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1. WO1993005180 - FORMATION OF TRIPLE HELIX COMPLEXES OF DOUBLE STRANDED DNA USING NUCLEOSIDE OLIGOMERS WHICH COMPRISE PURINE BASE ANALOGS

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Claims
1. A method off detecting or recognizing a specific segment of double-stranded nucleic acid without interrupting base-pairing of the duplex which comprises contacting said nucleic acid segment with an Oligomer which comprises at least one nucleosidyl unit which comprises an 8-modified purine base modified to favor the syn conformation, and which is sufficiently complementary to said nucleic segment or a portion thereof, to form a triple helix structure wherein one strand of the duplex comprises a polypurine sequence of at least about 7 purine bases and the Oligomer is parallel to the strand having the polypurine sequence, and, further, wherein guanine in the polypurine sequence is read by a base in the Oligomer selected from 8-oxo-adenine and cytosine or a cytosine analog either of which is protonated at N-3 under physiological pH so as to be capable of hydrogen bonding with guanine and wherein adenine in the polypurine sequence is read by a base in the Oligomer selected from 8-oxo-guanine, thymine and uracil.

2. A method according to claim 1 wherein said polypurine sequence comprises at least about 12 purine bases.

3. A method according to claim 1 wherein nucleosides of the Oligomer which comprise 8-oxoadenine or

8-oxoguanine are in the syn conformation.

4. A method according to claim 1 wherein said polypurine sequence includes up to 50% pyrimidine bases and wherein cytosine in the polypurine sequence is read by a base in the Oligomer selected from 8-fluoroguanine, 8-methoxyguanine and 8-azaguanine and wherein thymine in the polypurine sequence is read by a base in the Oligomer selected from 8-fluoroadenine, 8-methoxyadenine and 8-azaadenine.

5. A method according to claim 4 wherein nucleosides of the Oligomer which comprise 8-oxoadenine, 8-oxoguanine, 8-fluoroadenine, 8-fluoroguanine, 8- methoxyadenine, 8-methoxyguanine, 8-azaadenine, or 8- azaguanine are in the syn conformation.

6. A method according to either of claims 1 or 4 wherein said Oligomer comprises an oligonucleotide, an alkyl- or aryl-phosphonothioate Oligomer, a phosphorothioate Oligomer, an alkyl- or aryl-phosphonate Oligomer, a phosphotriester Oligomer, a phosphoramidate Oligomer, a carbamate Oligomer, a sulfamate Oligomer, a morpholino Oligomer, or a formacetal Oligomer.

7. A method according to claim 7 wherein nucleosidyl units of said Oligomer comprise sugar moieties selected from ribose, deoxyribose, 2'-O-alkylribose, 2'-O- arylribose and 2'-halogenribose, all optionally substituted with halogen, alkyl or aryl.

8. A method according to claim 7 wherein nucleosidyl units of said Oligomer comprise sugar moieties selected from ribose, deoxyribose and 2'-O-methyl ribose.

9. A method of preventing expression or function of a specific segment of double-stranded nucleic acid having a given sequence of each of the two strands in the complementary nucleic acid duplex which comprises contacting said nucleic acid segment with an Oligomer which comprises at least one nucleosidyl unit which comprises an 8-modified purine base modified to favor the syn conformation, and which is sufficiently complementary to said nucleic acid segment, or a portion thereof, to form a triple helix structure, wherein one strand of the duplex comprises a polypurine sequence of at least about 7 purine bases and the Oligomer is parallel to the strand having the polypurine sequence and, further, wherein guanine in the polypurine sequence is read by a base in the Oligomer selected from 8-oxoadenine and cytosine or a cytosine analog either of which is protonated at N-3 under physiological pH so as to be capable of hydrogen bonding with guanine and wherein adenine of the polypurine sequence is read by a base in the Oligomer selected form 8-oxo-guanine, thymine and uracil.

10. A method according to claim 9 wherein said polypurine sequence comprises at least about 12 purine bases.

11. A method according to claim 9 wherein nucleosides of the Oligomer which comprise 8-oxoadenine or 8-oxoguanine are in the syn conformation.

12. A method according to claim 9 wherein said polypurine sequence includes up to about 50% pyrimidine bases and wherein cytosine in the polypurine sequence is read by a base in the Oligomer selected from 8-fluoroguanine, 8-methoxyguanine and 8-azaguanine, and wherein thymine in the polypurine sequence is read by a base in the Oligomer selected from 8-fluoroadenine, 8-methoxyadenine and 8-azadenine.

13. A method according to claim 12 wherein nucleosides of the Oligomer which comprise 8-oxoguanine, 8-oxoadenine, 8-fluoroadenine, 8-fluoroguanine, 8-methoxyadenine, 8-methoxyguanine, 8-azaadenine or 8-azaguanine are in the syn conformation.

14. A method according to claim 9 wherein said Oligomer is modified to include a nucleic acid modifying group which may be caused to react with said nucleic acid duplex and irreversibly modify the structure of said nucleic acid.

15. A method according to claim 9 wherein said Oligomer includes a nucleic acid modifying group which can be caused to react with said nucleic acid segment or a target sequence therein and irreversibly modify said nucleic acid and thereby irreversibly inhibit the expression or function of said nucleic acid segment.

16. A method according to claim 15 wherein said modification comprises covalently linking of said Oligomer with one strand of the nucleic acid duplex strand of the nucleic acid duplex or crosslinking said nucleic acid.

17. A method according to claim 15 wherein said modification comprises cleaving one or both strands of nucleic acid segment.

18. A method according to claim 15 wherein said nucleic acid segment comprises a gene in a living cell and formation of said triple helix structure permanently inhibits or inactivates said gene.

19. A method according to either of claims 9 or 12 wherein said Oligomer comprises an Oligonucleotide, an alkyl- or aryl- phosphonothioate Oligomer, a phosphorothioate Oligomer, an alkyl- or aryl-phosphonate Oligomer, a phosphotriester Oligomer, a phosphoramidate Oligomer, a carbamate Oligomer, a sulfamate Oligomer, a morpholino Oligomer, or a formacetal Oligomer.

20. A method according to claim 19 wherein nucleosidyl units of said Oligomer comprise sugar moieties selected from ribose, deoxyribose, 2'-O-alkylribose, 2'-O-arylribose, 2'-halogenribose all optionally substituted with halogen, alkyl or aryl.

21. A method according to claim 20 wherein nucleosidyl units of said Oligomer comprise sugar moieties selected from ribose, deoxyribose and 2'-O-meth╬│lribose.

22. A triple helix structure which comprises a selected double stranded nucleic acid sequence and an

Oligomer which comprises at least one nucleosidyl unit which comprises an 8-modified purine base modified to favor the syn conformation, and which is sufficiently complementary to read a polypurine sequence in one strand of the nucleic acid sequence and thus form triplets, wherein the Oligomer is parallel to the strand having the polypurine sequence and wherein guanine in the polypurine sequence is read by a base in the Oligomer selected from 8-oxo-adenine and cytosine or a cytosine analog either of which is protonated at N-3 under physiological pH so as to be capable of hydrogen bonding with guanine and wherein adenine in the polypurine sequence is read by a base in the Oligomer selected from 8-oxo-guanine, thymine and uracil.

23. A structure according to claim 22 wherein nucleosides of the Oligomer which comprise 8-oxo-adenine or 8-oxoguanine are in the syn conformation.

24. A structure according to claim 22 wherein said polypurine sequence includes up to about 50% pyrimidine bases and wherein cytosine in the polypurine sequence is read by a base in the Oligomer selected from 8-fluoroguanine, 8-methoxyguanine and 8-azaguanine; and wherein thymine in the polypurine sequences is read by a base in the Oligomer selected from 8-fluoroadenine, 8-methoxyadenine and 8-azaadenine.

25. A structure according to claim 24 wherein nucleosides of the Oligomer which comprise 8-oxoadenine, 8-oxoguanine, 8-fluoroadenine, 8-fluoroguanine, 8- methoxyadenine, 8-methoxyguanine, 8-azaadenine or 8- azaguanine are in the syn conformation.

26. A structure according to either of claims 22 or 24 wherein said Oligomer comprises an oligonucleotide, an alkyl- or aryl-phosphonothiate Oligomer, a phosphorothioate Oligomer, a phosphotriester Oligomer, a phosphoramidate Oligomer a carbamate Oligomer, a sulfamate Oligomer, a morpholino Oligomer, an alkyl or a formacetal Oligomer.

27. A structure according to claim 26 wherein nucleosidyl units of said Oligomer comprise sugar moieties selected from ribose, deoxyribose, 2'-O-alkylribose, 2'-O- aryl ribose or 2'-halogen ribose all optionally substituted with halogen, alkyl or aryl.

28. A structure according to claim 27 wherein nucleosidyl units of said Oligomer comprises sugar moieties selected from ribose, deoxyribose and 2'-O-methylribose.

29. A structure according to claim 27 wherein said Oligomer comprises about 12 to about 16 nucleosidyl units.

30. A structure according to any of claims 22 or 24 wherein said Oligomer is an alkyl or aryl phosphonate oligomer.

31. An Oligomer capable of reading a polypurine sequence of one strand of a double stranded nucleic acid sequence which comprises at least one nucleosidyl unit which comprises an 8-modified purine base modified to favor the syn conformation and wherein guanine in the polypurine sequence is read by a base in the Oligomer selected from 8-oxoadenine and cytosine or a cytosine analog either of which is protonated at N-3 at physiologi cal pH so as to" be capable of hydrogen bonding with guanine, and wherein adenine in the polypurine sequence is read by a base in the Oligomer selected from 8-oxoguanine, thymine and uracil.

32. An Oligomer according to claim 31 wherein said polypurine sequence includes up to about 50% pyrimidine bases and wherein cytosine in the polypurine sequence is read by a base in the Oligomer selected from 8- fluoroguanine, 8-methoxyguanine, and 8-azaguanine and wherein thymine in the polypurine sequence is read by a base in the Oligomer selected from 8-fluoroadenine, 8- methoxyadenine and 8-azaadenine.

33. An Oligomer to either of claims 31 or 32 wherein said neutral Oligomer comprises an oligonucleotide, an alkyl- or aryl-phosphonothioate Oligomer, a phosphorothioate Oligomer, an alkyl- or aryl-phosphonate Oligomer, a phosphotriester Oligomer, a phosphoramidite Oligomer a carbamate Oligomer, a sulfamate Oligomer, a morpholino Oligomer, or a formacetal Oligomer.

34. An Oligomer according to claim 33 wherein nucleosidyl units of said Oligomer comprise a sugar moiety selected from ribose, deoxyribose, 2'-O-alkyl-ribose, 2'-O-arylribose or 2'-halogen ribose all optionally substituted with halogen, alkyl or aryl.

35. An Oligomer according to claim 34 wherein nucleosidyl units of said Oligomer comprise a sugar moiety selected from ribose, deoxyribose and 2'-O-methylribose.

36. An Oligomer according to claim 34 which comprises from about 12 to about 16 nucleosidyl units.

37. An Oligomer according to either of claim 31 or 32 which comprises an alkyl- or aryl- phosphonate Oligomer.

38. An Oligomer according to claim 37 which comprises a methylphosphonate Oligomer.