Human papillomavirus 56 nucleic acid hybridization probes and methods for employing the same

• US 4,908,306 A
• Filed: 04/27/1989
• Issued: 03/13/1990
• Est. Priority Date: 06/12/1987
• Status: Expired due to Term

• Current Assignee: Digene Dianostics Incorporated
• Original Assignee: Life Technologies Incorporated (Thermo Fisher Scientific Incorporated)
• Inventors: Lorincz, Attila T.
• Primary Examiner(s): Warden, Robert J.
• Assistant Examiner(s): Spiegel, J.
• Application Number:
  US07/343,699
• Time in Patent Office: 320 Days
• Field of Search: 435/5, 435/6, 435/7, 435/21, 435/28, 435/172.1, 435/948, 436/501, 536/26-28, 935/77, 935/78
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/708 for papilloma
• CPC Class Codes: Y10S 435/948 using viruses or cell lines

Abstract

Nucleic acid hybridization probes for human papillomavirus types and particularly human papillomavirus type 56; and methods for employing the same.

Claims

1. A recombinant DNA of HPV 56 comprising a cloning vector and substantially all of HPV 56 DNA or fragments thereof.

2. The recombinant DNA of HPV 56 as claimed in claim 1, wherein said cloning vector is selected from the group consisting of pBR322, pUC11, λ

charon, λ

L47, M13 derived bacteriophage, pZIP-Neo SV [X1], pBKTK-1, pT712 and pT713.

3. The recombinant DNA of HPV 56 as claimed in claim 1, wherein said fragments are about 15 to about 8000 base pairs in size.

4. The recombinant DNA of HPV 56 as claimed in claim 3, wherein said fragments are about 300 to about 800 base pairs in size.

5. The recombinant DNA of HPV 56 as claimed in claim 1, wherein said recombinant DNA has the identifying characteristics of a member selected from the group consisting of HPV 56 clones 2A, 2B and 2C (ATCC Nos. 40341, 40379 and 40549, respectively).

6. The recombinant DNA of HPV 56 as claimed in claim 1, wherein the HPV DNA of said recombinant DNA is labelled with a marker.

7. The recombinant DNA of HPV 56 as claimed in claim 6, wherein said marker is a radioactive marker.

8. The recombinant DNA of HPV 56 as claimed in claim 7, wherein said marker is a radioactive marker selected from the group consisting of ³² P, ¹⁴ C, ³ H, ¹²⁵ I and ³⁵ S.

9. The recombinant DNA of HPV 56 as claimed in claim 6, wherein said marker is a non-radioactive marker selected from the group consisting of biotin, an enzyme and a fluorescent molecule.

10. The recombinant DNA of HPV 56 as claimed in claim 9, wherein said enzyme is selected from the group consisting of alkaline phosphatase and horseradish peroxidase.

11. The recombinant DNA of HPV 56 as claimed in claim 9, wherein said fluorescent molecule is selected from the group consisting of fluorescein and rhodamine.

12. Essentially pure HPV 56 DNA or fragments thereof.

13. The essentially pure HPV 56 DNA as claimed in claim 12, wherein said HPV 56 DNA or fragments thereof are produced biologically.

14. The essentially pure HPV 56 DNA as claimed in claim 12, wherein said HPV 56 DNA or fragments thereof are produced chemically.

15. The essentially pure HPV 56 DNA as claimed in claim 12, wherein said fragments are about 15 to about 8000 bases or base pairs in size.

16. The essentially pure HPV 56 DNA as claimed in claim 15, wherein said fragments are about 300 to about 800 bases or base pairs in size.

17. The essentially pure HPV 56 DNA as claimed in claim 12, wherein said HPV 56 DNA or fragments thereof are labelled with a marker.

18. The essentially pure HPV 56 DNA as claimed in claim 17, wherein said marker is a radioactive marker.

19. The essentially pure HPV 56 DNA as claimed in claim 18, wherein said marker is a radioactive marker selected from the group consisting of ³² P, ¹⁴ C, ³ H, ¹²⁵ I and ³⁵ S.

20. The essentially pure HPV 56 DNA as claimed in claim 17, wherein said marker is a non-radioactive marker selected from the group consisting of biotin, an enzyme and a fluorescent molecule.

21. The essentially pure HPV 56 DNA as claimed in claim 20, wherein said enzyme is selected from the group consisting of alkaline phosphatase and horseradish peroxidase.

22. The essentially pure HPV 56 DNA as claimed in claim 20, wherein said fluorescent molecule is selected from the group consisting of fluorescein and rhodamine.

23. Essentially pure HPV 56 RNA or fragments thereof.

24. The essentially pure HPV 56 RNA as claimed in claim 23, wherein said HPV 56 RNA or fragments thereof are produced biologically.

25. The essentially pure HPV 56 RNA as claimed in claim 23, wherein said HPV 56 RNA or fragments thereof are produced chemically.

26. The essentially pure HPV 56 RNA as claimed in claim 23, wherein said fragments are about 15 to about 8000 bases or base pairs in size.

27. The essentially pure HPV 56 RNA as claimed in claim 26, wherein said fragments are about 300 to about 800 bases or base pairs in size.

28. The essentially pure HPV 56 RNA as claimed in claim 23, wherein said HPV 56 RNA or fragments thereof are labelled with a marker.

29. The essentially pure HPV 56 RNA as claimed in claim 28, wherein said marker is a radioactive marker.

30. The essentially pure HPV 56 RNA as claimed in claim 29, wherein said marker is a radioactive marker selected from the group consisting of ³² P, ¹⁴ C, ³ H, ¹²⁵ I and ³⁵ S.

31. The essentially pure HPV 56 RNA as claimed in claim 28, wherein said marker is a non-radioactive marker selected from the group consisting of biotin, an enzyme and a fluorescent molecule.

32. The essentially pure HPV 56 RNA as claimed in claim 31, wherein said enzyme is selected from the group consisting of alkaline phosphatase and horseradish peroxidase.

33. The essentially pure HPV 56 RNA as claimed in claim 31, wherein said fluorescent molecule is selected from the group consisting of fluorescein and rhodamine.

34. An HPV 56 hybridization probe comprising a member selected from the group consisting of (i) HPV 56 DNA or fragments thereof labelled with a marker and (ii) HPV 56 RNA or fragments thereof labelled with a marker.

35. The HPV 56 hybridization probe as claimed in claim 34, wherein said fragments are about 15 to about 8000 bases or base pairs in size.

36. The HPV 56 hybridization probe as claimed in claim 35, wherein said fragments are about 300 to about 800 bases or base pairs in size.

37. The HPV 56 hybridization probe as claimed in claim 34, wherein said marker is a radioactive marker.

38. The HPV 56 hybridization probe as claimed in claim 37, wherein said marker is a radioactive marker selected from the group consisting of ³² P, ¹⁴ C, ³ H, ¹²⁵ I and ³⁵ S.

39. The HPV 56 hybridization probe as claimed in claim 34, wherein said marker is a non-radioactive marker selected from the group consisting of biotin, an enzyme and a fluorescent molecule.

40. The HPV 56 hybridization probe as claimed in claim 39, wherein said enzyme is selected from the group consisting of alkaline phosphatase and horseradish peroxidase.

41. The HPV 56 hybridization probe as claimed in claim 39, wherein said fluorescent molecule is selected from the group consisting of fluorescein and rhodamine.

42. An HPV hybridization probe composition comprising (a) a member selected from the group consisting of (i) HPV 56 DNA or fragments thereof labelled with a marker and (ii) HPV 56 RNA or fragments thereof labelled with a marker and, (b) DNA or RNA or fragments thereof of at least one other HPV type labelled with a marker.

43. The HPV hybridization probe composition as claimed in claim 42, wherein at least any one of said fragments are about 15 to about 8000 bases or base pairs in size.

44. The HPV hybridization probe composition as claimed in claim 43, wherein at least any one of said fragments are about 300 to about 800 bases or base pairs in size.

45. The HPV hybridization probe composition as claimed in claim 42, wherein at least any one of said marker is a radioactive marker.

46. The HPV hybridization probe composition as claimed in claim 45, wherein at least any one of said marker is a radioactive marker selected from the group consisting of ³² P, ¹⁴ C, ³ H, ¹²⁵ I and ³⁵ S.

47. The HPV hybridization probe composition as claimed in claim 42, wherein at least any one of said marker is a non-radioactive marker selected from the group consisting of biotin, an enzyme and a fluorescent molecule.

48. The HPV hybridization probe composition as claimed in claim 47, wherein said enzyme is selected from the group consisting of alkaline phosphatase and horseradish peroxidase.

49. The HPV hybridization probe composition as claimed in claim 47, wherein said fluorescent molecule is selected from the group consisting of fluorescein and rhodamine.

50. The HPV hybridization probe composition as claimed in claim 42, wherein said other HPV type is at least one member selected from the group consisting of HPV 6, HPV 11, HPV 16, HPV 18 and HPV 31.

51. The HPV hybridization probe composition as claimed in claim 50, wherein said other HPV type is at least one member selected from the group consisting of HPV 16, HPV 18 and HPV 31.

52. The HPV hybridization probe composition as claimed in claim 51, wherein said other HPV type is HPV 16, HPV 18 and HPV 31.

53. A method for detecting HPV DNA or RNA comprising:

(1) carrying out hybridization, under non-stringent conditions, with

(a) a labelled HPV 56 nucleic acid selected from the group consisting of

(i) HPV 56 DNA or fragments thereof labelled with a marker, and

(ii) HPV 56 RNA or fragments thereof labelled with a marker;

(b) an unknown sample of DNA or RNA; and

(c) at least one other labelled HPV type nucleic acid, and

(2) assaying for the presence of cross-hybridization between all labelled nucleic acids and said unknown sample so as to detect HPV DNA or RNA in said sample.

54. The method as claimed in claim 53, wherein said unknown sample of DNA or RNA is derived from a genital, throat, oral or skin lesion.

55. The method as claimed in claim 54, wherein said unknown sample of DNA or RNA is derived from a genital lesion.

56. The method as claimed in claim 55, wherein said unknown sample of DNA or RNA derived from a genital lesion is obtained by biopsying an epithelial lesion, scraping the cervix or by swabbing the cervix to obtain exfoliated cells or is DNA derived from a genital lesion which has been cloned in a cloning vector.

57. The method as claimed in claim 53, wherein at least any one of said fragments are about 15 to about 8000 bases or base pairs in size.

58. The method as claimed in claim 57, wherein at least any one of said fragments are about 300 to about 800 bases or base pairs in size.

59. The method as claimed in claim 53, wherein said other labelled HPV type nucleic acid is selected from the group consisting of:

(i) HPV 6 DNA or fragments thereof labelled with a marker;

(ii) HPV 6 RNA or fragments thereof labelled with a marker;

(iii) HPV 11 DNA or fragments thereof labelled with a marker;

(iv) HPV 11 RNA or fragments thereof labelled with a marker;

(v) HPV 16 DNA or fragments thereof labelled with a marker;

(vi) HPV 16 RNA or fragments thereof labelled with a marker;

(vii) HPV 18 DNA or fragments thereof labelled with a marker; and

(viii) HPV 18 RNA or fragments thereof labelled with a marker.

60. The method as claimed in claim 59, wherein said other HPV type is at least one member selected from the group consisting of HPV 16 and HPV 18.

61. The method as claimed in claim 60, wherein said other HPV type is HPV 16 and HPV 18.

62. The method as claimed in claim 53, wherein at least any one of said markers is a radioactive marker.

63. The method as claimed in claim 62, wherein at least any one of said markers is a radioactive marker selected from the group consisting of ³² P, ¹⁴ C, ³ H, ¹²⁵ I and ³⁵ S.

64. The method as claimed in claim 53, wherein at least any one of said markers is a non-radioactive marker selected from the group consisting of biotin, an enzyme and a fluorescent molecule.

65. The method as claimed in claim 64, wherein said enzyme is selected from the group consisting of alkaline phosphatase and horseradish peroxidase.

66. The method as claimed in claim 64, wherein said fluorescent molecule is selected from the group consisting of fluorescein and rhodamine.

67. The method as claimed in claim 53, wherein said cross-hybridization produces DNA-DNA hybrids.

68. The method as claimed in claim 53, wherein said cross-hybridization produces DNA-RNA hybrids.

69. A method for detecting HPV 56 DNA or RNA comprising:

(1) carrying out hybridization, under stringent conditions, with

(a) a member selected from the group consisting of

(i) HPV 56 DNA or fragments thereof labelled with a marker, and

(ii) HPV 56 RNA or fragments thereof labelled with a marker;

(b) an unknown sample of DNA or RNA, and

(2) assaying for the presence of cross-hybridization so as to detect HPV 56 DNA or RNA in said sample.

70. The method as claimed in claim 69, wherein said unknown sample of DNA or RNA is derived from a genital, throat, oral or skin lesion.

71. The method as claimed in claim 70, wherein said unknown sample of DNA or RNA is derived from a genital lesion.

72. The method as claimed in claim 71, wherein said unknown sample of DNA or RNA derived from a genital lesion is obtained by biopsying an epithelial lesion, scraping the cervix or by swabbing the cervix to obtain exfoliated cells or is DNA derived from a genital lesion which has been cloned in a cloning vector.

73. The method as claimed in claim 69, wherein said fragments are about 15 to about 8000 bases or base pairs in size.

74. The method as claimed in claim 73, wherein said fragments are about 300 to about 800 bases or base pairs in size.

75. The method as claimed in claim 69, wherein said HPV 56 DNA comprises substantially all of the HPV 56 genome.

76. The method as claimed in claim 69, wherein said markers is a radioactive marker.

77. The method as claimed in claim 76, wherein said markers is a radioactive marker selected from the group consisting of ³² P, ¹⁴ C, ³ H, ¹²⁵ I and ³⁵ S.

78. The method as claimed in claim 69, wherein said markers is a non-radioactive marker selected from the group consisting of biotin, an enzyme and a fluorescent molecule.

79. The method as claimed in claim 78, wherein said enzyme is selected from the group consisting of alkaline phosphatase and horseradish peroxidase.

80. The method as claimed in claim 78, wherein said fluorescent molecule is selected from the group consisting of fluorescein and rhodamine.

81. The method as claimed in claim 69, wherein said cross-hybridization produces DNA-DNA hybrids.

82. The method as claimed in claim 69, wherein said cross-hybridization produces DNA-RNA hybrids.

83. A method for detecting HPV 56 DNA or RNA comprising:

(1) carrying out hybridization, under stringent conditions, with

(a) a first fraction of DNA or RNA derived from each individual genital lesion of a sampling of genital lesions, which sampling shows an epidemiological progression to cervical cancer, and

(b) a member selected from the group consisting of

(i) HPV 56 DNA or fragments thereof labelled with a marker, and

(ii) HPV 56 RNA or fragments thereof labelled with a marker; and

assaying for the presence of cross-hybridization with the DNA or RNA derived from each individual genital lesion of said sampling of genital lesions;

(2) carrying out hybridization, under stringent conditions, with

(a) a second fraction of DNA or RNA derived from each individual genital lesion of said sampling of genital lesions, and

(b) an unknown sample of DNA or RNA derived from a genital lesion which has been labelled with a marker;

and assaying for the presence of cross-hybridization with the DNA or RNA derived from each individual genital lesion of said sampling of genital lesions;

(3) comparing the overall patterns of cross-hybridization of said sampling of genital lesions obtained in Step (1) with that obtained in Step (2); and

(4) comparing the cross-hybridizations of each individual genital lesion of said sampling of genital lesions obtained in Step (1) with that obtained in Step (2);

wherein the presence of HPV 56 DNA or RNA in said unknown sample is detected when both (i) the overall patterns of cross-hybridization of said sampling of genital lesions are essentially the same, and (ii) the cross-hybridizations of each individual genital lesion of said sampling of genital lesions are essentially the same.

84. The method as claimed in claim 83, wherein at least any one of said fragments are about 15 to about 8000 bases or base pairs in size.

85. The method as claimed in claim 84, wherein at least any one of said fragments are about 300 to about 800 bases or base pairs in size.

86. The method as claimed in claim 83, wherein at least any one of said HPV 56 DNA comprises substantially all of the HPV 56 genome.

87. The method as claimed in claim 83, wherein at least any one of said markers is a radioactive marker.

88. The method as claimed in claim 87, wherein at least any one of said markers is a radioactive marker selected from the group consisting of ³² P, ¹⁴ C, ³ H, ¹²⁵ I and ³⁵ S.

89. The method as claimed in claim 83, wherein at least any one of said markers is a non-radioactive marker selected from the group consisting of biotin, an enzyme and a fluorescent molecule.

90. The method as claimed in claim 89, wherein said enzyme is selected from the group consisting of alkaline phosphatase and horseradish peroxidase.

91. The method as claimed in claim 89, wherein said fluorescent molecule is selected from the group consisting of fluorescein and rhodamine.

92. The method as claimed in claim 83, wherein said unknown sample of DNA or RNA derived from a genital lesion is obtained by biopsying an epithelial lesion, scraping the cervix or by swabbing the cervix to obtain exfoliated cells or is DNA derived from a genital lesion which has been cloned in a cloning vector.

93. The method as claimed in claim 83, wherein at least any one of said cross-hybridization produces DNA-DNA hybrids.

94. The method as claimed in claim 83, wherein at least any one of said cross-hybridization produces DNA-RNA hybrids.