Oligonucleotide compositions and methods thereof

Abstract

The present disclosure provides, inter alia, oligonucleotides, compositions, and methods thereof, which are useful for adenosine modification. In some embodiments, the disclosure provides methods for treating various conditions, disorders, or diseases that can benefit from adenosine modification.

Claims

1. An oligonucleotide comprising: a first domain, wherein the first domain is about 10 nucleobases in length or more; a second domain, wherein the second domain is about 10 nucleobases in length or more; and 2'-F modified sugar; in: The base sequence of the first domain is complementary to the first part of the base sequence of the target nucleic acid; The base sequence of the second domain is complementary to the second portion of the base sequence of the target RNA nucleic acid; The first portion and the second portion of the base sequence of the target RNA nucleic acid are separated by a gap of about or at least about 50, 100, 200, 500, or 1000 nucleobases in the target nucleic acid; and The oligonucleotide is about 25-50 nucleobases in length.

2. An oligonucleotide comprising: A first domain; and The second domain, in: The base sequence of the first domain is complementary to the first part of the base sequence of the target nucleic acid; The base sequence of the second domain is complementary to the second part of the base sequence of the target nucleic acid; and The first part and the second part of the base sequence of the target nucleic acid are separated by a gap.

3. An oligonucleotide comprising: A first domain; and The second domain, in: The first domain is characterized in that it can form a duplex with a first portion of a target nucleic acid; The second domain is characterized in that it can form a duplex with a second portion of the target nucleic acid; and The first part and the second part of the base sequence of the target nucleic acid are separated by a gap.

4. The oligonucleotide of any one of claims 1 to 3, wherein the oligonucleotide comprises 5'-N1N0N -1 -3', where N -1 , N0 and N1 are each independently a nucleoside; and wherein the nucleobase of N0 is BA, wherein BA is 5. The oligonucleotide of any one of claims 1 to 3, wherein the oligonucleotide comprises 5'-N1N0N -1 -3', where N -1 , N0 and N1 are each independently a nucleoside; and wherein the nucleobase of N0 is BA, wherein BA comprises a ring BA or a tautomer thereof, wherein the ring BA has a structure of formula BA-III-e: in: X 1 is -N(-)- or -C(-)=; W X2 and W X6 Each of is independently O, S or Se; R B4 Is halogen, -CN, -NO2 or -L B4 -R B41 , where R B41 It is R'; R B5 Is halogen, -CN, -NO2 or -L B5 -R B51 , where R B51 is -R', -N(R')2, -OR' or -SR', L B4 and L B5 Each of which is independently L B ; Each L B is independently a covalent bond, or an optionally substituted divalent C 1-10 a saturated or partially unsaturated chain in which one or more methylene units are optionally and independently replaced by -Cy-, -O-, -S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, -C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)O-, -S(O)-, -S(O)2-, -S(O)2N(R')-, -C(O)S-, or -C(O)O-; Each -Cy- is independently an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms; each R' is independently -R, -C(O)R, -C(O)OR, -C(O)N(R)2, or -SO2R; and Each R is independently -H, or an optionally substituted group selected from the following: C 1-20 Aliphatic, C with 1-10 heteroatoms 1-20 Heteroaliphatic, C 6-20 Aryl, C 6-20 Aryl aliphatic group, C 6-20 arylheteroaliphatic, 5-20 membered heteroaryl having 1-10 heteroatoms, and 3-20 membered heterocyclyl having 1-10 heteroatoms, or Two R groups optionally and independently join together to form a covalent bond, or Two or more R groups on the same atom are optionally and independently taken together with that atom to form an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms in addition to that atom; or Two or more R groups on two or more atoms are optionally and independently taken together with the atoms between them to form an optionally substituted 3-30 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms in addition to the atoms between them.

6. The oligonucleotide of claim 4 or 5, wherein the sugar of NO comprises a 2'-OR modification, wherein R is an optionally substituted C 1-6 Aliphatic group.

7. The oligonucleotide of any one of claims 1 to 3, wherein the oligonucleotide comprises 5'-N1N0N -1 -3', where N -1 , N0 and N1 are each independently a nucleoside; and wherein the nucleobase of N0 is BA, wherein BA is 8. The oligonucleotide of any one of claims 1 to 3, wherein the oligonucleotide comprises 5'-N1N0N -1 -3', where N -1 , N0 and N1 are each independently a nucleoside; and wherein the nucleobase of N0 is BA, wherein BA comprises cyclic BA or a tautomer thereof, wherein cyclic BA has a structure of formula BA-VI: in: Each are independently a single bond or a double bond; X 1' is -N(-)- or -C(-)=; X 2’ Yes-C(W X2’ )-、-C(R B2’ )=、-C(OR B2’ )=, -N= or optionally substituted -CH= or -CH2-, wherein R B2’ Is a halogen, -CN, -NO2, or -L B2’ -R', and W X2’ is O, S or Se; X 3’ Yes-N(R B3’ )-、-N=、-C(R B3’ )= or optionally substituted -NH- or -CH=, wherein R B3’ Is a halogen, -CN, -NO2, or -L B3’ -R'; X 4’ Yes-C(R B4’ )=,-C(OR B4’ )=,-C(-N(R B4’ )2)=,-C(R B4’ )2-,-C(W X4’ )-,-C(=NR B4’ )-,-N(R B4’ )-, -N= or optionally substituted -CH=, -NH- or -CH2-, wherein each R B4’ are independently halogen, -CN, -NO2, or -L B4’ -R B41’ , or two R on the same atom B4’ Combined to form =O, =C(-L B4’ -R B41’ )2, =NL B4’ -R B41’ , or optionally substituted =CH2 or =NH, wherein each R B41’ are independently -R', and W X4’ is O, S or Se; X 5’ Yes-C(R B5’ )2-,-N(R B5’ )-,-C(R B5’ )=,-C(W X5’ )-, -N=, or optionally substituted -NH-, -CH2-, or -CH=, wherein each R B5’ are independently halogen, -CN, -NO2, or -L B5’ -R B51’ , where R B51’ is -R', -N(R')2, -OR', or -SR', and W X5’ is O, S, or Se; X 6’ Yes-C(R B6’ )=,-C(OR B6’ )=,-C(R B6’ )2-,-C(W X6’ )-,-C(-N(R B6’ )2)=, -N= or optionally substituted -NH-, -CH2- or -CH=, wherein each R B6’ are independently halogen, -CN, -NO2, or -L B6’ -R B61’ , or two R on the same atom B6’ Combined to form =O, =C(-L B6’ -R B61’ )2, =NL B6’ -R B61’ , or optionally substituted =CH2 or =NH, wherein each R B61’ are independently R', and W X6’ is O, S or Se; X 7’ Yes-C(R B7’ )=,-C(OR B7’ )=,-C(R B7’ )2-,-C(W X7’ )-,-C(-N(R B7’ )2)=,-N(R B7’ )-, -N= or optionally substituted -NH-, -CH2- or -CH=, wherein each R B7’ are independently halogen, -CN, -NO2, or -L B7’ -R B71’ , or two R on the same atom B7’ Combined to form =O, =C(-L B7’ -R B71’ )2, =NL B7’ -R B71’ , or optionally substituted =CH2 or =NH, wherein each R B71’ are independently R', and where W X7’ is O, S or Se; X 8’ and X 9’ each independently is C or N; L B2’ , L B3’ , L B4’ , L B5’ , L B6’ and L B7’ Each is independently L B ;and Each L B is independently a covalent bond, or an optionally substituted divalent C 1-10 a saturated or partially unsaturated chain in which one or more methylene units are optionally and independently replaced by -Cy-, -O-, -S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, -C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)O-, -S(O)-, -S(O)2-, -S(O)2N(R')-, -C(O)S-, or -C(O)O-; Each -Cy- is independently an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms; each R' is independently -R, -C(O)R, -C(O)OR, -C(O)N(R)2, or -SO2R; and Each R is independently -H, or an optionally substituted group selected from the following: C 1-20 Aliphatic, C with 1-10 heteroatoms 1-20 Heteroaliphatic, C 6-20 Aryl, C 6-20 Aryl aliphatic group, C 6-20 arylheteroaliphatic, 5-20 membered heteroaryl having 1-10 heteroatoms, and 3-20 membered heterocyclyl having 1-10 heteroatoms, or Two R groups optionally and independently join together to form a covalent bond, or Two or more R groups on the same atom are optionally and independently taken together with that atom to form an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms in addition to that atom; or Two or more R groups on two or more atoms are optionally and independently taken together with the atoms between them to form an optionally substituted 3-30 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms in addition to the atoms between them.

9. The oligonucleotide of any one of the preceding claims, wherein the first domain is about 10-30 nucleobases in length.

10. The oligonucleotide of any one of the preceding claims, wherein the second domain is about 10-30 nucleobases in length.

11. The oligonucleotide of any of the preceding claims, wherein the gap is about or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 50, 60, 70, 80, 90, or 100 nucleobases in length.

12. The oligonucleotide of any one of the preceding claims, wherein the first domain is linked to the second domain via a linker, optionally wherein the linker is or comprises an oligonucleotide ("linker oligonucleotide").

13. The oligonucleotide of any of the preceding claims, wherein the adaptor oligonucleotide has no more than about 30%, 25%, 20%, 10%, or 5% complementarity to the gap in the target nucleic acid.

14. The oligonucleotide of any of the preceding claims, wherein the linker comprises polyvinyl ether, polyethylene, polypropylene, polyethylene glycol (PEG), polypropylene glycol (PEG), polyvinyl alcohol (PVA), polyglycolide (PGA), polylactic acid (PLA), polycaprolactone (PCL), or a copolymer thereof.

15. The oligonucleotide of any one of the preceding claims, wherein the target nucleic acid is mRNA.

16. The oligonucleotide of any one of the preceding claims, wherein when the oligonucleotide is contacted with a target nucleic acid comprising a target adenosine in a system, the target adenosine in the target nucleic acid is modified.

17. The oligonucleotide of any one of the preceding claims, wherein the target adenosine is a mutation from guanine.

18. The oligonucleotide of any of the preceding claims, wherein the oligonucleotide has about 10-200 (e.g., about 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-120, 10-150, 20-30, 20-40, 20-50, 20-60, 20-70, 20-80, 20-90, 20-100, 20-120, 20-150, 20-200, 25-30, 25-40 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, 70, 75, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100 19. The oligonucleotide of any one of the preceding claims, wherein the oligonucleotide has a length of about 30-40 nucleobases.

20. The oligonucleotide of any of the preceding claims, wherein the first domain has a length of about 2-50 (e.g., about 5, 6, 7, 8, 9, or 10 to about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40, or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40, or 50, etc.) nucleobases.

21. The oligonucleotide of any of the preceding claims, wherein at least about 1-50 (e.g., about 5, 6, 7, 8, 9, or 10 to about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40, or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40, or 50, etc., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40, or 50, etc.) chiral internucleotide linkages in the first domain are chirality controlled.

22. The oligonucleotide of any of the preceding claims, wherein the second domain has a length of about 2-50 (e.g., about 5, 6, 7, 8, 9, or 10 to about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40, or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40, or 50, etc.) nucleobases.

23. An oligonucleotide as described in any of the preceding claims, wherein the second domain comprises one or more (e.g., 1-10, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10, etc.) wobble pairs when the oligonucleotide is complementarily aligned with the target nucleic acid.

24. The oligonucleotide of any of the preceding claims, wherein the second domain comprises a nucleoside opposite to the target adenosine when the oligonucleotide is complementarily aligned with the target nucleic acid.

25. The oligonucleotide of claim 95, wherein the first and second domains each independently comprise a nucleoside opposite to the target adenosine when the oligonucleotide is complementarily aligned with a target nucleic acid.

26. The oligonucleotide of claim 25, wherein the first and second domains each independently comprise a nucleobase opposite to the target adenosine, wherein each opposite nucleobase comprises nucleobase BA, wherein BA is or comprises cyclic BA or a tautomer thereof, wherein cyclic BA has the structure of formula BA-III-e: in: X 1 is -N(-)- or -C(-)=; W X2 and W X6 Each of is independently O, S or Se; R B4 Is halogen, -CN, -NO2 or -L B4 -R B41 , where R B41 It is R'; R B5 Is halogen, -CN, -NO2 or -L B5 -R B51 , where R B51 is -R', -N(R')2, -OR' or -SR', L B4 and L B5 Each of which is independently L B ; Each L B is independently a covalent bond, or an optionally substituted divalent C 1-10 a saturated or partially unsaturated chain in which one or more methylene units are optionally and independently replaced by -Cy-, -O-, -S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, -C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)O-, -S(O)-, -S(O)2-, -S(O)2N(R')-, -C(O)S-, or -C(O)O-; Each -Cy- is independently an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms; each R' is independently -R, -C(O)R, -C(O)OR, -C(O)N(R)2, or -SO2R; and Each R is independently -H, or an optionally substituted group selected from the following: C 1-20 Aliphatic, C with 1-10 heteroatoms 1-20 Heteroaliphatic, C 6-20 Aryl, C 6-20 Aryl aliphatic group, C 6-20 arylheteroaliphatic, 5-20 membered heteroaryl having 1-10 heteroatoms, and 3-20 membered heterocyclyl having 1-10 heteroatoms, or Two R groups optionally and independently join together to form a covalent bond, or Two or more R groups on the same atom are optionally and independently taken together with that atom to form an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms in addition to that atom; or Two or more R groups on two or more atoms are optionally and independently taken together with the atoms between them to form an optionally substituted 3-30 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms in addition to the atoms between them.

27. The oligonucleotide of any one of claims 1-3, wherein the first and second domains each independently comprise a nucleobase opposite to the target adenosine, wherein each opposite nucleobase comprises nucleobase BA, wherein BA is or comprises cyclic BA or a tautomer thereof, wherein cyclic BA has the structure of formula BA-VI: in: Each are independently a single bond or a double bond; X 1' is -N(-)- or -C(-)=; X 2’ Yes-C(W X2’ )-、-C(R B2’ )=、-C(OR B2’ )=, -N= or optionally substituted -CH= or -CH2-, wherein R B2’ Is a halogen, -CN, -NO2, or -L B2’ -R', and W X2’ is O, S or Se; X 3’ Yes-N(R B3’ )-、-N=、-C(R B3’ )= or optionally substituted -NH- or -CH=, wherein R B3’ Is a halogen, -CN, -NO2, or -L B3’ -R'; X 4’ Yes-C(R B4’ )=,-C(OR B4’ )=,-C(-N(R B4’ )2)=,-C(R B4’ )2-,-C(W X4’ )-,-C(=NR B4’ )-,-N(R B4’ )-, -N= or optionally substituted -CH=, -NH- or -CH2-, wherein each R B4’ are independently halogen, -CN, -NO2, or -L B4’ -R B41’ , or two R on the same atom B4’ Combined to form =O, =C(-L B4’ -R B41’ )2, =NL B4’ -R B41’ , or optionally substituted =CH2 or =NH, wherein each R B41’ are independently -R', and W X4’ is O, S or Se; X 5’ Yes-C(R B5’ )2-,-N(R B5’ )-,-C(R B5’ )=,-C(W X5’ )-, -N=, or optionally substituted -NH-, -CH2-, or -CH=, wherein each R B5’ are independently halogen, -CN, -NO2, or -L B5’ -R B51’ , where R B51’ is -R', -N(R')2, -OR', or -SR', and W X5’ is O, S, or Se; X 6’ Yes-C(R B6’ )=,-C(OR B6’ )=,-C(R B6’ )2-,-C(W X6’ )-,-C(-N(R B6’ )2)=, -N= or optionally substituted -NH-, -CH2- or -CH=, wherein each R B6’ are independently halogen, -CN, -NO2, or -L B6’ -R B61’ , or two R on the same atom B6’ Combined to form =O, =C(-L B6’ -R B61’ )2, =NL B6’ -R B61’ , or optionally substituted =CH2 or =NH, wherein each R B61’ are independently R', and W X6’ is O, S or Se; X 7’ Yes-C(R B7’ )=,-C(OR B7’ )=,-C(R B7’ )2-,-C(W X7’ )-,-C(-N(R B7’ )2)=,-N(R B7’ )-, -N= or optionally substituted -NH-, -CH2- or -CH=, wherein each R B7’ are independently halogen, -CN, -NO2, or -L B7’ -R B71’ , or two R on the same atom B7’ Combined to form =O, =C(-L B7’ -R B71’ )2, =NL B7’ -R B71’ , or optionally substituted =CH2 or =NH, wherein each R B71’ are independently R', and where W X7’ is O, S or Se; X 8’ and X 9’ each independently is C or N; L B2’ , L B3’ , L B4’ , L B5’ , L B6’ and L B7’ Each is independently L B ;and Each L B is independently a covalent bond, or an optionally substituted divalent C 1-10 a saturated or partially unsaturated chain in which one or more methylene units are optionally and independently replaced by -Cy-, -O-, -S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, -C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)O-, -S(O)-, -S(O)2-, -S(O)2N(R')-, -C(O)S-, or -C(O)O-; Each -Cy- is independently an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms; each R' is independently -R, -C(O)R, -C(O)OR, -C(O)N(R)2, or -SO2R; and Each R is independently -H, or an optionally substituted group selected from the following: C 1-20 Aliphatic, C with 1-10 heteroatoms 1-20 Heteroaliphatic, C 6-20 Aryl, C 6-20 Aryl aliphatic group, C 6-20 arylheteroaliphatic, 5-20 membered heteroaryl having 1-10 heteroatoms, and 3-20 membered heterocyclyl having 1-10 heteroatoms, or Two R groups optionally and independently join together to form a covalent bond, or Two or more R groups on the same atom are optionally and independently taken together with that atom to form an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms in addition to that atom; or Two or more R groups on two or more atoms are optionally and independently taken together with the atoms between them to form an optionally substituted 3-30 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms in addition to the atoms between them.

28. The oligonucleotide of any one of claims 1-26, wherein the sugar of the nucleoside comprising the opposite nucleobase comprises a 2'-OR modification, wherein R is an optionally substituted C 1-6 Aliphatic group.

29. The oligonucleotide of any one of claims 1-26, wherein the sugar of the nucleoside comprising the opposite nucleobase comprises a natural DNA sugar.

30. A phosphoramidite, wherein the nucleobase of the phosphoramidite is a nucleobase or a tautomer thereof as described in any one of claims 1-28, wherein the nucleobase or tautomer thereof is optionally substituted or protected.

31. The phosphoramidite of claim 30, wherein the phosphoramidite has or the structure of a salt thereof.

32. A method for preparing an oligonucleotide or composition, the method comprising coupling an -OH group of an oligonucleotide or nucleoside with a phosphoramidite as claimed in any one of claims 30 to 31.

33. A method for deaminating a target adenosine in a target nucleic acid, the method comprising contacting the target nucleic acid with an oligonucleotide or composition as claimed in any one of the preceding claims, wherein the oligonucleotide targets the target adenosine.

34. A method for producing a specific nucleic acid or its product, or restoring or increasing the level of a specific nucleic acid or its product, the method comprising contacting a target nucleic acid with an oligonucleotide or composition as described in any one of the preceding claims, wherein the target nucleic acid comprises a target adenosine, and the specific nucleic acid differs from the target nucleic acid in that the specific nucleic acid has an I or a G instead of the target adenosine.

35. A method comprising: Contacting the oligonucleotide or composition of any one of the preceding claims with a sample comprising a target nucleic acid and adenosine deaminase, wherein: The base sequence of one or more oligonucleotides in the oligonucleotide composition is substantially complementary to the base sequence of the target nucleic acid; and The target nucleic acid comprises a target adenosine; wherein the target adenosine is modified.

36. A method comprising obtaining a first modification level of a target adenosine in a target nucleic acid that is observed when a first oligonucleotide composition is contacted with a sample comprising the target nucleic acid and adenosine deaminase, wherein the first oligonucleotide composition comprises a first plurality of oligonucleotides that share the same base sequence that is substantially complementary to the base sequence of the target nucleic acid; and wherein the first modification level of the target adenosine is greater than a reference modification level of the target adenosine, wherein the reference level is observed when a reference oligonucleotide composition is contacted with a sample comprising the target nucleic acid and adenosine deaminase, wherein the reference oligonucleotide composition comprises a plurality of reference oligonucleotides that share the same base sequence that is substantially complementary to the base sequence of the target nucleic acid; in: The first plurality of oligonucleotides comprises one or more chiral controlled chiral internucleotide linkages; and The plurality of reference oligonucleotides contains no chiral internucleotide linkages that are chirality controlled (the reference oligonucleotide composition is a "stereorandom composition").

37. A method for preventing a condition, disorder or disease associated with a G to A mutation, the method comprising administering or delivering to a subject susceptible to the condition, disorder or disease an effective amount of an oligonucleotide or composition as described in any one of the preceding claims, wherein the oligonucleotide targets the G to A mutation for editing.

38. A method for treating a condition, disorder or disease associated with a G to A mutation, the method comprising administering or delivering to a subject suffering from the condition, disorder or disease an effective amount of an oligonucleotide or composition as described in any one of the preceding claims, wherein the oligonucleotide targets the G to A mutation for editing.

39. An oligonucleotide, composition, phosphoramidite, use or method as described in any one of the specification or example examples 1-2349.

Images