Oligonucleotides having modified nucleoside units

• US 20040014108A1
• Filed: 05/23/2003
• Published: 01/22/2004
• Est. Priority Date: 05/24/2002
• Status: Abandoned Application

• Current Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Cook, Phillip Dan, Eldrup, Anne B., Parshall, B. Lynne
• Application Number:
  US10/444,298
• Publication Number:
  US 20040014108A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2310/317 with an inverted bond, e.g. a cap structure
• CPC Class Codes: C12N 2310/33 of the base
• CPC Class Codes: C12N 2310/3527 Other alkyl chain
• CPC Class Codes: Y02P 20/582 Recycling of unreacted starting or intermediate materials

Abstract

Disclosed are oligonucleotide that include one or more modified nucleoside units. The oligonucleotides are particularly useful as antisense agents, ribozymes, aptamer, siRNA agents, probes and primers or, when hybridized to an RNA, as a substrate for RNA cleaving enzymes including RNase H and dsRNase.

Claims

1. A compound comprising a plurality of linked nucleoside units, at least one of said nucleoside units comprising a modified nucleoside of structural formula I of the indicated stereochemical configuration:

2. A compound of claim 1 wherein said plurality of linked nucleoside units comprises an oligonucleotide, the nucleosides of said oligonucleotide linked together by phosphodiester, phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methyl or alkyl phosphonate, 3′

-alkylene phosphonate, 5′

-alkylene phosphonate, chiral phosphonate, phosphinate, 3′

-amino phosphoramidate, aminoalkylphosphoramidate, thionophosphoramidate, thionoalkylphosphonate, thionoalkylphosphotriester, selenophosphates or boranophosphate linkages.

3. A compound of claim 2 wherein one of said linkages comprise an inverted internucleotide linkages that is a 3′

to 3′

or 5′

to 5′

linkage.

4. A compound of claim 3 wherein said inverted polarity linkage comprises a single 3′

to 3′

linkage at the 3′

-most internucleotide linkage of said compound.

5. A compound of claim 1 wherein said plurality of linked nucleoside units comprises an oligonucleoside, the nucleosides of said oligonucleoside linked together by morpholino, siloxane, sulfide, sulfoxide, sulfone;

formacetyl, thioformacetyl, methylene formacetyl, thioformacetyl, riboacetyl, alkene, sulfamate, methyleneimino, methylenehydrazino, sulfonate, sulfonamide or amide linkages.

6. A compound of claim 1 wherein said plurality of linked nucleoside units comprise a chimeric oligonucleotide having a first region capable of serving as a substrate for an RNA cleaving enzyme and a second region containing said nucleoside of structural formula I.

7. A compound of claim 6 wherein said RNA cleaving enzyme is an RNase H enzyme.

8. A compound of claim 6 wherein said RNA cleaving enzyme is a dsRNase.

9. A compound of claim 1 wherein a further of said linked nucleoside units comprises a 2′

-deoxy nucleoside.

10. A compound of claim 1 wherein a further of said linked nucleoside units comprises a 2′

-ribonucleoside.

11. A compound of claim 1 wherein a further of said linked nucleoside unites comprise a nucleoside having a 2′

substituent group and wherein said substituent group is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, C₅-C₂₀ aryl, —

O-alkyl, —

O-alkenyl, —

O-alkynyl, —

O-alkylamino, —

O-alkylalkoxy, —

O-alkylaminoalkyl, —

O-alkyl imidazole, —

OH, —

SH, —

S-alkyl, —

S-alkenyl, —

S-alkynyl, —

N(H)-alkyl, —

N(H)-alkenyl, —

N(H)-alkynyl, —

N(alkyl)₂, —

O-aryl, —

S-aryl, —

NH-aryl, —

O-aralkyl, —

S-aralkyl, —

N(H)-aralkyl, phthalimido (attached at N), halogen, amino, keto (—

C(═

O)—

R), carboxyl (—

C(═

O)OH), nitro (—

NO₂), nitroso (—

N═

O), cyano (—

CN), trifluoromethyl (—

CF₃), trifluoromethoxy (—

O—

CF₃), imidazole, azido (—

N₃), hydrazino (—

N(H)—

NH₂), aminooxy (—

O—

NH₂), isocyanato (—

N═

C═

O), sulfoxide (—

S(═

O)—

R), sulfone (—

S(═

O)₂—

R), disulfide (—

S—

S—

R), silyl, heterocycle, carbocycle, intercalator, reporter group, conjugate, polyamine, polyamide, polyalkylene glycol, and polyethers of the formula (—

O-alkyl)_m, where m is 1 to about 10;

wherein each R is, independently, hydrogen, a protecting group or substituted or unsubstituted alkyl, alkenyl, or alkynyl wherein said substituted alkyl, alkenyl, or alkynyl are substituted with haloalkyl, alkenyl, alkoxy, thioalkoxy, haloalkoxy, aryl groups as well as halogen, hydroxyl, amino, azido, carboxy, cyano, nitro, mercapto, sulfides, sulfones, or sulfoxides.

12. A compound of claim 11 wherein said 2′

substituent group —

O—

CH₂—

CH₂—

O—

CH₃.

13. A compound of claim 1 wherein Y¹ is alkyl unsubstituted or substituted with hydroxy, amino, C_1-4 alkoxy, C_1-4 alkylthio, or one to three fluorine atoms.

14. A compound of claim 13 wherein Y¹ is methyl or trifluoromethyl.

15. A compound of claim 1 wherein

Y¹ is alkyl unsubstituted or substituted with hydroxy, amino, C_1-4 alkoxy, C_1-4 alkylthio, or one to three fluorine atoms;

and

Y² is hydrogen, fluorine, methoxy or hydroxyl.

16. A compound of claim 15 wherein Y² is hydrogen or hydroxyl.

17. An antisense oligonucleotide comprising a compound of claim 1.

18. A ribozyme comprising a compound of claim 1.

19. An aptamers comprising a compound of claim 1.

20. A substrate strand for a RNase H or a RNA dsRNase cleaving enzyme comprising a compound of claim 1.

21. A nucleic acid probe comprising a compound of claim 1.

22. A PCR primer comprising a compound of claim 1.

23. A diagnostic oligonucleotide comprising a compound of claim 1.

24. A siRNA molecule having first and second strands, at least one of said strands comprising a compound of claim 1.

25. An oligomeric compound comprising a plurality of linked nucleoside units, at least one of said nucleoside units comprising a modified nucleoside of structural formula II of the indicated stereochemical configuration:

26. An oligonucleotide of claim 25 wherein Y¹ is alkyl unsubstituted or substituted with hydroxy, amino, C_1-4 alkoxy, C_1-4 alkylthio, or one to three fluorine atoms.

27. An oligonucleotide of claim 26 wherein Y¹ is methyl or trifluoromethyl.

28. An oligonucleotide of claim 26 wherein Y¹ is alkyl unsubstituted or substituted with hydroxy, amino, C_1-4 alkoxy, C_1-4 alkylthio, or one to three fluorine atoms;

and Y² is hydrogen, fluorine, methoxy or hydroxyl.

29. An oligonucleotide of claim 28 wherein Y² is hydrogen or hydroxyl.