DOUBLE STRAND COMPOSITIONS COMPRISING DIFFERENTIALLY MODIFIED STRANDS FOR USE IN GENE MODULATION
First Claim
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 second oligomeric compounds is a symmetric gapped oligomeric compound;
the other of the first and second oligomeric compounds is a fully modified oligomeric compound; and
the composition optionally further comprises one or more overhangs, phosphate moieties, conjugate groups or capping groups.
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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 a gapped motif and another strand having a gapped motif, a hemimer motif, a blockmer motif, a fully modified motif, a positionally modified motif or an alternating 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 some 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.
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Citations
45 Claims
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1. A composition comprising first and second chemically synthesized oligomeric compounds wherein:
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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 second oligomeric compounds is a symmetric gapped oligomeric compound;
the other of the first and second oligomeric compounds is a fully modified oligomeric compound; and
the composition optionally further comprises one or more overhangs, phosphate moieties, conjugate groups or capping groups.
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2. The composition of claim 1 wherein each symmetric gapped oligomeric compound independently comprises a contiguous sequence of nucleosides divided into an internal region flanked by two external regions wherein:
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the sugar groups within each region are identical, the sugar groups of each external region are identical and are different from the sugar modifications of the nucleosides in the internal region;
the nucleosides of the internal region are β
-D-ribonucleosides or sugar modified nucleosides and the nucleosides of the external regions are sugar modified nucleosides; and
the sugar modified nucleosides are each independently selected from 2′
-modified nucleosides, 4′
-thio modified nucleosides, 4′
-thio-2′
-modified nucleosides and nucleosides having bicyclic sugar moieties.
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3. The composition of claim 2 wherein each nucleoside of the internal region of the symmetric gapped oligomeric compound is a β
- -D-ribonucleoside.
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4. The composition of claim 2 wherein each nucleoside of the internal region of the symmetric gapped oligomeric compound is a sugar modified nucleoside.
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5. The composition of claim 4 wherein each sugar modified nucleoside of the internal region is a 2′
- -F modified nucleoside or 4′
-thio modified nucleoside.
- -F modified nucleoside or 4′
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6. The composition of claim 2 wherein each nucleoside of the external regions of the symmetric gapped oligomeric compound is a 2′
- -modified nucleoside.
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7. The composition of claim 6 wherein each of the 2′
- -modifications is halogen, allyl, amino, azido, —
O-allyl, —
O-C1-C10 alkyl, —
OCF3, —
O—
(CH2)2—
OCH3, —
O(CH2)2—
SCH3, —
O—
(CH2)2—
ON(Rm)(Rn) or —
O—
CH2—
C(═
O)N(Rm)(Rn), where each Rm and Rn is, independently, H, an amino protecting group or substituted or unsubstituted —
C1-C10 alkyl.
- -modifications is halogen, allyl, amino, azido, —
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8. The composition of claim 7 wherein each of the 2′
- -modifications is —
F, —
OCH3 or —
O—
(CH2)2—
OCH3.
- -modifications is —
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9. The composition of claim 8 wherein each of the 2′
- -modifications is —
O—
(CH2)2—
OCH3.
- -modifications is —
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10. The composition of claim 2 wherein each sugar modified nucleoside of the external regions of the symmetric gapped oligomeric compound is a 4′
- -thio modified nucleosides.
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11. The composition of claim 2 wherein each sugar modified nucleoside of the external regions of the symmetric gapped oligomeric compound is a 4′
- -thio-2′
-modified nucleosides.
- -thio-2′
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12. The composition of claim 11 wherein each 2-modification of the 4′
- -thio-2′
-modified nucleosides is halogen, allyl, amino, azido, —
O-allyl, —
O-C1-C10 alkyl, —
OCF3, —
O—
(CH2)2—
OCH3, —
O(CH2)2—
SCH3, —
O—
(CH2)2—
ON(Rm)(Rn) or —
O—
CH2—
C(═
O)N(Rm)(Rn), where each Rm and Rn is, independently, H, an amino protecting group or substituted or unsubstituted —
C1-C10 alkyl.
- -thio-2′
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13. The composition of claim 12 wherein each 2′
- -modification is —
F, —
OCH3, —
OCF3 or —
O—
(CH2)2—
OCH3.
- -modification is —
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14. The composition of claim 13 wherein each 2′
- -modification is —
OCH3 or —
O—
(CH2)2—
OCH3.
- -modification is —
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15. The composition of claim 2 wherein each sugar modified nucleoside of the external regions of the symmetric gapped oligomeric compound is a bicyclic sugar moiety.
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16. The composition of claim 15 wherein each bicyclic sugar moiety has a 2′
- -O—
(CH2)n-4′
bridge wherein n is 1 or 2.
- -O—
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17. The composition of claim 1 wherein the first oligomeric compound is the symmetric gapped oligomeric compound.
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18. The composition of claim 17 wherein each sugar modified nucleoside of the external regions of the symmetric gapped oligomeric compound is a 4′
- -thio modified nucleoside or a 2′
-modified nucleoside.
- -thio modified nucleoside or a 2′
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19. The composition of claim 18 wherein each 2′
- -modified nucleoside is a 2′
-OCH3 or a 2′
-F modified nucleosides.
- -modified nucleoside is a 2′
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20. The composition of claim 18 wherein each sugar modified nucleoside of the external regions of the symmetric gapped oligomeric compound is a 4′
- -thio modified nucleoside.
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21. The composition of claim 20 wherein each nucleoside of the fully modified oligomeric compound is a 2′
- -OCH3 modified nucleoside.
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22. The composition of claim 21 wherein each of the first and second oligomeric compounds comprises 19 nucleosides.
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23. The composition of claim 1 wherein the second oligomeric compound is the symmetric gapped oligomeric compound.
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24. The composition of claim 23 wherein each sugar modified nucleoside of the external regions of the symmetric gapped oligomeric compound is a 2′
- -modified nucleoside wherein the 2′
-modification is selected from allyl, —
O-allyl, —
O—
C2-C10 alkyl, —
O—
(CH2)2—
OCH3 and —
O(CH2)2—
SCH3.
- -modified nucleoside wherein the 2′
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25. The composition of claim 24 wherein each 2′
- -modification is —
O—
(CH2)2—
OCH3.
- -modification is —
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26. The composition of claim 2 wherein each external region of the symmetric gapped oligomeric compound independently comprises from 1 to about 6 nucleosides.
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27. The composition of claim 2 wherein each external region of the symmetric gapped oligomeric compound independently comprises from 1 to about 4 nucleosides.
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28. The composition of claim 2 wherein each external region of the symmetric gapped oligomeric compound independently comprises from 1 to about 3 nucleosides.
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29. The composition of claim 1 wherein each nucleoside of the fully modified oligomeric compound is a sugar modified nucleoside and wherein each sugar modification is the same.
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30. The composition of claim 29 wherein each sugar modified nucleoside of the fully modified oligomeric compound is selected from 2′
- -modified nucleosides, 4′
-thio modified nucleosides, 4′
-thio-2′
-modified nucleosides and nucleosides having bicyclic sugar moieties.
- -modified nucleosides, 4′
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31. The composition of claim 30 wherein each sugar modified nucleoside is a 2′
- -modified nucleoside.
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32. The composition of claim 31 wherein each sugar modified nucleoside is a 2′
- -OCH3 or a 2′
-F modified nucleoside.
- -OCH3 or a 2′
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33. The composition of claim 32 wherein each sugar modified nucleoside is a 2′
- -OCH3 modified nucleoside.
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34. The composition of claim 32 wherein each sugar modified nucleoside is a 2′
- -F modified nucleoside.
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35. The composition of claim 29 wherein one or both of the 3′
- and 5′
-termini of the fully modified oligomeric compound further includes a β
-D-ribonucleoside.
- and 5′
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36. The composition of claim 1 having at least 2 phosphorothioate internucleoside linking groups at the 3′
- -end of the first oligomeric compound.
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37. The composition of claim 36 having about 7 phosphorothioate internucleoside linking groups at the 3′
- -end of the first oligomeric compound.
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38. The composition of claim 1 wherein the first oligomeric compound further comprises a 5′
- -thiophosphate group.
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39. 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.
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40. The composition of claim 1 wherein each of the first and second oligomeric compounds independently comprises from about 12 to about 30 nucleosides.
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41. The composition of claim 1 wherein each of the first and second oligomeric compounds independently comprises from about 17 to about 23 nucleosides.
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42. The composition of claim 1 wherein each of the first and second oligomeric compounds independently comprises from about 19 to about 21 nucleosides.
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43. The composition of claim 1 wherein the first and the second oligomeric compounds form a complementary antisense/sense siRNA duplex.
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44. The composition of claim 1 wherein the first oligomeric compound is an antisense oligomeric compound and the second oligomeric compound is a sense oligomeric compound.
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45. A method of inhibiting gene expression comprising contacting one or more cells, a tissue or an animal with a composition of claim 1.
Specification