2' Modified Oligonucleotides

• US 5,792,847 A
• Filed: 06/06/1995
• Issued: 08/11/1998
• Est. Priority Date: 10/24/1989
• Status: Expired due to Term

• Current Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Original Assignee: Gilead Sciences Inc.
• Inventors: Buhr, Chris A., Matteucci, Mark
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US08/467,422
• Time in Patent Office: 1,162 Days
• Field of Search: 536/25.3, 536/25.33, 536/25.34, 536/25.6, 536/23.1, 536/22.1, 536/25.5
• US Class Current: 536/23.1
• 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. An oligonucleotide having the formula ##STR6## or a salt thereof, wherein each B is independently a protected or unprotected purine or pyrimidine base in the β

-anomeric configuration;

W₃ and W₄ are each independently H, PO₃^-2, a protecting group, or an intermediate moiety in the formation of an internucleotide link which when reacted with the appropriate --OH results in Z;

each Z independently is P(O)O, P(O)S or P(O)N(R)₂ ;

each R is independently H or alkyl (1-6 C);

n is an integer of 1-200;

each A is independently selected from the group consisting of --X--Y, H, OH or --OPr wherein Pr is a protecting group wherein

X is O;

Y is substituted alkyl (2-20 C) or substituted or unsubstituted alkenyl (2-20 C), wherein the substituents are a halogen, OH, NH₂, SH, --O--, --CH₂ CONH₂, --CH₂ COOCH₂ CH₃ or --CH₂ CONHCH₂ CH₂ NH₂ ; and

wherein at least one A is X--Y.

2. The oligonucleotide of claim 1 wherein the substituents are --CH₂ COONH₂, --CH₂ COOCH₂ CH₃ or --CH₂ CONHCH₂ CH₂ NH₂.

3. The oligonucleotide of claim 1 wherein each Z is independently P(O)O or P(O)S.

4. The oligonucleotide of claim 1 wherein each Z is P(O)O.

5. The oligonucleotide of claim 1 wherein each Z is P(O)S.

6. The oligonucleotide of claim 1 wherein each B is independently thymine, adenine, guanine, cytosine, uracil, 5-methylcytosine, 5-bromouracil, or a protected derivative thereof.

7. The oligonucleotide of claim 1 wherein W₃ is 4,4'"'"'-dimethoxytrityl, 4-monomethoxytrityl or trityl.

8. The oligonucleotide of claim 1 wherein the oligonucleotide is a dimer or trimer.

9. The oligonucleotide of claim 1 wherein at least one A has the formula X--Y and all remaining A are H or OH.

10. The oligonucleotide of claim 1 wherein W₃ and W₄ are hydrogen.

11. The oligonucleotide of claim 10 wherein each Z is independently P(O)O or P(O)S.

12. The oligonucleotide of claim 11 wherein the oligonucleotide is a dimer or trimer.

13. The oligonucleotide of claim 11 wherein each Z is P(O)S.

14. The oligonucleotide of claim 1 wherein Y is substituted alkyl (2-6 C).

15. The oligonucleotide of claim 14 wherein Y is substituted with a halogen, --O--, OH or NH₂.

16. The oligonucleotide of claim 1 wherein Y is substituted or unsubstituted alkenyl (2-6 C).

17. The oligonucleotide of claim 16 wherein Y is substituted with a halogen, --O--, OH or NH₂.

18. The oligonucleotide of claim 1 wherein Y is substituted alkyl (2-20 C) and the carbon atoms in Y are methylene groups.

19. The oligonucleotide of claim 18 wherein Y contains --CH₂ --O--CH₂ --CH₂ --O--.

20. The oligonucleotide of claim 18 wherein Y contains --CH₂ --O--CH₂ --CH₂ --NH--.

21. The oligonucleotide of claim 18 wherein Y contains --COO--CH₂ --CH₂ --O--.

22. The oligonucleotide of claim 18 wherein Y is substituted alkyl (2-6 C).

23. The oligonucleotide of claim 18 wherein Y is substituted with a halogen, --O--, OH or NH₂.

24. The oligonucleotide of claim 23 wherein Y is substituted with --O--.

25. The oligonucleotide of claim 23 wherein Y is substituted with a halogen or OH.

26. The oligonucleotide of claim 1 wherein Y is substituted alkyl (2-20 C) or substituted or unsubstituted alkenyl (2-20 C), wherein the substituents are a halogen, OH, --O--, --CH₂ CONH₂, --CH₂ COOCH₂ CH₃ or --CH₂ CONHCH₂ CH₂ NH₂.

27. The oligonucleotide of claim 1 wherein each B is independently an unprotected purine or pyrimidine base.

28. An oligonucleotide having the formula ##STR7## or a salt thereof, wherein each B is independently a protected or unprotected purine or pyrimidine base in the β

-anomeric configuration;

W₃ and W₄ are each independently H, PO₃^-2, a protecting group, or an intermediate moiety in the formation of an internucleotide link which when reacted with the appropriate --OH results in Z;

each Z independently is --P(O)O--, --P(O)S-- or --P(O)N(R)₂ --;

each R is independently H or alkyl (1-6 C);

n is an integer of 1-200;

each A is independently selected from the group consisting of --X--Y, --H, --OH or --OPr wherein Pr is a protecting group, wherein

X is --CH₂ --, --S-- or --NH--;

Y is substituted alkyl (2-20 C) or substituted or unsubstituted alkenyl (2-20 C), wherein the substituents are a halogen, --OH, --NH₂, --SH, --O--, --CH₂ CONH₂, --CH₂ COOCH₂ CH₃ or --CH₂ CONHCH₂ CH₂ NH₂ ; and

wherein at least one A is --X--Y.

29. The oligonucleotide of claim 28 wherein Y is substituted alkyl (2-20 C) and the carbon atoms in Y are methylene groups.

30. The oligonucleotide of claim 28 wherein Y contains --CH₂ --O--CH₂ --CH₂ --O--.

31. The oligonucleotide of claim 28 wherein Y contains --CH₂ --O--CH₂ --CH₂ --NH--.

32. The oligonucleotide of claim 28 wherein Y contains --COO--CH₂ --CH₂ --O--.

33. The oligonucleotide of claim 29 wherein Y is substituted with --NH₂ or --SH.

34. The oligonucleotide of claim 29 wherein Y is substituted with a halogen, --O-- or --OH.

35. An oligonucleotide having the formula ##STR8## or a salt thereof, wherein each B is independently a protected or unprotected purine or pyrimidine base in the β

anomeric configuration;

W₃ and W₄ are each independently H, PO₃^-2, a protecting group, or an intermediate moiety in the formation of an internucleotide link which when reacted with the appropriate --OH results in Z;

each Z independently is --P(O)O--, --P(O)S-- or --P(O)N(R)₂ --;

each R is independently --H or alkyl (1-6 C);

n is an integer of 1-200;

each A is independently selected from the group consisting of --X--Y, --H, --OH or --OPr wherein Pr is a protecting group wherein

X is --O--;

Y is substituted alkyl (2-20 C) or substituted or unsubstituted alkenyl (2-20 C), wherein the substituents are a halogen, --OH, --NH₂, --SH, --O--, --COOH, --C(O)--, --CH₂ COOH, --CH₂ CONH₂, --CH₂ COOCH₂ CH₃ or --CH₂ CONHCH₂ CH₂ NH₂ ; and

wherein at least one A is --X--Y.