Compositions and methods using platinum compounds for nucleic acid labeling

• US 20020165369A1
• Filed: 03/01/2002
• Published: 11/07/2002
• Est. Priority Date: 03/02/2001
• Status: Active Grant

• Current Assignee: Stratagene California (Agilent Technologies, Inc.)
• Original Assignee: Stratagene California (Agilent Technologies, Inc.)
• Inventors: Braman, Jeffrey, Huang, Haoqiang
• Granted Patent: US 6,825,330 B2
• Time in Patent Office: Days
• US Class Current: 536/17.1
• CPC Class Codes: C07F 15/0093 without a metal-carbon linkage

Abstract

The invention relates to novel platinum-based compounds for labeling biomolecules. Platinum based labeling compounds according to the invention irreversibly attach to a target biomolecule via coordination of a platinum (II) metal center with N or S atoms on the target biomolecule. The invention relates to the novel compounds themselves, methods of making the platinum-based labeling compounds, probes labeled with such compounds, methods of making such labeled probes, and kits comprising the novel platinum-based labeling compounds and/or probes labeled with them. The invention also relates to methods of using probes labeled with platinum-based labeling compounds of the invention, particularly array and microarray hybridization methods.

Claims

1. A composition comprising the formula:

2. The composition of claim 1, wherein said leaving group is selected from the group consisting of NO₃, halogen CN, OCOR₇, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-demethyl-phenyl-4-sulfate, wherein R₇ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₆, —

(C═

O)OR₆, —

OCH₂(C═

O)R₆ and a salt.

3. The composition of claim 1 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)_q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_nO)_m(CH₂)_tQ, NH₂(CH₂)_mAr(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

4. The composition of claim 1 wherein the detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

5. A nucleic acid comprising a composition of claim 1.

6. The nucleic acid of claim 5 wherein said composition forms a non-covalent adduct with said nucleic acid.

7. A probe comprising a composition of claim 1.

8. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 1 with said nucleic acid.

9. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 6 and detecting signal from said detectable marker.

10. A composition comprising the formula:

11. The composition of claim 10, wherein said leaving group is selected from the group consisting of NO₃, halogen, CN, OCOR₇, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-dimethyl-phenyl-4-sulfate, wherein R₇ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₆, —

(C═

O)OR₆, —

OCH₂(C═

O)R₆ and a salt.

12. The composition of claim 10 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)_q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_nO)_m(CH₂)_tQ, NH₂(CH₂)_mAr(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

13. The composition of claim 10 wherein the detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

14. A nucleic acid comprising a composition of claim 10.

15. The nucleic acid of claim 14 wherein said composition forms a non-covalent adduct with said nucleic acid.

16. A probe comprising a composition of claim 10.

17. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 10 with said nucleic acid.

18. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 15 and detecting signal from said detectable marker.

20. The composition of claim 19, wherein said leaving group is selected from the group consisting of NO₃, halogen, CN, OCOR₃, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-dimethyl-phenyl-4-sulfate, wherein R₃ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₂, —

(C═

O)OR₂, or —

OCH₂(C═

O)R₂ and a salt.

21. The composition of claim 19 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)_q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_nO)_m(CH₂)_tQ, NH₂(CH₂)_mAr(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

22. The composition of claim 19 wherein said detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

23. A nucleic acid comprising a composition of claim 19.

24. The nucleic acid of claim 23 wherein said composition forms a non-covalent adduct with said nucleic acid.

25. A probe comprising a composition of claim 19.

26. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 19 with said nucleic acid.

27. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 25 and detecting signal from said detectable marker.

29. The composition of claim 28, wherein said leaving group is selected from the group consisting of No₃, halogen, CN, OCOR₅, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-dimethyl-phenyl-4-sulfate wherein R₅ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₄, —

(C═

O)OR₄, —

OCH₂(C═

O)R₄ and a salt.

30. The composition of claim 28 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)_q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_nO)_m(CH₂)_tQ, NH₂(CH₂)_mAr(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

31. The composition of claim 28 wherein said detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

32. A nucleic acid comprising a composition of claim 28.

33. The nucleic acid of claim 32 wherein said composition forms a non-covalent adduct with said nucleic acid.

34. A probe comprising a composition of claim 28.

35. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 28 with said nucleic acid.

36. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 34 and detecting signal from said detectable marker.

38. The composition of claim 37, wherein said leaving group is selected from the group consisting of No₃, halogen, CN, OCOR₅, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-dimethyl-phenyl-4-sulfate, wherein R₅ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₄, —

(C═

O)OR₄, —

OCH₂(C═

O)R₄ and a salt.

39. The composition of claim 37 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)_q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_nO)_m(CH₂)_tQ, NH₂(CH₂)_mA(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

40. The composition of claim 37 wherein said detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

41. A nucleic acid comprising a composition of claim 37.

42. The nucleic acid of claim 41 wherein said composition forms a non-covalent adduct with said nucleic acid.

43. A probe comprising a composition of claim 37.

44. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 37 with said nucleic acid.

45. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 43 and detecting signal from said detectable marker.

47. The composition of claim 46, wherein said leaving group is selected from the group consisting of No₃, halogen, CN, OCOR₃, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-dimethyl-phenyl-4-sulfate, wherein R₃ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₂, —

(C═

O)OR₂, —

OCH₂(C═

O)R₂ and a salt.

48. The composition of claim 46 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_nO)_m(CH₂)_tQ, NH₂(CH₂)_mAr(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

49. The composition of claim 46 wherein said detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

50. A nucleic acid comprising a composition of claim 46.

51. The nucleic acid of claim 50 wherein said composition forms a non-covalent adduct with said nucleic acid.

52. A probe comprising a composition of claim 46.

53. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 46 with said nucleic acid.

54. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 52 and detecting signal from said detectable marker.

19. A composition comprising the formula:

28. A composition comprising the formula:

37. A composition comprising the formula:

46. A composition comprising the formula

55. A composition comprising the formula

56. The composition of claim 55, wherein said leaving group is selected from the group consisting of NO₃, halogen, CN, OCOR₄, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-dimethyl-phenyl-4-sulfate, wherein R₄ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₃, —

(C═

O)OR₃, —

OCH₂(C═

O)R₃ and a salt.

57. The composition of claim 55 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)_q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_nO)_m(CH₂)_tQ, NH₂(CH₂)_mAr(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

58. The composition of claim 55 wherein said detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

59. A nucleic acid comprising a composition of claim 55.

60. The nucleic acid of claim 59 wherein said composition forms a non-covalent adduct with said nucleic acid.

61. A probe comprising a composition of claim 55.

62. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 55 with said nucleic acid.

63. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 61 and detecting signal from said detectable marker.

64. A composition comprising the formula:

65. The composition of claim 64, wherein said leaving group is selected from the group consisting of No₃, halogen, CN, OCOR₈, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-dimethyl-phenyl-4-sulfate, wherein R₈ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₇, —

(C═

O)OR₆, —

OCH₂(C═

O)R₇ and a salt.

66. The composition of claim 64 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)_q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_nO)_m(CH₂)_tQ, NH₂(CH₂)_mAr(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

67. The composition of claim 64 wherein the detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

68. A nucleic acid comprising a composition of claim 64.

69. The nucleic acid of claim 68 wherein said composition forms a non-covalent adduct with said nucleic acid.

70. A probe comprising a composition of claim 64.

71. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 67 with said nucleic acid.

72. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 70 and detecting signal from said detectable marker.

73. A composition comprising the formula

74. The composition of claim 73, wherein said leaving group is selected from the group consisting of No₃, halogen, CN, OCOR₈, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-dimethyl-phenyl-4-sulfate, wherein R₈ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₇, —

(C═

O)OR₆, —

OCH₂(C═

O)R₇ and a salt.

75. The composition of claim 73 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)_q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_nO)_m(CH₂)_tQ, NH₂(CH₂)_mAr(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

76. The composition of claim 73 wherein the detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

77. A nucleic acid comprising a composition of claim 73.

78. The nucleic acid of claim 77 wherein said composition forms a non-covalent adduct with said nucleic acid.

79. A probe comprising a composition of claim 73.

80. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 73 with said nucleic acid.

81. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 79 and detecting signal from said detectable marker.

82. A composition comprising the formula:

83. The composition of claim 82 wherein said leaving group is selected from the group consisting of No₃, halogen, CN, OCOR₆, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-dimethyl-phenyl-4-sulfate, wherein R₆ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₅, —

(C═

O)OR₅, —

OCH₂(C═

O)R₅ and a salt.

84. The composition of claim 82 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)_q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_m(CH₂)_tQ, NH₂(CH₂)_mAr(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

85. The composition of claim 82 herein the detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

86. nucleic acid comprising a composition of claim 82.

87. The nucleic acid of claim 86 wherein said composition forms a non-covalent adduct with said nucleic acid.

88. A probe comprising a composition of claim 82.

89. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 82 with said nucleic acid.

90. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 88 and detecting signal from said detectable marker.

91. A composition comprising the formula:

92. The composition of claim 91, wherein said leaving group is selected from the group consisting of NO₃, halogen, CN, OCOR₆, OCO-Phenyl, OCOCH₂OC(Phenyl)₃, O-Trityl and 3,5-dimethyl-phenyl-4-sulfate, wherein R₆ is selected from the group consisting of H, methyl, benzyl, sulfonate, phosphonate, NO₂, CF₃, halogen, O—

R₅, —

(C═

O)OR₅, —

OCH₂(C═

O)R₅ and a salt.

93. The composition of claim 91 wherein said linker is selected from the group consisting of:

(CH₂)n, (CH₂)_n(CH═

CH)_mO(CH═

CH)_p(CH₂)_q, CO(CH₂)_n(CH═

CH)_m(CH₂)_p, COAr(CH₂)_n(CH═

CH)_m(CH₂)_p, NH₂(CH₂)_nQ, NH₂((CH₂)_nO)_m(CH₂)_tQ, NH₂(CH₂)_mAr(CH₂)_nQ, wherein m, n, p, q and t are integers from 0 to 8, inclusive, and m, n, p, q and t are the same or different, wherein Q is selected from the group consisting of CONH, NHCO, —

S—

S—

, NHCSNH, NHCSO, wherein

94. The composition of claim 91 wherein the detectable marker, D, is selected from the group consisting of a fluorophore, a chromophore, a radiolabel, an enzyme and an affinity tag.

95. A nucleic acid comprising a composition of claim 91.

96. The nucleic acid of claim 95 wherein said composition forms a non-covalent adduct with said nucleic acid.

97. A probe comprising a composition of claim 91.

98. A method of labeling a nucleic acid, said method comprising the step of contacting a composition of claim 91 with said nucleic acid.

99. A method of probing a nucleic acid array, said method comprising the steps of contacting said array with a probe of claim 97 and detecting signal from said detectable marker.

100. A method of making a platinum labeling compound that comprises a stabilizing bridge, the method comprising the step of contacting potassium tetrachloroplatinate (II) with an aliphatic diamine labeled with a detectable marker, wherein said contacting results in a cis-platinum dichloride labeling compound.

101. The method of claim 100 wherein said aliphatic diamine is a cycloaliphatic diamine.

102. The method of claim 101 wherein said cycloaliphatic diamine is a 1,2-cycloaliphatic diamine.

103. The method of claim 101 wherein said cycloaliphatic diamine is a cyclohexyl diamine.

104. The method of claim 103 wherein said cyclohexyl diamine is a 1,2-cyclohexyl diamine.

105. The method of claim 100 wherein said contacting is performed in aqueous solution at a pH of about 1.5 to 5.5 and at a temperature of about 65°

C.