Closed antisense and sense oligonucleotides and their applications

• US 6,369,038 B1
• Filed: 11/23/1993
• Issued: 04/09/2002
• Est. Priority Date: 04/25/1991
• Status: Expired due to Fees

• Current Assignee: Serono Genetics Institute S.A. (Merck & Co., Inc.)
• Original Assignee: Genset SA
• Inventors: Brandys, Pascal, dʼAuriol, Luc, Vasseur, Marc, Blumenfeld, Marta
• Primary Examiner(s): Martinell, James
• Application Number:
  US08/137,134
• Time in Patent Office: 3,059 Days
• Field of Search: 435/91.1, 435/6, 536/23.1, 536/24.2, 536/24.3, 536/24.31, 514/44, 514/2
• US Class Current: 514/44.00R
• CPC Class Codes: A61K 31/70 Carbohydrates; Sugars; Derivatives thereof sorbitol A61K31/047
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/00 Drugs for immunological or allergic disorders
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/13 Decoys
• CPC Class Codes: C12N 2310/53 partially self-complementary or closed

Abstract

An antisense or sense agent of the oligonucleotide type, includes a single-stranded oligonucleotide sequence having a binding affinity for DNA, RNA, or protein selected from the group consisting of (a) a sequence whose ends are linked to one another via covalent linkage to form a closed, single-stranded structure, and (b) a sequence wherein one free end is linked to an internal nucleotide via covalent linkage to form a closed, single-stranded branched structure.

Claims

1. An antisense or sense agent of the oligonucleotide type, comprising a single-stranded oligonucleotide sequence having a binding affinity for DNA, RNA, or protein selected from the group consisting of (a) a sequence whose ends are linked to one another via covalent linkage to form a closed, single-stranded structure, and (b) a sequence wherein one free end is linked to an internal nucleotide via covalent linkage to form a closed, single-stranded branched structure wherein the nucleotide sequence does not contain sequences capable of self-pairing.

2. The antisense or sense agent as claimed in claim 1, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked via a non-nucleoside monophosphate linkage as a covalent part of the backbone.

3. The antisense or sense agent as claimed in claim 2, wherein a compound is coupled to the non-nucleoside monophosphate linkage, where the compound is a bridging agent, an intercalating agent, or a cleaving agent or a molecule increasing intracellular penetration.

4. The antisense or sense agent as claimed in claim 3, wherein the, non-nucleoside monophosphate linkage is a peptide.

5. The antisense or sense agent as claimed in claim 3, wherein the non-nucleoside monophosphate linkage is a lipid.

6. A method of using the agent as claimed in claim 2, as an antiviral or anticancer agent or as an inducer of natural immuno-modulators, comprising administering to a patient in need thereof a therapeutically effective amount of the agent.

7. A method of using the agent of claim 2 in the treatment of dermatological pathology comprising topically administering to a patient in need thereof a pharmaceutically effective amount of the agent.

11. The antisense or sense agent as claimed in claim 1, wherein the single-stranded oligonucleotide sequence is a sequence whose ends are covalently linked.

12. The antisense or sense agent as claimed in claim 1, wherein the nucleotide sequence contains sequences capable of pairing to form double-stranded self-pairings.

13. The antisense or sense agent as claimed in claim 12, wherein the sequences capable of pairing are separated by sequences incapable of pairing.

14. The antisense or sense agent as claimed in claim 12, wherein the single-stranded oligonucleotide sequence comprises a sequence that can affinity-bind a protein.

15. The antisense or sense agent as claimed in claim 1, wherein a compound is coupled to the single-stranded oligonucleotide, wherein the compound is a bridging agent, an intercalating agent, or a cleaving agent of molecular increasing intracellular penetration.

16. The antisense or sense agent as claimed in claim 1, wherein the single-stranded sequence is a sequence complementary to a region of a messenger RNA or of a natural DNA fragment.

18. The antisense or sense agent as claimed in claim 1, which contains a polyribonucleotide portion capable of exerting a trans cleavage activity on an RNA.

19. The antisense or sense agent as claimed in claim 1, wherein the oligonucleotide sequence contains between 10 and 100 nucleotides.

20. The antisense or sense agent as claimed in claim 19, wherein the oligonucleotide sequence contains between 20 and 50 nucleotide.

21. The method for preparing an agent as claimed in claim 1, wherein the partial or total chemical synthesis of the single-stranded chain of the compound has been performed before the latter is cvilized.

22. A method of using the agent as claimed in claim 1, as an antiviral or anticancer agent or as an inducer of natural immuno-modulators, comprising administering to a patient in need thereof a therapeutically effective amount of the agent.

23. A method as claimed in claim 22, wherein the agent is an interferon inducer.

24. A method of using the agent of claim 1 in the treatment of dermatological pathology comprising topically administering to a patient in need thereof a pharmaceutically effective amount of the agent.

25. In a method of in vitro diagnosis using an oligonucleotide agent, the improvement wherein the agent is the agent of claim 1.

26. A pharmaceutical composition comprising a pharmaceutically effective amount of the agent of claim 1 and a pharmaceutically acceptable carrier.

27. The composition as claimed in claim 26 in a form suitable for external topical administration.

28. In a cosmetic including a therapeutic agent, the improvement wherein the agent is the agent of claim 1.

29. The antisense or sense agent as claimed in claim 1, wherein the single-stranded oligonucleotide sequence comprises a sequence that can affinity-bind a protein.

8. The antisense or sense agent as claimed in claimed 1, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked to one another via a phosphodiester internucleotide bond.

9. A method of using the agent as claimed in claim 8, as an antiviral or anticancer agent or as an inducer of natural immuno-modulators, comprising administering to a patient in need thereof a therapeutically effective amount of the agent.

10. A method of using the agent of claim 8 in the treatment of dermatological pathology comprising topically administering to a patient in need thereof a pharmaceutically effective amount of the agent.

17. The antisense or sense agent as claimed in claime 1, wherein the single-stranded oligonucleotide sequence comprises a sequence that can affinity-bind a protein.

30. An antisense or sense agent of the oligonucleotide type, comprising a single-stranded oligonucleotide sequence having a binding affinity for DNA, RNA, or protein selected from the group consisting of (a) a sequence whose ends are linked to one another via covalent linkage to form a closed, single-stranded structure, and (b) a sequence wherein one free end is linked to an internal nucleotide via covalent linkage to form a closed single-stranded branched structure wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked via a non-nucleoside monophosphate linkage as a covalent part of the backbone and a compound selected from the group consisting of a bridging agent, an intercalating agent, a cleaving agent, and a molecule increasing intracellular penetration compound is coupled to the non-nucleoside monophosphate linkage and the non-nucleoside monophosphate linkage is a peptide or lipid linkage.

31. The antisense or sense agent of claim 30, wherein said linkage is a peptide linkage.

32. The antisense or sense agent of claim 30, wherein said linkage is a lipid linkage.

33. The antisense or sense agent of claim 30, wherein said compound is a bridging agent.

34. The antisense or sense agent of claim 30, wherein said compound is an intercalating agent.

35. The antisense or sense agent of claim 30, wherein said compound is a cleaving agent.

36. The antisense or sense agent of claim 30, wherein said compound is a molecule increasing intracellular penetration.

37. The antisense or sense agent as claimed in claim 30, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked via a non-nucleoside monophosphate linkage as a covalent part of the backbone.

38. The antisense or sense agent as claimed in claim 30, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked to one another via a phosphodiester intemucleotide bond.

39. The antisense or sense agent as claimed in claim 30, wherein the single-stranded oligonucleotide sequence is a sequence whose ends are covalently linked.

40. The antisense or sense agent as claimed in claim 30, wherein the nucleotide sequence does not contain sequences capable of self-pairing.

41. The antisense or sense agent as claimed in claim 40, wherein the single-stranded oligonucleotide sequence comprises a sequence that can affinity-bind a protein.

42. The antisense or sense agent as claimed in claim 30, wherein the nucleotide sequence contains sequences capable of pairing to form double-stranded self-pairings.

43. The antisense or sense agent as claimed in claim 42, wherein the fragments capable of pairing are separated by sequences incapable of pairing.

44. The antisense or sense agent as claimed in claim 42, wherein the single-stranded oligonucleotide sequence comprises a sequence that can affinity-bind a protein.

45. The antisense or sense agent as claimed in claim 30, wherein a compound is coupled to the single-stranded oligonucleotide, wherein the compound is a bridging agent, an intercalating agent, or a cleaving agent of molecular increasing intercellular penetration.

46. The antisense or sense agent as claimed in claim 30, wherein the single-stranded sequence is a sequence complementary to a region of a messenger RNA or of a natural DNA fragment.

47. The antisense or sense agent as claimed in claim 30, wherein the single-stranded oligonucleotide sequence comprises a sequence that can affinity-bind a protein.

48. The antisense or sense agent as claimed in claim 30, which contains a polyribonucleotide portion capable of exerting a trans cleavage activity on an RNA.

49. The antisense or sense agent as claimed in claim 30, wherein the oligonucleotide sequence contains between 10 and 100 nucleotides.

50. The antisense or sense agent as claimed in claim 30, wherein the oligonucleotide sequence contains between 20 and 50 nucleotides.

51. A method for preparing an agent as claimed in claim 30, wherein the partial or total chemical synthesis of the single-stranded chain of the compound has been performed before the latter is cyclized.

52. In a method of in vitro diagnosis using an oligonucleotide agent, the improvement wherein the agent is the agent of claim 30 and comprises contacting a biological sample with the agent of claim 30 in a hybridization assay.

53. A pharmaceutical composition comprising a pharmaceutically effective amount of the agent of claim 30 and a pharmaceutically acceptable carrier.

54. The composition as claimed in claim 53 in a form suitable for external topical administration.

55. In a cosmetic including a therapeutic agent, the improvement wherein the agent is the agent of claim 30.

56. A method of using an antisense or sense agent of the oligonucleotide type, comprising a single-stranded oligonucleotide sequence having a binding affinity for DNA, RNA, or protein selected from the group consisting of (a) a sequence whose ends are linked to one another via covalent linkage to form a closed, single-stranded structure, and (b) a sequence wherein one free end is linked to an internal nucleotide via covalent linkage to form a closed single-stranded branched structure wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked via a non-nucleoside monophosphate linkage as a covalent part of the backbone and a compound selected from the group consisting of a bridging agent, an intercalating agent, a cleaving agent, and a molecule increasing intracellular penetration compound is coupled to the non-nucleoside monophosphate linkage and the non-nucleoside monophosphate linkage is a peptide or lipid linkage, as an antiviral or anticancer agent or as an inducer of natural immuno-modulators, comprising administering to a patient in need thereof a therapeutically effective amount of the agent.

57. The method of claim 56, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked via a non-nucleoside monophosphate linkage as a covalent part of the backbone.

58. The method of claim 56, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked to one another via a phosphodiester internucleotide bond.

59. The method as claimed in claim 56, wherein the agent is an interferon inducer.

60. A method of using an antisense or sense agent of the oligonucleotide type, comprising a single-stranded oligonucleotide sequence having a binding affinity for DNA, RNA, or protein selected from the group consisting of (a) a sequence whose ends are linked to one another via covalent linkage to form a closed, single-stranded structure, and (b) a sequence wherein one free end is linked to an internal nucleotide via covalent linkage to form a closed single-stranded branched structure wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked via a non-nucleoside monophosphate linkage as a covalent part of the backbone and a compound selected from the group consisting of a bridging agent, an intercalating agent, a cleaving agent, and a molecule increasing intracellular penetration compound is coupled to the non-nucleoside monophosphate linkage and the non-nucleoside monophosphate linkage is a peptide or lipid linkage, as an antiviral or anticancer agent or as an inducer of natural immuno-modulators in the treatment of dermatological pathology comprising topically administering to a patient in need thereof a pharmaceutically effective amount of the agent.

61. The method of claim 60, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked via a non-nucleoside monophosphate linkage as a covalent part of the backbone.

62. The method of claim 60, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked to one another via a phosphodiester intemucleotide bond.

63. An antisense or sense agent of the oligonucleotide type, comprising a single-stranded oligonucleotide sequence having a binding affinity for DNA, RNA, or protein selected from the group consisting of (a) a sequence whose ends are linked to one another via covalent linkage to form a closed, single-stranded structure, and (b) a sequence wherein one free end is linked to an internal nucleotide via covalent linkage to form a closed single-stranded branched structure and a polyribonucleotide portion capable of exerting a trans cleavage activity on an RNA.

64. The antisense or sense agent as claimed in claim 63, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked via a non-nucleoside monophosphate linkage as a covalent part of the backbone.

65. The antisense or sense agent as claimed in claim 64, wherein a compound is coupled to the single-stranded oligonucleotide, wherein the compound is a bridging agent, an intercalating agent, or a cleaving agent or a molecule increasing intracellular penetration.

66. The antisense or sense agent as claimed in claim 65, wherein the non-nucleoside monophosphate linkage is a peptide.

67. The antisense or sense agent as claimed in claim 65, wherein the non-nucleoside monophosphate linkage is a lipid.

68. The antisense or sense agent as claimed in claim 63, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked to one another via a phosphodiester internucleotide bond.

69. The antisense or sense agent as claimed in claim 63, wherein the single-stranded oligonucleotide sequence is a sequence whose ends are covalently linked.

70. The antisense or sense agent as claimed in claim 63, wherein the nucleotide sequence does not contain sequences capable of self-pairing.

71. The antisense or sense agent as claimed in claim 70, wherein the single-stranded oligonucleotide sequence comprises a sequence that can affinity-bind a protein.

72. The antisense or sense agent as claimed in claim 63, wherein the nucleotide sequence contains sequences capable of pairing to form double-stranded self-pairings.

73. The antisense or sense agent as claimed in claim 72, wherein the fragments capable of pairing are separated by sequences incapable of pairing.

74. The antisense or sense agent as claimed in claim 72, wherein the single-stranded oligonucleotide sequence comprises a sequence that can affinity-bind a protein.

75. The antisense or sense agent as claimed in claim 63, wherein a compound is coupled to the single-stranded oligonucleotide, wherein the compound is a bridging agent, an intercalating agent, or a cleaving agent, or a molecule increasing intracellular penetration.

76. The antisense or sense agent as claimed in claim 63, wherein the single-stranded sequence is a sequence complementary to a region of a messenger RNA or of a natural DNA fragment.

77. The antisense or sense agent as claimed in claim 63, wherein the single-stranded oligonucleotide sequence comprises a sequence that can affinity-bind a protein.

78. The antisense or sense agent as claimed in claim 63, wherein the oligonucleotide sequence contains between 10 and 100 nucleotides.

79. The antisense or sense agent as claimed in claim 78, wherein the oligonucleotide sequence contains between 20 and 50 nucleotides.

80. A method for preparing an agent as claimed in claim 63, wherein the partial or total chemical synthesis of the single-stranded chain of the compound has been performed before the latter is cyclized.

81. In a method of in vitro diagnosis using an oligonucleotide agent, the improvement wherein the agent is the agent of claim 63 and comprises contacting a biological sample with the agent of claim 63 in a hybridization assay.

82. A pharmaceutical composition comprising a pharmaceutically effective amount of the agent of claim 63 and a pharmaceutically acceptable carrier.

83. The composition of claim 82 in a form suitable for external topical administration.

84. In a cosmetic including a therapeutic agent, the improvement wherein the agent is the agent of claim 63.

85. A method of using an antisense or sense agent of the oligonucleotide type, comprising a single-stranded oligonucleotide sequence having a binding affinity for DNA, RNA, or protein selected from the group consisting of (a) a sequence whose ends are linked to one another via covalent linkage to form a closed, single-stranded structure, and (b) a sequence wherein one free end is linked to an internal nucleotide via covalent linkage to form a closed single-stranded branched structure and a polyribonucleotide portion capable of exerting a trans cleavage activity on an RNA, as an antiviral or anticancer agent or as an inducer of natural immuno-modulators, comprising administering to a patient in need thereof a therapeutically effective amount of the agent.

86. The method according to claim 85, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked via a non-nucleoside monophosphate linkage as a covalent part of the backbone.

87. The method of claim 85, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked to one another via a phosphodiester intemucleotide bond.

88. The method of claim 85, wherein the agent is an interferon inducer.

89. A method of using an antisense or sense agent of the oligonucleotide type, comprising a single-stranded oligonucleotide sequence having a binding affinity for DNA, RNA, or protein selected from the group consisting of (a) a sequence whose ends are linked to one another via covalent linkage to form a closed, single-stranded structure, and (b) a sequence wherein one free end is linked to an internal nucleotide via covalent linkage to form a closed single-stranded branched structure and a polyribonucleotide portion capable of exerting a trans cleavage activity on an RNA in the treatment of dermatological pathology comprising topically administering to a patient in need thereof a pharmaceutically effective amount of the agent.

90. The method of claim 89, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked via a non-nucleoside monophosphate linkage as a covalent part of the backbone.

91. The method of claim 89, wherein the single-stranded oligonucleotide sequence is a sequence whose 5′

and 3′

ends are linked to one another via a phosphodiester internucleotide bond.