Chemically modified multifunctional short interfering nucleic acid molecules that mediate RNA interference

1. A chemically modified multifunctional short interfering nucleic acid (siNA), the structure of which is represented by Formula MF-III:

wherein:

each X, X′, Y, and Y′ is independently an oligonucleotide of length about 18 to about 28 nucleotides;

X comprises a nucleotide sequence that is complementary to a nucleotide sequence present in region Y′;

X′ comprises a nucleotide sequence that is complementary to a nucleotide sequence present in region Y;

one or more of X, X′, Y, and Y′ is independently complementary to a first or second target sequence, respectively, or a portion thereof; and

W represents a nucleotide or non-nucleotide linker that connects sequences Y′ and Y,

wherein the siNA directs cleavage of the first and/or second target sequence via RNA interference,

wherein X is annealed to Y′ and X′ is annealed to Y,

wherein, when Y′ or Y is an antisense strand, and when the 5′ end of one or both of Y′ and Y is connected by the linker W, W is a biodegradable linker such that the 5′ end of the antisense strand has a free 5′ end suitable to mediate RNA interference-based cleavage of a target RNA, and

wherein the chemically modified multifunctional siNA comprises one or more chemical modifications.

2. The chemically modified multifunctional siNA of claim 1 , wherein each X and X′ is independently an antisense strand complementary to the first and second target sequences, respectively, or a portion thereof.

3. The chemically modified multifunctional siNA of claim 1 , wherein each Y and Y′ is independently an antisense strand complementary to the first and second target sequences, respectively, or a portion thereof.

4. The chemically modified multifunctional siNA of claim 1 , wherein the first and second target sequences are present in the same target nucleic acid molecule.

5. The chemically modified multifunctional siNA of claim 1 , wherein the first and second target sequences are present in different target nucleic acid molecules.

6. The chemically modified multifunctional siNA of claim 2 , wherein W connects the 3′-end of the sequence Y′ with the 3′-end of the sequence Y, and the 5′-end of the sequences X and X′ face each other.

7. The chemically modified multifunctional siNA of claim 2 , wherein W connects the 3′-end of the sequence Y′ with the 5′-end of the sequence Y, and the 5′-end of the sequences X faces the 3′-end of the sequence X′.

8. The chemically modified multifunctional siNA of claim 2 , wherein W connects the 5′-end of the sequence Y′ with the 3′-end of the sequence Y, and the 3′-end of the sequences X faces the 5′-end of the sequence X′.

9. The chemically modified multifunctional siNA of claim 2 , wherein W connects the 5′-end of the sequence Y′ with the 5′-end of the sequence Y, and the 5′-end of the sequences X and X′ point away from each other.

10. The chemically modified multifunctional siNA of claim 1 , further comprising one or more terminal phosphate groups at the end of sequence X, X′, Y or Y′.

11. The chemically modified multifunctional siNA of claim 1 , wherein W is a biodegradable linker.

12. The chemically modified multifunctional siNA of claim 11 , wherein W is a biodegradable nucleic acid linker molecule containing 2 to 20 nucleotides in length.

13. The chemically modified multifunctional siNA of claim 12 , wherein W contains ribonucleotides, deoxyribonucleotides, 2′-modified nucleotides selected from the group consisting of 2′-O-methyl, 2′-fluoro, 2′-amino, 2′-O-amino, 2′-C-allyl, 2′-O-allyl, or combination thereof.

14. The chemically modified multifunctional siNA of claim 1 , wherein W contains a non-nucleotide linker selected from the group consisting of an abasic moiety, polyether, polyamine, polyamide, peptide, carbohydrate, lipid, and polyhydrocarbon.

15. The chemically modified multifunctional siNA of claim 14 , wherein W comprises one or more carbohydrates.

16. The chemically modified multifunctional siNA of claim 15 , W comprises one or more N-acetyl-galactosamine.

17. A pharmaceutical composition comprising the chemically modified multifunctional siNA of claim 1 alone or in combination with a pharmaceutically acceptable carrier or excipient.

18. The chemically modified multifunctional siNA of claim 1 , wherein the one or more chemical modifications are selected from the group consisting of phosphorothioate internucleotide linkage, 2′-deoxy modification, 2′-O-methyl modification, 2′-deoxy-2′-fluoro modification, 4′-thio modification, 2′-O-trifluoromethyl modification, 2′-O-ethyl-trifluoromethoxy modification, 2′-O-difluoromethoxy-ethoxy modification, 2′-deoxy-2′-fluoroarabino modification, universal base modification, acyclic modification, 5-C-methyl modification, glyceryl modification, abasic modification, inverted deoxy abasic modification, and combinations thereof.

19. A method for inhibiting the expression of a target gene comprising the step of administering the chemically modified multifunctional siNA of claim 1 , in an amount sufficient to inhibit expression of the target gene.