DOUBLE STRAND COMPOSITIONS COMPRISING DIFFERENTIALLY MODIFIED STRANDS FOR USE IN GENE MODULATION

• US 20070166734A1
• Filed: 12/01/2006
• Published: 07/19/2007
• Est. Priority Date: 06/03/2004
• Status: Abandoned Application

• Current Assignee: Balkrishen Bhat, Charles Allerson, Eric Swayze, Richard Griffey, Thazha Prakash
• Original Assignee: Balkrishen Bhat, Charles Allerson, Eric Swayze, Richard Griffey, Thazha Prakash
• Inventors: Bhat, Balkrishen, Allerson, Charles, Swayze, Eric, Griffey, Richard, Prakash, Thazha
• Application Number:
  US11/565,770
• Publication Number:
  US 20070166734A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding 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 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/32 of the sugar
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/3231 having an additional ring, e.g. LNA, ENA
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/346 having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2320/30 Special therapeutic applications
• CPC Class Codes: C12N 2320/51 modulating the chemical stability, e.g. nuclease-resistance

Abstract

The present invention provides double stranded compositions wherein each strand is modified to have a motif defined by positioning of β-D-ribonucleosides and sugar modified nucleosides. More particularly, the present compositions comprise one strand having an alternating motif and another strand having a hemimer motif, a blockmer motif, a fully modified motif or a positionally modified motif. At least one of the strands has complementarity to a nucleic acid target. The compositions are useful for targeting selected nucleic acid molecules and modulating the expression of one or more genes. In preferred embodiments the compositions of the present invention hybridize to a portion of a target RNA resulting in loss of normal function of the target RNA. The present invention also provides methods for modulating gene expression.

Claims

1. A composition comprising first and second chemically synthesized oligomeric compounds wherein:

at least a portion of the first oligomeric compound is complementary to and capable of hybridizing to a selected nucleic acid target;

a portion of from about 12 to about 24 nucleosides of the first oligomeric compound is complementary to the second oligomeric compound;

one of the first and the second oligomeric compounds comprises nucleosides linked by internucleoside linking groups wherein the sequence of linked nucleosides defines an alternating motif having the formula;

5′

-A(-L-B-L-A)_n(-L-B)_nn-3′

wherein;

each L is, independently, an internucleoside linking group;

each A or each B is a β

-D-ribonucleoside;

the other of each A or each B is a sugar modified nucleoside wherein the sugar modification of the other of each A or each B nucleoside is identical;

n is from about 7 to about 11;

nn is 0 or 1;

the other of the first and the second oligomeric compound is a fully modified oligomeric compound comprising a contiguous sequence of sugar modified nucleosides linked by internucleoside linking groups wherein each sugar modification fully modified oligomeric compound is identical; and

the composition optionally further comprises one or more overhangs, phosphate moieties, conjugate groups or capping groups.

2. The composition of claim 1 wherein each A or each B is a 2′

-modified nucleoside having a 2′

-substituent selected from halogen, allyl, amino, azido, —

O-allyl, —

O—

C₁-C₁₀ alkyl, —

OCF₃, —

O—

(CH₂)₂—

OCH₃, —

O(CH₂)₂—

SCH₃, —

O—

(CH₂)₂—

ON(R_m)(R_n) and —

O—

CH₂—

C(═

O)N(R_m)(R_n), where each R_m and R_n is, independently, H, an amino protecting group or substituted or unsubstituted —

C₁-C₁₀ alkyl.

3. The composition of claim 2 wherein the 2′

-substituent is allyl, —

O-allyl, —

O—

C₁-C₁₀ alkyl, —

O—

(CH₂)₂—

OCH₃ or —

O—

(CH₂)₂—

SCH₃.

4. The composition of claim 3 wherein the 2′

-substituent is —

O—

(CH₂)₂—

OCH₃.

5. The composition of claim 3 wherein the 2′

-substituent is —

OCH₃.

6. The composition of claim 1 wherein the second oligomeric compound comprises the alternating motif.

7. The composition of claim 6 wherein each A or each B is a 2′

-modified nucleoside having a 2′

-substituent selected from allyl, —

O-allyl, —

O—

C₁-C₁₀ alkyl, —

O—

(CH₂)₂—

OCH₃ and —

O(CH₂)₂—

SCH₃.

8. The composition of claim 7 wherein each 2′

-substituent of the 2′

-modified nucleosides is —

O—

(CH₂)₂—

OCH₃.

9. The composition of claim 1 wherein the fully modified oligomeric compound comprises sugar modified nucleosides selected from 2′

-modified nucleosides, 4′

-thio modified nucleosides, 4′

-thio-2′

-modified nucleosides or nucleosides having bicyclic sugar moieties.

10. The composition of claim 1 further comprising a β

-D-ribonucleoside at one or both of the 3′ and

5′

-termini of the fully modified oligomeric compound.

11. The composition of claim 9 wherein each sugar modified nucleoside of the fully modified oligomeric compound is a 2′

-modified nucleoside.

12. The composition of claim 11 wherein each sugar modified nucleoside of the fully modified oligomeric compound is a 2′

-OCH₃ or a 2′

-F modified nucleoside.

13. The composition of claim 11 wherein each sugar modified nucleoside of the fully modified oligomeric compound is a 2′

-F modified nucleoside.

14. The composition of claim 10 wherein each sugar modified nucleoside of the fully modified oligomeric compound is a 2′

-OCH₃ modified nucleoside.

15. The composition of claim 14 wherein the second oligomeric compound is the oligomeric compound having the alternating motif.

16. The composition of claim 15 wherein each A or each B of the oligomeric compound having the alternating motif is a 2′

-O(CH₂)₂—

OCH₃ modified nucleoside.

17. The composition of claim 1 wherein each of the internucleoside linking groups of the first and second oligomeric compounds is, independently, selected from phosphodiester and phosphorothioate.

18. The composition of claim 1 having at least 2 phosphorothioate internucleoside linking groups at the 3′

-end of the first oligomeric compound.

19. The composition of claim 18 having about 7 phosphorothioate internucleoside linking groups at the 3′

-end of the first oligomeric compound.

20. The composition of claim 1 wherein the first oligomeric compound further comprises a 5′

-thiophosphate group.

21. The composition of claim 1 wherein each of the first and second oligomeric compounds independently comprises from about 12 to about 30 nucleosides.

22. The composition of claim 1 wherein each of the first and second oligomeric compounds independently comprises from about 17 to about 23 nucleosides.

23. The composition of claim 1 wherein each of the first and second oligomeric compounds independently comprises from about 19 to about 21 nucleosides.

24. The composition of claim 1 wherein the first and the second oligomeric compounds form a complementary antisense/sense siRNA duplex.

25. The composition of claim 1 wherein each sugar modified nucleoside is independently, selected from 2′

-modified nucleosides, 4′

-thio modified nucleosides, 4′

-thio-2′

-modified nucleosides and nucleosides having bicyclic sugar moieties.

26. A method of inhibiting gene expression comprising contacting one or more cells, a tissue or an animal with a composition of claim 1.