, 2-methoxy-5-methyl- cytidine, 4-methoxy-pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine, lysidine, α-thio-cytidine, 2′-O- methyl-cytidine, 5,2′-O-dimethyl-cytidine, N4-acetyl-2′-O-methyl-cytidine, N4,2′-O-dimethyl-cytidine, 5-formyl- 2′-O-methyl-cytidine, N4,N4,2′-O-trimethyl-cytidine, 1-thio-cytidine, 2’‐F‐ara‐cytidine, 2’‐F‐cytidine, and 2’‐ OH‐ara‐cytidine.

49. The nucleic acid of any one of claims 44 and 46-48, wherein the modified adenosine of the open reading frame is selected from the group consisting of 2-amino-purine, 2, 6-diaminopurine, 2-amino-6-halo- purine, 6-halo-purine, 2-amino-6-methyl-purine, 8-azido-adenosine, 7-deaza-adenine, 7-deaza-8-aza- adenine, 7-deaza-2-amino-purine, 7-deaza-8-aza-2-amino-purine, 7-deaza-2,6-diaminopurine, 7-deaza-8- aza-2,6-diaminopurine, 1-methyl-adenosine, 2-methyl-adenine, N6-methyl-adenosine, 2-methylthio-N6- methyl-adenosine, N6-isopentenyl-adenosine, 2-methylthio-N6-isopentenyl-adenosine, N6-(cis- hydroxyisopentenyl)adenosine, 2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine, N6-glycinylcarbamoyl- adenosine, N6-threonylcarbamoyl-adenosine, N6-methyl-N6-threonylcarbamoyl-adenosine, 2-methylthio-N6- threonylcarbamoyl-adenosine, N6,N6-dimethyl-adenosine, N6-hydroxynorvalylcarbamoyl-adenosine, 2- methylthio-N6-hydroxynorvalylcarbamoyl-adenosine, N6-acetyl-adenosine, 7-methyl-adenine, 2-methylthio-PATENT ATTORNEY DOCKET NO.50858-164WO2 adenine, 2-methoxy-adenine, α-thio-adenosine, 2′-O-methyl-adenosine, N6,2′-O-dimethyl-adenosine, N6,N6,2′-O-trimethyl-adenosine, 1,2′-O-dimethyl-adenosine, 2′-O-ribosyladenosine, 2-amino-N6-methyl- purine, 1-thio-adenosine, 8-azido-adenosine, 2’‐F‐ara‐adenosine, 2’‐F‐adenosine, 2’‐OH‐ara‐adenosine, and N6‐(19‐amino‐pentaoxanonadecyl)-adenosine.

50. The nucleic acid of any one of claims 44 and 46-49, wherein the modified guanosine of the open reading frame is selected from the group consisting of inosine, 1-methyl-inosine, wyosine, methylwyosine, 4- demethyl-wyosine, isowyosine, wybutosine, peroxywybutosine, hydroxywybutosine, 7-deaza-guanosine, queuosine, epoxyqueuosine, galactosyl-queuosine, mannosyl-queuosine, 7-cyano-7-deaza-guanosine, 7- aminomethyl-7-deaza-guanosine, archaeosine, 7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza- guanosine, 6-thio-7-deaza-8-aza-guanosine, 7-methyl-guanosine, 6-thio-7-methyl-guanosine, 7-methyl- inosine, 6-methoxy-guanosine, 1-methyl-guanosine, N2-methyl-guanosine, N2,N2-dimethyl-guanosine, N2,7- dimethyl-guanosine, N2, N2,7-dimethyl-guanosine, 8-oxo-guanosine, 7-methyl-8-oxo-guanosine, 1-methyl-6- thio-guanosine, N2-methyl-6-thio-guanosine, N2,N2-dimethyl-6-thio-guanosine, α-thio-guanosine, 2′-O- methyl-guanosine, N2-methyl-2′-O-methyl-guanosine, N2,N2-dimethyl-2′-O-methyl-guanosine, 1-methyl-2′- O-methyl-guanosine, N2,7-dimethyl-2′-O-methyl-guanosine, 2′-O-methyl-inosine, 1,2′-O-dimethyl-inosine, 2′- O-ribosylguanosine, 1-thio-guanosine, O6-methyl-guanosine, 2’‐F‐ara‐guanosine, and 2’‐F‐guanosine.

51. A synthetic composition comprising the Cas nuclease of any one of claims 1-36 or the nucleic acid of any one of claims 37-50.

52. The composition of claim 51, further comprising one or more carriers, diluents, or excipients.

53. The composition of claim 51 or 52, wherein the composition further comprises a guide RNA (gRNA) comprising (i) a CRISPR RNA (crRNA) and (ii) a trans activating RNA (tracrRNA).

54. The composition of claim 53, wherein the crRNA and the tracrRNA are separate RNA molecules.

55. The composition of claim 53, wherein the crRNA and the tracrRNA are present within a single RNA molecule (sgRNA).

56. The composition of any one of claims 53-55, wherein the crRNA comprises a polynucleotide having a nucleic acid sequence that is at least 60% identical to the nucleic acid sequence of any one of SEQ ID NOs: 216 and 292-319.

57. The composition of claim 56, wherein the nucleic acid sequence of the crRNA polynucleotide is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 the nucleic acid sequence of any one of SEQ ID NOs: 216 and 292-319.

58. The composition of any one of claims 53-57, wherein the tracrRNA comprises a polynucleotide having a nucleic acid sequence that is at least 60% identical to the nucleic acid sequence of any one of SEQ ID NOs: 163-215 and 270-291.PATENT ATTORNEY DOCKET NO.50858-164WO2 59. The composition of claim 58, wherein the nucleic acid sequence of the tracrRNA polynucleotide is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 the nucleic acid sequence of any one of SEQ ID NOs: 163-215 and 270-291.

60. The composition of any one of claims 55-59, wherein the sgRNA comprises a polynucleotide having a nucleic acid sequence that is at least 60% identical to the nucleic acid sequence of any one of SEQ ID NOs: 217-269 and 320-371.

61. The composition of claim 60, wherein the nucleic acid sequence of the sgRNA polynucleotide is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 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 the nucleic acid sequence of any one of SEQ ID NOs: 217-269 and 320-371.

62. The composition of any one of claims 51-61, further comprising a base editor enzyme.

63. The composition of claim 62, wherein the base editor enzyme is an adenosine deaminase or a cytidine deaminase.

64. The composition of any one of claims 51-63, further comprising a reverse transcriptase enzyme.

65. The composition of any one of claims 51-64, further comprising a template DNA polynucleotide for homology-directed repair (HDR) of a target DNA polynucleotide.

66. The composition of any one of claims 51-65, wherein the composition is a population of lipid nanoparticles (LNPs).

67. The composition of claim 66, wherein the LNPs comprise one or more, or all, of (i) a neutral lipid; (ii) a cationic lipid; (iii) a PEGylated lipid; and (iv) a sterol.

68. The composition of claim 66 or 67, wherein the population of LNPs has a mean particle size of from 80 nm to 160 nm.

69. The composition of any one of claims 66-68, wherein the population of LNPs has a polydispersity index PDI of from 0.02 to 0.2, 70. The composition of any one of claims 66-69, wherein the population of LNPs has a mean lipid to polynucleotide ratio (wt / wt) of from 10 to 20.

71. A genetically engineered host cell comprising the Cas nuclease of any one of claims 1-36, the nucleic acid of any one of claims 37-50, or the composition of any one of claims 51-70, wherein the Cas nuclease is heterologous with respect to the host cell.

72. The host cell of claim 71, wherein the host cell is a eukaryotic cell.

73. The host cell of claim 72, wherein the eukaryotic cell is a mammalian cell.PATENT ATTORNEY DOCKET NO.50858-164WO2 74. The host cell of claim 73, wherein the mammalian cell is a modified human cell.

75. A method of modifying the nucleic acid sequence of a target DNA polynucleotide, the method comprising contacting the target DNA polynucleotide with the Cas nuclease of any one of claims 1-36, the nucleic acid of any one of claims 37-50, or the composition of any one of claims 51-70.

76. A method of introducing a single nucleotide substitution into a target DNA polynucleotide, the method comprising contacting the target DNA polynucleotide with the Cas nuclease of any one of claims 1- 36, the nucleic acid of any one of claims 37-50, or the composition of any one of claims 51-70, wherein (i) the Cas nuclease comprises a base editor domain or (ii) the composition further comprises a base editor enzyme.

77. A method of replacing a target nucleic acid sequence with a template nucleic acid sequence in a target DNA polynucleotide, the method comprising contacting the target DNA polynucleotide with the Cas nuclease of any one of claims 1-36, the nucleic acid of any one of claims 37-50, or the composition of any one of claims 51-70, wherein (i) the Cas nuclease comprises a reverse transcriptase domain or (ii) the composition further comprises a reverse transcriptase enzyme.

78. A kit comprising the Cas nuclease of any one of claims 1-36, the nucleic acid of any one of claims 37-50, or the composition of any one of claims 51-70.

79. The kit of claim 78, wherein the kit further comprises a package insert instructing a user of the kit to conduct the method of any one of claims 75-77.