RNA aptamers and methods for identifying the same

1. An RNA aptamer which binds to the coagulation pathway factor IXa, the RNA aptamer comprising a secondary structure wherein the secondary structure consists essentially of, in a 5′ to 3′ direction, a first stem region, a first loop region, a second stem region, a second loop region, and a third loop region, wherein the first loop region comprises a consensus sequence comprising NNAUA, wherein N is selected from the group consisting of A, U, G, and C.

2. The aptamer of claim 1 , having a dissociation constant of about 20 nanomolar (nM) or less.

3. The aptamer of claim 2 , wherein the dissociation constant ranges from about 400 pM to about 10 nM.

4. The aptamer of claim 2 , wherein the dissociation constant ranges from about 100 pM to about 10 nM.

5. The aptamer of claim 1 , which comprises at least one modified nucleotide.

6. An RNA aptamer comprising a nucleotide sequence selected from SEQ ID NO:3 or a truncate thereof.

7. The aptamer of claim 6 , wherein the nucleotide sequence is SEQ ID NO: 70.

8. The aptamer of claim 6 , wherein the sequence is SEQ ID NO:3.

9. A pharmaceutical composition comprising a therapeutically effective amount of an RNA aptamer which binds to the coagulation pathway factor IXa, in a pharmaceutically acceptable diluent or vehicle, the RNA aptamer comprising a secondary structure wherein the secondary structure consists essentially of, in a 5′ to 3′ direction, a first stem region, a first loop region, a second stem region, a second loop region, and a third loop region, wherein the first loop region comprises consensus sequence comprising NNAUA, wherein N is selected from the group consisting of A, U, G, and C.

10. The aptamer of claim 5 , wherein the aptamer comprises at least one 2′-modified nucleotide.

11. The aptamer of claim 5 , wherein the aptamer comprises at least one 2′-halo-modified nucleotide.

12. The aptamer of claim 5 , wherein the aptamer comprises at least one 2′-fluoro-modified nucleotide.

13. The aptamer of claim 5 , wherein the aptamer comprises at least one 2′-O-alkyl-modified nucleotide.

14. The aptamer of claim 5 , wherein the aptamer comprises at least one 2′-methoxy-modified nucleotide.

15. The aptamer of claim 5 wherein at least one cytidine is 2′-deoxy-2′-fluorocytidine.

16. The aptamer of claim 5 wherein at least one uridine is 2′-deoxy-2′-fluorouridine.

17. The aptamer of claim 5 wherein all uridines are 2′-deoxy-2′-fluorouridine.

18. The aptamer of claim 1 , that comprises a 3′ chain terminator.

19. The aptamer of claim 1 , that comprises about 15 to 100 bases.

20. The aptamer of claim 1 , that has less than about 100 bases.

21. The aptamer of claim 1 , that has less than about 40 bases.

22. The aptamer of claim 1 , that comprises a covalently linked earner.

23. The aptamer of claim 22 wherein the carrier is a soluble polymer.

24. The aptamer of claim 22 wherein the carrier is a biodegradable polymer.

25. The aptamer of claim 22 wherein the carrier is polyethylene glycol.

26. The aptamer of claim 1 additionally comprising covalently linked cholesterol.

27. The aptamer of claim 1 , wherein the first stem region comprises at least about 5 nucleotides at a 5′ end of the aptamer that form base pairs with at least about 5 nucleotides at a 3′ end of the aptamer.

28. The pharmaceutical composition of claim 9 wherein the composition is in a unit dose.

29. The pharmaceutical composition of claim 9 , wherein the first stem region comprises at least about 5 nucleotides at a 5′ end of the aptamer that form base pairs with at least about 5 nucleotides at a 3′ end of the aptamer.

30. An RNA aptamer comprising a nucleotide sequence at least 80% homologous to a nucleotide sequence selected from SEQ ID NO:3 or a truncate thereof.

31. The aptamer of claim 30 , wherein the aptamer comprises at least one modified nucleotide.

32. The aptamer of claim 30 , wherein the aptamer comprises at least one 2′-modified nucleotide.

33. The aptamer of claim 30 , wherein the aptamer comprises at least one 2′-halo-modified nucleotide.

34. The aptamer of claim 30 , wherein the aptamer comprises at least one 2′-fluoro-modified nucleotide.

35. The aptamer of claim 30 , wherein the aptamer comprises at least one 2′-O-alkyl-modified nucleotide.

36. The aptamer of claim 30 , wherein the aptamer comprises at least one 2′-methoxy-modified nucleotide.

37. The aptamer of claim 30 , wherein at least one cytidine is 2′-deoxy-2′-fluorocytidine.

38. The aptamer of claim 30 , wherein at least one uridine is 2′-deoxy-2′-fluorouridine.

39. The aptamer of claim 30 , wherein all uridines are 2′-deoxy-2′-fluorouridine.

40. The aptamer of claim 30 , that comprises a 3′ chain terminator.

41. The aptamer of claim 30 , that comprises about 15 to 100 bases.

42. The aptamer of claim 30 , that has less than about 100 bases.

43. The aptamer of claim 30 , that has less than about 40 bases.

44. The aptamer of claim 30 , that comprises a covalently linked carrier.

45. The aptamer of claim 44 , wherein the carrier is a soluble polymer.

46. The aptamer of claim 44 , wherein the carrier is a biodegradable polymer.

47. The aptamer of claim 44 , wherein the carrier is polyethylene glycol.

48. The aptamer of claim 30 , additionally comprising covalently linked cholesterol.

49. The aptamer of claim 30 , that comprises a 3′ chain terminator.

50. The aptamer of claim 30 , that comprises about 15 to 100 bases.

51. The aptamer of claim 30 , that has less than about 100 bases.

52. The aptamer of claim 30 , that has less than about 40 bases.

53. The aptamer of claim 30 , wherein the aptamer includes a first stem region that comprises at least about 5 nucleotides at a 5′ end of the aptamer that form base pairs with at least about 5 nucleotides at a 3′ end of the aptamer.

54. A pharmaceutical composition comprising a therapeutically effective amount of an RNA aptamer which binds to the coagulation pathway factor IXa, the aptamer comprising a nucleotide sequence at least 80% homologous to a nucleotide sequence selected from SEQ ID NO:3 or a truncate thereof.

55. The pharmaceutical composition of claim 54 , wherein the composition is in a unit dose.