Compounds and methods for modulating protein expression

1. A method of modulating expression of a target protein in a cell by altering splicing of a target pre-mRNA encoding the target protein comprising contacting the cell with an oligomeric compound comprising a contiguous sequence of nucleosides having the formula I:

T 1 -(Nu 1 ) n1 -(Nu 2 ) n2 -(Nu 3 ) n3 -(Nu 4 ) n4 -(Nu 5 ) n5 -T 2 , wherein:

Nu 1 and Nu 5 are, independently, 2′ stabilizing nucleosides;

Nu 2 and Nu 4 are β-D-2′-deoxy-2′-fluororibofuranosyl nucleosides;

Nu 3 is a 2′-modified nucleoside;

each of n1 and n5 is, independently, from 0 to 3;

the sum of n2 plus n4 is between 10 and 25;

n3 is from 0 to 5; and

each T 1 and T 2 is, independently, H, a hydroxyl protecting group, an optionally linked conjugate group or a capping group;

wherein the oligomeric compound has a nucleobase sequence complementary to the target pre-mRNA; and thereby altering splicing of the pre-mRNA and thereby modulating expression of the target protein.

2. The method of claim 1 , wherein, Nu 1 and Nu 5 are, independently, 2% modified nucleosides.

3. The method of claim 2 , wherein, each of the 2′-modified nucleosides independently comprises a 2′-substituent group selected from halogen, O—C 1 -C 12 alkyl, substituted O—C 1 -C 12 alkyl, O—C 2 -C 12 alkenyl, substituted O—C 2 -C 12 alkenyl, O—C 2 -C 12 alkynyl, substituted O—C 2 -C 12 alkynyl, amino, substituted amino, amide, substituted amide, aralkyl, substituted aralkyl, O-aralkyl, substituted O-aralkyl, N 3 , SH, CN, OCN, CF 3 , OCF 3 , SOCH 3 , —SO 2 CH 3 , heterocycloalkyl, heterocycloalkaryl, aminoalkylamino and polyalkylamino; and

wherein each substituent group is, independently, halogen, C 1 -C 12 alkyl, substituted C 1 -C 12 alkyl, C 2 -C 12 alkenyl, substituted C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, substituted C 2 -C 12 alkynyl, O—C 1 -C 12 alkyl, substituted O—C 1 -C 12 alkyl, S—C 1 -C 12 alkyl, substituted S—C 1 -C 12 alkyl, acyl (C(═O)—H), substituted acyl, amino, substituted amino, amide, substituted amide, C 1 -C 12 alkylamino, substituted C 1 -C 12 alkylamino, C 1 -C 12 aminoalkoxy, substituted C 1 -C 12 aminoalkoxy, C 1 -C 12 alkylaminooxy, substituted C 1 -C 12 alkylaminooxy, guanidinyl, substituted guanidinyl or a protecting group.

4. The method of claim 3 , wherein, each 2′-substituent group is, independently, halogen, O(CH 2 ) 0-2 CH 3 , O(CH 2 ) 2 OCH 3 , O(CH 2 ) 2 SCH 3 , OCH 2 C(H)CH 2 , O(CH 2 ) 2 ON(CH 3 ) 2 or OCH 2 C(═O)N(H)CH 3 .

5. The method of claim 4 , wherein, each 2′-substituent group is, independently, OCH 3 or O—(CH 2 ) 2 —OCH 3 .

6. The method of claim 5 , wherein, each 2′-substituent group is O—(CH 2 ) 2 —OCH 3 .

7. The method of claim 2 , wherein, the 2′-modified nucleoside is a bicyclic sugar modified nucleoside.

8. The method of claim 4 , wherein, each of the bicyclic sugar modified nucleosides independently comprises a bridge group between the 2′ and the 4′-carbon atoms comprising from 1 to 8 linked biradical groups independently selected from —O—, —S—, —N(R 1 )—, —C(R 1 )(R 2 )—, —C(R 1 )═C(R 1 )—, —C(R 1 )═N—, —C(═NR 1 )—, —Si(R 1 )(R 2 )—, —S(═O) 2 —, —S(═O)—, —C(═O)— and —C(═S)—;

each R 1 and R 2 is, independently, H, hydroxyl, C 1 -C 12 alkyl, substituted C 1 -C 12 alkyl, C 2 -C 12 alkenyl, substituted C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, substituted C 2 -C 12 alkynyl, C 5 -C 20 aryl, substituted C 5 -C 20 aryl, a heterocycle radical, a substituted heterocycle radical, heteroaryl, substituted heteroaryl, C 5 -C 7 alicyclic radical, substituted C 5 -C 7 alicyclic radical, halogen, substituted oxy (—O—), amino, substituted amino, azido, carboxyl, substituted carboxyl, acyl, substituted acyl, CN, thiol, substituted thiol, sulfonyl (S(═O) 2 —H), substituted sulfonyl, sulfoxyl (S(═O)—H) or substituted sulfoxyl; and

wherein each substituent group is, independently, halogen, C 1 -C 12 alkyl, substituted C 1 -C 12 alkyl, C 2 -C 12 alkenyl, substituted C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, substituted C 2 -C 12 alkynyl, amino, substituted amino, acyl, substituted acyl, C 1 -C 12 aminoalkyl, C 1 -C 12 aminoalkoxy, substituted C 1 -C 12 aminoalkyl, substituted C 1 -C 12 aminoalkoxy or a protecting group.

9. The method of claim 8 , wherein, each bicyclic sugar modified nucleoside independently comprises 2 or 3 of the linked biradical groups.

10. The method of claim 9 , wherein, each bicyclic sugar modified nucleoside comprises 2 of the linked biradical groups.

11. The method of claim 8 , wherein, each bridge group is, independently, —CH 2 —, —(CH 2 ) 2 —, —CH 2 —O—, —(CH 2 ) 2 —O— or —CH 2 —N(R 3 )—O— wherein R 3 is H or C 1 -C 12 alkyl.

12. The method of claim 11 , wherein, each bridge group is, independently, —CH 2 —O— or —(CH 2 ) 2 —O—.

13. The method of claim 1 wherein the oligomeric compound comprises at least one phosphorothioate internucleoside linkage.

14. The method of claim 1 wherein each internucleoside linkage comprises a phosphorothioate internucleoside linkage.

15. The method of claim 1 , wherein the target protein is selected from SMN2, Bcl-x, MyD88, Lamin-A, and TNF.

16. The method of any of claim 1 , wherein the cell is in an animal.

17. The method of claim 16 , wherein the animal is a human.