Phosphorous-linked oligomeric compounds and their use in gene modulation

• US 20050042647A1
• Filed: 06/03/2004
• Published: 02/24/2005
• Est. Priority Date: 06/06/1996
• Status: Abandoned Application

• Current Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Bhat, Balkrishen, Griffey, Richard H., Swayze, Eric E., Baker, Brenda F., Prakash, Thazha P., Manoharan, Muthiah, Crooke, Stanley T., Eldrup, Anne B.
• Application Number:
  US10/860,455
• Publication Number:
  US 20050042647A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/319 linked by 2'-5' linkages, i.e. having a free 3'-position
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/335 Modified T or U
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/342 Hemimers, i.e. of the type ====----
• CPC Class Codes: C12N 2310/343 having patterns, e.g. ==--==--==--
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy

Abstract

Oligonucleotide compositions comprising first and second oligonucleotides are provided wherein at least a portion of the first oligonucleotide is capable of hybridizing with at least a portion of the second oligonucleotide, at least a portion of the first oligonucleotide is complementary to and capble of hybridizing to a selected target nucleic acid, and at least one of the first or second oligonucleotides includes at least one nucleotide having a modified phosphorous-containing internucleoside linkage. Oligonucleotide/protein compositions are also provided comprising an oligonucleotide complementary to and capable of hybridizing to a selected target nucleic acid and at least one protein comprising at least a portion of an RNA-induced silencing complex (RISC), wherein at least one nucleotide of the oligonucleotide has a modified phosphorous-containing internucleoside linkage.

Claims

1. A composition comprising a first oligomer and a second oligomer, wherein:

at least a portion of said first oligomer is capable of hybridizing with at least a portion of said second oligomer,

at least a portion of said first oligomer is complementary to and capable of hybridizing to a selected target nucleic acid, and

at least one of said first or said second oligomers includes at least one nucleotide having a modification comprising;

a phosphorothioate;

phosphorodithioate;

phosphonate;

phosphonothioate;

phosphotriester;

phosphorothiotriester;

phosphoramidate;

phosphorothioamidate;

phosphinate;

boronate;

α

-D-arabinoftiranosyl;

or 2′

-5′

internucleoside linkage;

or

at least one of said first or said second oligomers contains at least one region of chirally pure internucleoside linkages or includes at least one region of inverted polarity.

2. The composition of claim 1 wherein said first and said second oligomers are a complementary pair of siRNA oligomers.

3. The composition of claim 1 wherein said first and said second oligomers are an antisense/sense pair of oligomers.

4. The composition of claim 1, wherein each of said first and second oligomers has from about 8 to about 80 nucleobases.

5. The composition of claim 1 wherein each of said first and second oligomers has from about 10 to about 50 nucleobases.

6. The composition of claim 1 wherein each of said first and second oligomers has from about 12 to about 30 nucleobases.

7. The composition of claim 1 wherein each of said first and second oligomers has from about 12 to about 24 nucleobases.

8. The composition of claim 1 wherein each of said first and second oligomers has from about 19 to about 23 nucleobases.

9. The composition of claim 1 wherein said first oligomer is an antisense oligomer.

10. The composition of claim 9 wherein said second oligomer is a sense oligomer.

11. The composition of claim 9 wherein said second oligomer has a plurality of ribose nucleotide units.

12. The composition of claim 1 wherein said first oligomer includes said nucleotide having said modification.

13. The composition of claim 1 wherein said phosphonate internucleoside linkage is an alkylphosphonate, cyclohexylphosphonate, benzylphosphonate, or phenylphosphonate internucleoside linkage.

14. The composition of claim 13 wherein said alkylphosphonate linkage is a methylphosphonate linkage.

15. The composition of claim 1 wherein said phosphotriester internucleoside linkage is a methylphosphotriester, ethylphosphotriester, isopropylphosphotriester, or propylphosphotriester internucleoside linkage.

16. The composition of claim 1 wherein said phosphotriester internucleoside linkage is an aminoalkylphosphotriester internucleoside linkage.

17. The composition of claim 1 wherein said phosphotriester internucleoside linkage is an S-alkylphosphorothiotriester, S-arylphosphorothiotriester, O-alkylphosphorothiotriester, or O-arylphosphorothiotriester internucleotide linkage.

18. The composition of claim 1 wherein said phosphoramidate internucleoside linkage is a 3′

aminophosphoramidate, aminoalkylphosphoramidate, or aminoalkylphosphorthioamidate internucleoside linkage.

19. The composition of claim 1 wherein said 2′

-5′

internucleoside linkage is a 2′

-5′

adenosine linkage, 2′

-5′

adenosine phosphorothioate linkage, a 2′

-5′

xyloadenosine linkage, or a linkage of one of the following formulas

20. The composition of claim 1 wherein said chirally pure internucleoside linkage is a chirally pure phosphorothioate, alkylphosphonate, phosphotriester, phosphodiesterthioester, or phosphoramidate internucleoside linkage.

21. A pharmaceutical composition comprising the composition of claim 1 and a pharmaceutically acceptable carrier.

22. A method of modulating the expression of a target nucleic acid in a cell comprising contacting said cell with a composition of claim 1.

23. A method of treating or preveting a disease or disorder associated with a target nucleic acid comprising administering to an animal having or predisposed to said disease or disorder a therapeutically effective amount of a composition of claim 1.

24. A composition comprising an oligomer complementary to and capable of hybridizing to a selected target nucleic acid and at least one protein, said protein comprising at least a portion of a RNA-induced silencing complex (RISC), wherein:

said oligomer includes at least one nucleotide having a modification comprising;

a phosphorothioate;

phosphorodithioate;

phosphonate;

phosphonothioate;

phosphotriester;

phosphorothiotriester;

phosphoramidate;

phosphorothioamidate;

phosphinate;

boronate;

α

-D-arabinofuranosyl;

or 2′

-5′

internucleoside linkage, or

said oligomer includes at least one region of chirally pure internucleoside linkages or includes at least one region of inverted polarity.

25. The composition of claim 24 wherein said oligomer is an antisense oligomer.

26. The composition of claim 24, wherein said oligomer has from about 8 to about 80 nucleobases.

27. The composition of claim 24 wherein said oligomer has from about 10 to about 50 nucleobases.

28. The composition of claim 24 wherein said oligomer has from about 12 to about 30 nucleobases.

29. The composition of claim 24 wherein said oligomer has from about 12 to about 24 nucleobases.

30. The composition of claim 24 wherein said oligomer has from about 19 to about 23 nucleobases.

31. The composition of claim 24 including a further oligomer, wherein said further oligomer is complementary to and hydrizable to said oligomer.

32. The composition of claim 31 wherein said further oligomer is a sense oligomer.

33. The composition of claim 31 wherein said further oligomer is an oligomer having a plurality of ribose nucleotide units.

34. The composition of claim 24 wherein said phosphonate internucleoside linkage is an alkylphosphonate, cyclohexylphosphonate, benzylphosphonate, or phenylphosphonate internucleoside linkage.

35. The composition of claim 34 wherein said alkylphosphonate linkage is a methylphosphonate linkage.

36. The composition of claim 24 wherein said phosphotriester internucleoside linkage is a methylphosphotriester, ethylphosphotriester, isopropylphosphotriester, or propylphosphotriester internucleoside linkage.

37. The composition of claim 24 wherein said phosphotriester internucleoside linkage is an aminoalkylphosphotriester internucleoside linkage.

38. The composition of claim 24 wherein said phosphotriester internucleoside linkage is an S-alkylphosphorothiotriester, S-arylphosphorothiotriester, O-alkylphosphorothiotriester, or O-arylphosphorothiotriester internucleotide linkage.

39. The composition of claim 24 wherein said phosphoramidate internucleoside linkage is a 3′

aminophosphoramidate, aminoalkylphosphoramidate, or aminoalkylphosphorthioamidate internucleoside linkage.

40. The composition of claim 24 wherein said 2′

-5′

internucleoside linkage is a 2′

-5′

adenosine linkage, 2′

-5′

adenosine phosphorothioate linkage, a 2′

-5′

xyloadenosine linkage, or a linkage of one of the following formulas

41. The composition of claim 24 wherein said chirally pure internucleoside linkage is a chirally pure phosphorothioate, alkylphosphonate, phosphotriester, phosphodiesterthioester, or phosphoramidate internucleoside linkage.

42. A pharmaceutical composition comprising the composition of claim 24 and a pharmaceutically acceptable carrier.

43. A method of modulating the expression of a target nucleic acid in a cell comprising contacting said cell with a composition of claim 24.

44. A method of treating or preveting a disease or disorder associated with a target nucleic acid comprising administering to an animal having or predisposed to said disease or disorder a therapeutically effective amount of a composition of claim 24.

45. An oligomer having at least a first region and a second region wherein:

said first region of said oligomer is complementary to and capable of hybridizing with said second region of said oligomer,

at least a portion of said oligomer is complementary to and capable of hybridizing to a selected target nucleic acid, and

said oligomer includes at least two nucleosides having a modification comprising;

a phosphorothioate;

phosphorodithioate;

phosphonate;

phosphonothioate;

phosphotriester;

phosphorothiotriester;

phosphoramidate;

phosphorothioamidate;

phosphinate;

boronate;

α

-D-arabinofuranosyl;

or 2′

-5′

internucleoside linkage;

or

said oligomer contains at least one region of chirally pure internucleoside linkages or includes at least one region of inverted polarity.

46. The oligomer of claim 45 wherein each of said first and said second regions is at least 10 nucleosidic bases.

47. The oligomer of claim 45 wherein said first region in a 5′

to 3′

direction is complementary to said second region in a 3′

to 5′

direction.

48. The oligomer of claim 45 wherein said oligomer includes a hairpin structure.

49. The oligomer of claim 45 wherein said first region of said oligomer is spaced from said second region of said oligomer by a third region and where said third region comprises at least two nucleosidic bases.

50. The oligomer of claim 45 wherein said first region of said oligomer is spaced from said second region of said oligomer by a third region and where said third region comprises a non-nucleosidic base region.

51. A pharmaceutical composition comprising the oligomer of claim 45 and a pharmaceutically acceptable carrier.

52. A method of modulating the expression of a target nucleic acid in a cell comprising contacting said cell with an oligomer of claim 45.

53. A method of treating or preventing a disease or disorder associated with a target nucleic acid comprising administering to an animal having or predisposed to said disease or disorder a therapeutically effective amount of an oligomer of claim 45.