Targeted mutagenesis in living cells using modified oligonucleotides

• US 5,935,830 A
• Filed: 03/26/1997
• Issued: 08/10/1999
• Est. Priority Date: 06/07/1995
• Status: Expired due to Fees

• Current Assignee: Epoch Pharmaceuticals, Inc.
• Original Assignee: Epoch Pharmaceuticals, Inc.
• Inventors: Gall, Alexander A., Meyer, Rich B. Jr., Kutyavin, Igor V., Gamper, Howard B.
• Primary Examiner(s): LeGuyader, John L.
• Application Number:
  US08/827,116
• Time in Patent Office: 867 Days
• Field of Search: 514/44, 536/24.5, 536/24.3, 536/24.31, 536/24.32, 536/24.33, 536/91.1, 536/325, 435/6, 435/375, 435/172.3, 435/172.1
• US Class Current: 435/462
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61P 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12N 15/102 Mutagenizing nucleic acids
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/153 with the aid of a protein, e.g. recombinase
• CPC Class Codes: C12N 2310/311 Phosphotriesters
• CPC Class Codes: C12N 2310/335 Modified T or U
• CPC Class Codes: C12N 2310/3511 intercalating or cleaving agent
• CPC Class Codes: C12Q 1/6839 Triple helix formation or other higher order conformations in hybridisation assays
• CPC Class Codes: C12Q 2521/507 Recombinase
• CPC Class Codes: C12Q 2523/101 Crosslinking agents, e.g. psoralen
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine

Abstract

A method for introducing a site-specific mutation into a target polynucleotide sequence is presented. The method involves the use of an oligonucleotide capable of binding to the target sequence, either by triplex formation (mediated by Hoogsteen, reverse Hoogsteen or equivalent base pairing) or by Watson/Crick base pairing (in the presence of a recombinase enzyme). The oligonucleotide of the invention is modified by the covalent attachment of one or more electrophilic groups. When a modified oligonucleotide is bound to its target sequence, the electrophilic group is able to interact with a nearby nucleotide in the target sequence, causing a modification to the nucleotide that results in a change in nucleotide sequence. Compositions used in the practice of the method are also disclosed.

Claims

1. A method for site-directed mutagenesis of a target in a double-stranded DNA molecule, said double-stranded DNA molecule residing in a cell capable of replicating said double-stranded DNA molecule, said target comprising a sequence of nucleotides, said method comprising the steps of:

a) contacting said double-stranded DNA molecule with an oligonucleotide comprising one or more electrophilic groups, wherein the oligonucleotide and the double-stranded DNA molecule form a three-stranded complex in the region of the target;

b) allowing reaction to occur between an electrophilic group and a nucleotide in the target to generate one or more chemically modified sites; and

c) allowing the double-stranded DNA molecule comprising one or more chemically modified sites to undergo one or more rounds of replication, thereby generating one or more mutations at or in the vicinity of the target.

2. The method according to claim 1 performed in vitro.

3. The method according to claim 1 performed ex vivo.

4. The method according to claim 1 performed in vivo.

5. The method according to claim 1 wherein said cell is a cultured cell.

6. The method according to claim 1 wherein the oligonucleotide binds to the target sequence by triplex-formation.

7. The method according to claim 1 wherein the oligonucleotide comprises at least about 26 nucleotides and wherein the oligonucleotide forms a triple-stranded complex with the target according to the rules of Watson/Crick base pairing,

the method further comprising contacting the oligonucleotide with a recombinase.

8. The method according to claim 1 wherein the target sequence is in a chromosomal gene of a plant or animal, a viral genome, or the genome of a pathogen.

9. The method according to claim 1 wherein the electrophilic group is mutagenic.

10. The method according to claim 1 wherein the electrophilic group is an alkylating group.

11. The method according to claim 1 wherein the electrophilic group is part of an arm-leaving group structure having the formula -A-L, wherein the electrophilic group is part of the arm moiety A.

12. The method according to claim 11 wherein the -A-L structure is selected from the groups consisting of:

space="preserve" listing-type="equation">--(CH.sub.2).sub.q --Y--(CH.sub.2).sub.m -L,

space="preserve" listing-type="equation">--(CH.sub.2).sub.q --NH--CO--(CH.sub.2).sub.m --(X).sub.n'"'"' --N(R.sub.1)--(CH.sub.2).sub.p -L,

and

space="preserve" listing-type="equation">(CH.sub.2).sub.q'"'"' --O--(CH.sub.2).sub.q" --NH--CO--(CH.sub.2).sub.m --(X).sub.n'"'"' --N(R.sub.1)--(CH.sub.2).sub.p -L

wherein each of m and q is independently 0 to 8, inclusive, q'"'"' is 3 to 7 inclusive, q" is 1 to 7 inclusive,

Y is a linking group derived from a bifunctional molecule having a hydrocarbyl backbone and having at each end a functionality selected from --NH₂, --OH, --SH, --COOH and C.tbd.CH,

X is phenyl or phenyl substituted with chloro, bromo, lower alkyl or lower alkoxy groups,

n'"'"' is 0 or 1,

p is an integer from 1 to 6, and

R₁ is H, lower alkyl or CH₂)_p -L.

13. The method according to claim 12 wherein --(CH₂)_q --Y--(CH₂)_m -L is selected from the group consisting of 3-iodoacetamidopropyl, 3-(4-bromobutyr-amido)propyl, 4-iodoacetamidobutyl and 4-(4-bromobutyramido) butyl.

14. The method according to claim 11 wherein L is selected from the group consisting of chloro, bromo, iodo, SO₂ R'"'"'", and S⁺ R"", wherein each of R'"'"'" and R"" is independently C_1-6 alkyl, aryl or heteroaryl, or R'"'"'" and R"" together form a C_1-6 alkylene bridge.

15. The method according to claim 10 wherein the alkylating group is a nitrogen mustard.

16. The method according to claim 15 wherein the alkylating group is a bifunctional nitrogen mustard.

17. The method according to claim 1 wherein two or more electrophilic groups are attached to the oligonucleotide.

18. The method according to claim 17 wherein two or more alkylating groups are attached to the oligonucleotide.

19. The method according to claim 1 wherein an electrophilic group is attached to the 5'"'"' terminus of said oligonucleotide.

20. The method according to claim 1 wherein an electrophilic group is attached to the 3'"'"' terminus of said oligonucleotide.

24. The method according to claim 1 wherein an electrophilic group is attached to a base residue.

25. The method according to claim 1 wherein an electrophilic group is attached to a sugar residue.

26. The method according to claim 1 wherein an electrophilic group is attached to a phosphate group.

27. The method according to claim 24 wherein an electrophilic group is attached to the C5 position of a pyrimidine base.

28. The method according to claim 24 wherein an electrophilic group is attached to the C8 position of a purine base.

29. The method according to claim 24 wherein an electrophilic group is attached to the N2 position of guanine.

30. The method according to claim 24 wherein an electrophilic group is attached to the C3 position of a pyrazolopyrimidine.

31. The method according to claim 1 further comprising the use of a triplex stabilizer.

32. The method according to claim 31 wherein the triplex stabilizer is coralyne.

33. The method according to claim 1 wherein said one or more mutations alter the activity of the double-stranded DNA molecule.

21. The method according to claim 21 wherein one of said two or more electrophilic groups is attached to the 5'"'"' terminus of said oligonucleotide.

22. The method according to claim 21 wherein one of said two or more electrophilic groups is attached to the 3'"'"' terminus of said oligonucleotide.

23. The method according to claim 21 wherein one of said two or more electrophilic groups is attached to the 5'"'"' terminus of said oligonucleotide and another of said two or more electrophilic groups is attached to the 3'"'"' terminus of said oligonucleotide.

34. A method of inducing a mutation in a target, said target comprising a sequence of nucleotides, said method comprising:

contacting said target with a sequence-specific oligonucleotide to which is covalently attached one or more electrophilic groups; and

allowing reaction to occur between one of said electrophilic groups and one of said nucleotides, thereby resulting in a mutation in the target.

35. The method according to claim 34 performed in vitro.

36. The method according to claim 34 performed ex vivo.

37. The method according to claim 34 performed in vivo.

38. The method according to claim 34 wherein the target is located in a cell.

39. The method according to claim 34 wherein the oligonucleotide binds to the target sequence by triplex-formation.

40. The method according to claim 34 wherein the oligonucleotide comprises at least about 26 nucleotides and wherein the oligonucleotide forms a triple-stranded complex with the target according to the rules of Watson/Crick base pairing,

the method further comprising contacting the oligonucleotide with a recombinase.

41. The method according to claim 34 wherein the target sequence is in a chromosomal gene of a plant or animal, a viral genome, or the genome of a pathogen.

42. The method according to claim 34 wherein the electrophilic group is mutagenic.

43. The method according to claim 34 wherein the electrophilic group is an alkylating group.

44. The method according to claim 34 wherein the electrophilic group is part of an arm-leaving group structure having the formula -A-L, wherein the electrophilic group is part of the arm moiety A.

45. The method according to claim 44 wherein the -A-L structure is selected from the groups consisting of:

space="preserve" listing-type="equation">--(CH.sub.2).sub.q --Y--(CH.sub.2).sub.m -L,

space="preserve" listing-type="equation">--(CH.sub.2).sub.q --NH--CO--(CH.sub.2).sub.m --(X).sub.n'"'"' --N(R.sub.1)--(CH.sub.2).sub.p -L,

and

space="preserve" listing-type="equation">--(CH.sub.2).sub.q'"'"' --O--(CH.sub.2).sub.q" --NH--CO--(CH.sub.2).sub.m --(X).sub.n'"'"' --N(R.sub.1)--(CH.sub.2).sub.p -L

wherein each of m and q is independently 0 to 8, inclusive, q'"'"' is 3 to 7 inclusive, q" is 1 to 7 inclusive,

Y is a linking group derived from a bifunctional molecule having a hydrocarbyl backbone and having at each end a functionality selected from --NH₂, --OH, --SH, --COOH and C.tbd.CH,

X is phenyl or phenyl substituted with chloro, bromo, lower alkyl or lower alkoxy groups,

n'"'"' is 0 or 1,

p is an integer from 1 to 6, and

R₁ is H, lower alkyl or CH₂)_p -L.

46. The method according to claim 45 wherein --(CH₂)_q --Y--(CH₂)_m -L is selected from the group consisting of 3-iodoacetamidopropyl, 3-(4-bromobutyr-amido)propyl, 4-iodoacetamidobutyl and 4-(4-bromobutyramido)butyl.

47. The method according to claim 44 wherein L is selected from the group consisting of chloro, bromo, iodo, SO₂ R'"'"'", and S⁺ R"", wherein each of R'"'"'" and R"" is independently C_1-6 alkyl, aryl or heteroaryl, or R'"'"'" and R"" together form a C_1-6 alkylene bridge.

48. The method according to claim 43 wherein the alkylating group is a nitrogen mustard.

49. The method according to claim 48 wherein the alkylating group is a bifunctional nitrogen mustard.

50. The method according to claim 34 wherein two or more electrophilic groups are attached to the oligonucleotide.

51. The method according to claim 50 wherein two or more alkylating groups are attached to the oligonucleotide.

52. The method according to claim 34 wherein an electrophilic group is attached to the 5'"'"' terminus of said oligonucleotide.

53. The method according to claim 34 wherein an electrophilic group is attached to the 3'"'"' terminus of said oligonucleotide.

54. The method according to claim 50 wherein one of said two or more electrophilic groups is attached to the 5'"'"' terminus of said oligonucleotide.

55. The method according to claim 50 wherein one of said two or more alkylating groups is attached to the 3'"'"' terminus of said oligonucleotide.

56. The method according to claim 50 wherein one of said two or more electrophilic groups is attached to the 5'"'"' terminus of said oligonucleotide and another of said two or more electrophilic groups is attached to the 3'"'"' terminus of said oligonucleotide.

57. The method according to claim 34 wherein an electrophilic group is attached to a base residue.

58. The method according to claim 34 wherein an electrophilic group is attached to a sugar residue.

59. The method according to claim 34 wherein an electrophilic group is attached to a phosphate group.

60. The method according to claim 57 wherein an electrophilic group is attached to the C5 position of a pyrimidine base.

61. The method according to claim 57 wherein an electrophilic group is attached to the C8 position of a purine base.

62. The method according to claim 57 wherein an electrophilic group is attached the N2 position of guanine.

63. The method according to claim 57 wherein an electrophilic group is attached to the C3 position of a pyrazolopyrimidine.

64. The method according to claim 34 further comprising the use of a triplex stabilizer.

65. The method according to claim 59 wherein the triplex stabilizer is coralyne.

66. The method according to claim 34 wherein said mutation alters the activity of the double-stranded DNA molecule.