COMPOSITIONS AND METHODS FOR SPECIFICALLY SILENCING A TARGET NUCLEIC ACID

1 . A method for specifically silencing the expression of a target nucleic acid in a biological sample, the method comprising contacting the biological sample with an oligonucleotide comprising a duplex portion, the duplex portion comprising a sense region base paired with an antisense region, the antisense region having at least about 70% complementary to the target nucleic acid such that the target nucleic acid is silenced by RNA interference, wherein the antisense region comprises at least one 2′-5′ internucleotide linkage in the region from the second nucleotide to the eighth nucleotide from the 5′ end.

2 . The method of claim 1 , wherein the silencing of off-target nucleic acids is reduced.

3 . The method of claim 2 , wherein the internucleotide linkages of the oligonucleotide are selected from the group consisting of phosphorus-containing linkages, non-phosphorus-containing linkages, and combinations thereof.

4 . The method of claim 3 , wherein the oligonucleotide comprises at least one 3′ overhang, the overhang comprising from one to about six nucleotides.

5 . The method of claim 4 , wherein the oligonucleotide comprises one antisense strand and at least one sense stand, and the duplex portion comprises from about 15 to about 40 base pairs.

6 . The method of claim 4 , wherein the oligonucleotide is a single molecule comprising the duplex portion and a loop region, the loop region connecting the duplexed sense and the antisense regions, and the duplex portion comprising from about 15 to about 40 base pairs.

7 . The method of claim 5 , wherein there is a 5′ phosphate group on the first nucleotide from the 5′ end of the antisense strand.

8 . The method of claim 5 , wherein there is a 5′ amino group on the first nucleotide from the 5′ end of the sense strand or strands.

9 . The method of claim 5 , wherein the oligonucleotide further comprises a 2′ substituent on at least one nucleotide in the sense region, the 2′ substituent being selected from the group consisting of hydrogen, halogen, —R, —NHR, —NRR 1 , —SR, and —OR, wherein R and R 1 are independently selected from the group consisting of hydrogen, hydrocarbyl, and substituted hydrocarbyl.

10 . The method of claim 5 , wherein there is at least one 2′-5′ internucleotide linkage in the sense strand.

11 . The method of claim 10 , wherein at least one of the 2′-5′ linked nucleotides also comprises a 3′ substituent selected from the group consisting of hydrogen, halogen, —R, —NHR, —NRR 1 , —SR, and —OR, wherein R and R 1 are independently selected from the group consisting of hydrogen, hydrocarbyl, and substituted hydrocarbyl.

12 . The method of claim 5 , wherein the oligonucleotide comprises one sense strand, and the duplex portion comprises from about 17 to about 25 base pairs.

13 . The method of claim 12 , wherein the 2′-5′ linkage is between the second and third nucleotides from the 5′ end of the antisense strand.

14 . The method of claim 13 , wherein there is a 5′ phosphate group on the first nucleotide from the 5′ end of the antisense strand, and there is a 5′ amino group on the first nucleotide from the 5′ end of the sense strand.

15 . The method of claim 13 , wherein there is a 5′ phosphate group on the first nucleotide from the 5′ end of the antisense strand, and there a 2′-O-methyl group on each of the first and second nucleotides from the 5′ end of the sense strand.

16 . The method of claim 13 , wherein there is a 5′ phosphate group on the first nucleotide from the 5′ end of the antisense strand, there is a 2′-O-methyl group on the first nucleotide from the 5′ end of the sense strand, and there is a second 2′-5′ linkage between the second and third nucleotides from the 5′ end of the sense strand.

17 . The method of claim 1 , wherein the biological sample is a cell or an extract of a cell.

18 . The method of claim 17 , wherein the cell is disposed in a human or an animal.

19 . An oligonucleotide, the oligonucleotide comprising a duplex portion, the duplex portion comprising a sense region base paired with an antisense region, and the antisense region comprising a 5′ phosphate group on the first nucleotide and at least one 2′-5′ internucleotide linkage in the region from the second nucleotide to the eighth nucleotide from the 5′ end.

20 . The oligonucleotide of claim 19 , wherein the internucleotide linkages of the oligonucleotide are selected from the group consisting of phosphorus-containing linkages, non-phosphorus-containing linkages, and combinations thereof.

21 . The oligonucleotide of claim 20 , wherein the oligonucleotide comprises at least one 3′ overhang, the overhang comprising from one to about six nucleotides.

22 . The oligonucleotide of claim 21 , wherein the oligonucleotide comprises one antisense strand and at least one sense stand, and the duplex portion comprises from about 15 to about 40 base pairs.

23 . The oligonucleotide of claim 21 , wherein the oligonucleotide is a single molecule comprising the duplex portion and a loop region, the loop region connecting the duplexed sense and the antisense regions, and the duplex portion comprising from about 15 to about 40 base pairs.

24 . The oligonucleotide of claim 22 , further comprising a 5′ amino group on the first nucleotide at the 5′ end of the sense strand.

25 . The oligonucleotide of claim 22 , further comprising a 2′ substituent on at least one nucleotide in the sense region, the 2′ substituent being selected from the group consisting of hydrogen, halogen, —R, —NHR, —NRR 1 , —SR, and —OR, wherein R and R 1 are independently selected from the group consisting of hydrogen, hydrocarbyl, and substituted hydrocarbyl.

26 . The oligonucleotide of claim 22 , further comprising at least one 2′-5′ internucleotide linkage in the sense strand.

27 . The oligonucleotide of claim 26 , wherein at least one of the 2′-5′ linked nucleotides also comprises a 3′ substituent selected from the group consisting of hydrogen, halogen, —R, —NHR, —NRR 1 , —SR, and —OR, wherein R and R 1 are independently selected from the group consisting of hydrogen, hydrocarbyl, and substituted hydrocarbyl.

28 . The oligonucleotide of claim 22 , wherein the oligonucleotide comprises one sense strand, and the duplex portion comprises from about 17 to about 25 base pairs.

29 . The oligonucleotide of claim 28 , wherein the at least one 2′-5′ linkage is between the second and third nucleotides from the 5′ end of the antisense strand.

30 . The oligonucleotide of claim 29 , further comprising a 5′ amino group on the first nucleotide at the 5′ end of the sense strand or stands.

31 . The oligonucleotide of claim 29 , further comprising a 2′-O-methyl group on each of the first and second nucleotides at the 5′ end of the sense strand.

32 . The oligonucleotide of claim 29 , further comprising a 2′-O-methyl group on the first nucleotide at the 5′ end of the sense strand, and a second 2′-5′ linkage between the second and third nucleotides from the 5′ end of the sense strand.