2' modified oligonucleotides

• US 20030036649A1
• Filed: 06/27/2002
• Published: 02/20/2003
• Est. Priority Date: 10/24/1989
• Status: Active Grant

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Buhr, Chris A., Matteucci, Mark
• Granted Patent: US 6,911,540 B2
• Time in Patent Office: Days
• US Class Current: 536/26.1
• CPC Class Codes: C07H 19/04 Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/16 Purine radicals
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• 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 15/113 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 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/3517 Marker; Tag
• CPC Class Codes: C12N 2310/3527 Other alkyl chain
• CPC Class Codes: C12N 2310/353 linked to the nucleic acid via an atom other than carbon
• CPC Class Codes: C12N 2310/3535 Nitrogen

Abstract

Oligomers which have substituents on the 2′ position are resistant to oligonucleases and furthermore can be derivatized to deliver reagents or drugs, to carry label, or to provide other properties.

Claims

1. A monomer of the formula:

2. The monomer of claim 1 wherein X is O or S.

3. The monomer of claim 1 wherein X is NR.

4. The monomer of claim 1 wherein X is CR₂.

5. The monomer of claim 1 wherein Y is a nuclease-inhibiting substituent selected from the group consisting of substituted or unsubstituted alkyl(2-6C) and substituted or unsubstituted aryl (6-20C).

6. The monomer of claim 2 wherein Y is a nuclease-inhibiting substituent selected from the group consisting of substituted or unsubstituted alkyl(2-6C) and substituted or unsubstituted aryl (6-20C).

7. The monomer of claim 3 wherein Y is a nuclease-inhibiting substituent selected from the group consisting of substituted or unsubstituted alkyl(2-6C) and substituted or unsubstituted aryl (6-20C).

8. The monomer of claim 4 wherein Y is a nuclease-inhibiting substituent selected from the group consisting of substituted or unsubstituted alkyl(2-6C) and substituted or unsubstituted aryl (6-20C).

9. The monomer of claim 1 wherein Y is selected from the group consisting of —

CH₂COOEt;

—

CH₂COOH;

—

CH₂CONH₂; and

—

CH₂CONHCH₂CH₂NH₂.

10. The monomer of claim 1 wherein Y is a drug residue optionally attached through a linker moiety.

11. The monomer of claim 10 wherein Y is selected from the group consisting of netropsin and its derivatives, anthramycin, quinoxaline antibiotics, actinomycin, and pyrrolo (1-4) benzodiazepine derivatives optionally attached through a linker moiety.

12. The monomer of claim 1 wherein Y is a label optionally attached through a linker moiety.

13. The monomer of claim 1 wherein Y is a property-affecting residue optionally attached through a linker moiety.

14. The monomer of claim 1 wherein B is selected from the group consisting of A, T, G, C and U and the protected forms thereof.

15. The monomer of claim 1 wherein W₂ is a phosphonate residue.

16. The monomer of claim 1 wherein W₁ is a protecting group.

17. The monomer of claim 1 which is a salt of N⁴-benzoyl-5′

-O-(4,4′

-dimethoxytrityl)-2′

-O-(ethoxycarbonylmethyl)-cytidin-3′

-yl-hydrogen phosphonate.

18. The monomer of claim 1 which is a salt of 5′

-O-(4,4′

-dimethoxytrityl)-2′

-O-(ethoxycarbonylmethyl)-uridin-3′

-yl-hydrogen phosphonate.

19. The monomer of claim 1 which is a salt of N⁶-benzoyl-5′

-O-(4,4′

-dimethoxytrityl)-2′

-O-(ethoxycarbonylmethyl)-adenin-3′

-yl-hydrogen phosphonate.

20. The monomer of claim 1 which is a salt of N²-isobutyryl-5′

-O-(4,4′

-dimethoxytrityl)-2′

-O-(ethoxycarbonylmethyl)-guanosin-3′

-yl-hydrogen phosphonate.

21. The monomer of claim 1 which is a salt of 5-methyl-5′

-O-(4,4′

-dimethoxytrityl)-2′

-O-(ethoxycarbonylmethyl)-uridin-3′

-yl-hydrogen phosphonate.

22. The monomer of claim 1 which is a salt of 5-bromo-5′

-O-(4,4′

-dimethoxytrityl)-2′

-O-(ethoxycarbonylmethyl)-uridin-3′

-yl-hydrogen phosphonate.

23. The monomer of claim 1 which is a salt of 5-methyl-N⁴-benzoyl-5′

-O-(4,4-dimethoxytrityl)-2′

-O-(ethoxycarbonylmethyl)-cytidin-3′

-yl-hydrogen phosphonate.

24. The monomer of claim 1 which is a salt of 2′

-N-acylamino-5′

-O-(4,4′

-dimethoxytrityl)-uridin-3′

-yl-hydrogen phosphonate.

25. The monomer of claims 17-24 which is the triethylammonium salt.

27. The oligomer of claim 2 which is a dimer or trimer.

26. An oligomer of the formula:

28. The oligomer of claim 26 wherein Z is selected from the group consisting of P(O)O, P(O)S, P(O)NR₂, P(O)R, CO, CNR₂, wherein R is H or alkyl(1-6), P(O)OR′

, wherein R′

is alkyl(1-6C), and CX₂*, wherein each X* is independently an electron-withdrawing substituent.

29. The oligomer of claim 26 wherein all A have the formula X—

Y.

30. The oligomer of claim 26 wherein at least one A has the formula X—

Y and all remaining A are H or OH, or the phosphorylated form thereof.

31. The oligomer of claim 26 wherein X is O or S.

32. The oligomer of claim 26 wherein X is NR.

33. The oligomer of claim 26 wherein X is CR₂.

34. The oligomer of claim 26 wherein Y is a nuclease-inhibiting substituent selected from the group consisting of substituted or unsubstituted alkyl(2-6C) and substituted or unsubstituted aryl(6-20C).

35. The oligomer of claim 31 wherein Y is a nuclease-inhibiting substituent selected from the group consisting of substituted or unsubstituted alkyl(2-6C) and substituted or unsubstituted aryl (6-20C).

36. The oligomer of claim 32 wherein Y is a nuclease-inhibiting substituent selected from the group consisting of substituted or unsubstituted alkyl(2-6C) and substituted or unsubstituted aryl (6-20C).

37. The oligomer of claim 33 wherein Y is a nuclease-inhibiting substituent selected from the group consisting of substituted or unsubstituted alkyl(2-6C) and substituted or unsubstituted aryl (6-20C).

38. The oligomer of claim 26 wherein Y is a drug residue optionally attached through a linker moiety.

39. The oligomer of claim 38 wherein Y is selected from the group consisting of netropsin and its derivatives, anthramycin, quinoxaline antibiotics, actinomycin, and pyrrolo (1-4) benzodiazepine derivatives optionally attached through a linker moiety.

40. The oligomer of claim 26 wherein Y is a label optionally attached through a linker moiety.

41. The oligomer of claim 26 wherein Y is a property-affecting residue optionally attached through a linker meiety.

42. The oligomer of claim 26 wherein each B is independently selected from the group consisting of A, T, G, C and U and the protected forms thereof.

43. The oligomer of claim 26 which is 2′

-S-phenylthiocytidylyl-(3′

→

5′

)-thymidine.

44. The oligomer of claim 26 which is 2′

-O-(ethoxycarbonylmethyl)-cytidylyl-(3→

5′

)-thymidine.

45. The oligomer of claim 26 which is 2′

-O-aminocarbonylmethyl-(3→

5′

)-thymidine.

46. The oligomer of claim 26 which is 2′

-O-(hydroxycarbonylmethyl)-cytidylyl-(3→

5′

)-thymidine.

47. The oligomer of claim 26 which is 2′

-O-((2-aminoethyl)-aminocarbonylmethyl]-cytidylyl-(3′

→

5′

)-thymidine.

48. The oligomer of claim 26 which is 2′

-N-acylamino-2′

-deoxyuridylyl-(3′

→

5′

)-thymidine.

49. A method to treat diseases mediated by the presence of a nucleotide sequence which comprises administering to a subject in need of such treatment an amount of the modified oligomer of claim 26 capable of specifically binding said nucleotide sequence effective to inactivate said nucleotide sequence.