Thermostable ligase mediated DNA amplification system for the detection of genetic diseases

• US 5,830,711 A
• Filed: 06/05/1995
• Issued: 11/03/1998
• Est. Priority Date: 05/03/1990
• Status: Expired due to Term

• Current Assignee: California Institute of Technology, Cornell Research Foundation Incorporated (Cornell University)
• Original Assignee: California Institute of Technology, Cornell Research Foundation Incorporated (Cornell University)
• Inventors: Hood, Leroy, Kaiser, Robert J. Jr., Barany, Francis, Zebala, John, Nickerson, Deborah
• Primary Examiner(s): Marschel, Ardin H.
• Assistant Examiner(s): Riley, Jezia
• Application Number:
  US08/462,221
• Time in Patent Office: 1,247 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 536/22.1, 536/23.1, 536/24.3, 536/25.32, 536/25.4
• US Class Current: 435/91.1
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12N 9/93 Ligases (6)
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2531/137 Ligase Chain Reaction [LCR]
• CPC Class Codes: C12Q 2561/125 Ligase Detection Reaction [LDR]

Abstract

The present invention relates to the cloning of the gene of a thermophilic DNA ligase, from Thermus aquaticus strain HB8, and the use of this ligase for the detection of specific sequences of nucleotides in a variety of nucleic acid samples, and more particularly in those samples containing a DNA sequence characterized by a difference in the nucleic acid sequence from a standard sequence including single nucleic acid base pair changes, deletions, insertions or translocations.

Claims

1. A method for distinguishing a first nucleotide sequence which differs by at least a single base from a second nucleotide sequence comprising:

providing a sample potentially containing the first nucleotide sequence and the second nucleotide sequence;

providing a first oligonucleotide set of at least two oligonucleotides suitable for ligation together at a first ligation junction and for hybridization without mismatch at the first ligation junction to the first nucleotide sequence but not to the second nucleotide sequence, wherein the at least two oligonucleotides hybridize adjacent to one another on the first nucleotide sequence and have a hybridization temperature of about 50°

C. to 85°

C.;

providing a thermocyclable ligase which does not become irreversibly denatured and lose its catalytic activity when subjected to temperatures ranging from about 50°

C. to 105°

C.;

blending the sample, the at least two oligonucleotides, and the thermocyclable ligase to form an amplification mixture;

subjecting the amplification mixture to a series of cycles comprising a denaturation treatment, wherein the hybridized first oligonucleotide set is separated from the first nucleotide sequence or from the second nucleotide sequence, and a thermal hybridization treatment at a temperature of 50°

-85°

C., wherein the oligonucleotides of the first oligonucleotide set, when hybridized to the first nucleotide sequence, ligate to one another to amplify linearly a sequence of nucleotides complementary to the first nucleotide sequence and, when hybridized to the second nucleotide sequence, do not ligate together and individually separate from the second nucleotide sequence during the denaturation treatment; and

detecting the presence of the first nucleotide sequence in the sample by detecting the presence of ligated oligonucleotides of the first oligonucleotide set.

2. A method according to claim 1, wherein the denaturation treatment is at a temperature of about 90°

C. to 105°

C.

3. A method according to claim 1, wherein said subjecting amplifies the sequence of nucleotides complementary to the first nucleotide sequence by about 50 to about 500 fold more than if a single base mismatch were present at the first ligation junction.

4. A method according to claim 1, wherein said subjecting amplifies the sequence of nucleotides complementary to the first nucleotide sequence by at least about 100 fold more than if the first nucleotide sequence were not present in the sample.

5. A method according to claim 1, wherein said subjecting is repeated for 5 to 20 cycles.

6. A method according to claim 1, wherein the first nucleotide sequence can be distinguished in the sample when present in an amount down to 1 femtomole.

7. A method according to claim 1, wherein the thermal hybridization step discriminates between the first nucleotide sequence and the second nucleotide sequence based on a distinguishing nucleotide at the first ligation junction.

8. A method according to claim 7, wherein the difference between the first and second nucleotide sequences is a single nucleic acid base pair change.

9. A method according to claim 7, wherein the difference between the first and second nucleotide sequences is a nucleic acid deletion.

10. A method according to claim 7, wherein the difference between the first and second nucleotide sequences is a nucleic acid insertion.

11. A method according to claim 7, wherein A:

A mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 0.4 to <

0.1%.

12. A method according to claim 7, wherein T:

T mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 0.7 to 1.0%.

13. A method according to claim 7, wherein G:

T mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 1.0 to 1.5%.

14. A method according to claim 7, wherein C:

T mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 0.4 to <

0.1%.

15. A method according to claim 7, wherein G:

A mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 0.4 to <

0.1%.

16. A method according to claim 7, wherein C:

A mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 0.4 to <

0.1%.

17. A method according to claim 1, further comprising:

amplifying the first nucleotide sequence in the sample prior to said blending by subjecting the sample to a polymerase chain reaction process.

18. A method according to claim 7, wherein the distinguishing nucleotide is complementary to the oligonucleotide of the first oligonucleotide set having its 3'"'"' end at the first ligation junction.

19. A method according to claim 1, wherein the first oligonucleotide set is in molar excess of the first nucleotide sequence.

20. A method according to claim 1, wherein the ligase is isolated from Thermus aquaticus.

21. A method according to claim 20, wherein the ligase has an amino acid sequence corresponding to SEQ. ID. No. 2.

22. A method according to claim 1, wherein said detecting comprises:

capturing a hook attached to at least one of the oligonucleotides of the first oligonucleotide set.

23. A method according to claim 22, wherein the hook is selected from the group consisting of antigens, biotin, and DNA binding proteins.

24. A method according to claim 1, wherein said detecting comprises:

detecting a label attached to at least one of the oligonucleotides of the first oligonucleotide set.

25. A method according to claim 24, wherein the label is selected from the group consisting of chromophores, fluorescent moieties, enzymes, antigens, chemiluminescent moieties, and electrochemical detecting moieties.

26. A method according to claim 1, wherein said detecting comprises:

separating products of said subjecting by size.

27. A method according to claim 1, wherein the oligonucleotides of the first oligonucleotide set are deoxyribonucleic acids.

28. A method according to claim 1, wherein the oligonucleotides of the first oligonucleotide set each have a hybridization temperature of about 66°

to 70°

C.

29. A method according to claim 1, wherein the amplification mixture further includes a carrier DNA.

30. A method according to claim 29, wherein the carrier DNA is salmon sperm DNA.

31. A method according to claim 1, wherein the first nucleotide sequence is present as a first strand of a double stranded DNA molecule.

32. A method according to claim 31, further comprising:

providing a second oligonucleotide set of at least two oligonucleotides suitable for ligation together at a second ligation junction and for hybridization without mismatch at the second ligation junction to a first complementary nucleotide sequence but not to a second complementary nucleotide sequence, wherein the first complementary nucleotide sequence is complementary to the first nucleotide sequence and is present in the second strand of the DNA and the at least two oligonucleotides of the second oligonucleotide set hybridize adjacent to one another on the first complementary nucleotide sequence and have a hybridization temperature of about 50°

to 85°

C., wherein the first and second complementary nucleotide sequences differ by at least a single base at the second ligation junction, and

blending the second oligonucleotide set with the amplification mixture, whereby said subjecting exponentially amplifies the first and first complementary nucleotide sequences in the DNA and said detecting further comprises detecting the presence of the first complementary nucleotide sequence in the sample by detecting the presence of ligated oligonucleotides of the second oligonuclcotide set.

33. A method according to claim 32, wherein the thermal hybridization step discriminates between the first nucleotide sequence and the second nucleotide sequence and between the first complementary nucleotide sequence and the second complementary nucleotide sequence based on distinguishing nucleotides at the first ligation junction and the second ligation junction, respectively.

34. A method according to claim 33, wherein the difference between the first and second complementary nucleotide sequences is a single nucleic acid base pair change.

35. A method according to claim 33, wherein the difference between the first and second complementary nucleotide sequences is a nucleic acid deletion.

36. A method according to claim 33, wherein the difference between the first and second complementary nucleotide sequences is a nucleic acid insertion.

37. A method according to claim 33, wherein A:

A and T;

T mismatches at the distinguishing nucleotides have a mismatched/complementary percentage of 0.6 to 1.3%.

38. A method according to claim 33, wherein T:

T and A;

A mismatches at the distinguishing nucleotides have a mismatched/complementary percentage of <

0.2%.

39. A method according to claim 33, wherein G:

T and C;

A mismatches at the distinguishing nucleotides have a mismatched/complementary percentage of 0.6 to 1.3%.

40. A method according to claim 33, wherein G:

A and C;

T mismatches at the distinguishing nucleotides have a mismatched/complementary percentage of <

0.2%.

41. A method according to claim 31, wherein said subjecting is repeated for up to 40 cycles.

42. A method according to claim 31, wherein the first nucleotide sequence and the first complementary nucleotide sequence can be distinguished in the sample when present in an amount of 0.001 to 100 attomoles.

43. A method according to claim 31, wherein the ligase is isolated from Thermus aquaticus.

44. A method according to claim 43, wherein the ligase has an amino acid sequence corresponding to SEQ.ID.NO.2.

45. A method for together amplifying and distinguishing nucleotide sequences complementary to a first nucleotide sequence and a second nucleotide sequence, wherein the first and second nucleotide sequences differ by at least one base, comprising:

providing a sample potentially containing the first nucleotide sequence and the second nucleotide sequence;

providing a first oligonucleotide set of at least two oligonucleotides suitable for ligation together at a first ligation junction and for hybridization without mismatch at the first ligation junction to the first nucleotide sequence, but not to the second nucleotide sequence, wherein the oligonucleotides of the first set hybridize adjacent to one another on the first nucleotide sequence and have a hybridization temperature of about 50°

C. to 85°

C.;

providing a second oligonucleotide set of at least two oligonucleotides suitable for ligation together at a second ligation junction and for hybridization without mismatch at the second ligation junction to the second nucleotide sequence, but not to the first nucleotide sequence, wherein the oligonucleotides of the second set hybridize adjacent to one another on the second nucleotide sequence and have a hybridization temperature of about 50°

C. to 85°

C.;

providing a thermocyclable ligase which does not become irreversibly denatured and lose its catalytic activity when subjected to temperatures ranging from about 50°

C. to 105°

C.;

blending the sample, the first set of oligonucleotides, and the thermocyclable ligase to form a first amplification mixture;

blending the sample, the second set of oligonucleotides, and the thermocyclable ligase to form a second amplification mixture;

subjecting the first and second amplification mixtures to a series of cycles comprising a denaturation treatment, wherein the first oligonucleotide set is separated from the first nucleotide sequence while the second oligonucleotide set is separated from the second nucleotide sequence, and a thermal hybridization treatment at a temperature of about 50°

C. to 85°

C., wherein the first oligonucleotide set hybridizes to the first nucleotide sequence and its oligonucleotides ligate to one another while the second oligonucleotide set hybridizes to the second nucleotide sequence and its oligonucleotides ligate to one another, to amplify linearly nucleotide sequences complementary to the first nucleotide sequence and to the second nucleotide sequence;

detecting the presence of the first nucleotide sequence in the sample by detecting the presence of ligated oligonucleotides of the first oligonucleotide set; and

detecting the presence of the second nucleotide sequence in the sample by detecting the presence of ligated oligonucleotides of the second oligonucleotide set.

46. A method according to claim 45, wherein the denaturation treatment is at a temperature of about 90°

C. to 105°

C.

47. A method according to claim 45, wherein said subjecting amplifies the sequence of nucleotides complementary to the first and second nucleotide sequences by about 50 to about 500 fold more than if a single base mismatch were present at the first and second ligation junctions.

48. A method according to claim 45, wherein said subjecting amplifies the sequence of nucleotides complementary to the first and second nucleotide sequences by atleast about 100 fold more than if the first and second nucleotide sequences were not present in the sample.

49. A method according to claim 45, wherein said subjecting is repeated for 5 to 20 cycles.

50. A method according to claim 45, wherein the first nucleotide sequence can be distinguished in the sample when present in an amount down to 1 femtomole.

51. A method according to claim 45, wherein the first and second amplification mixtures are formed separately.

52. A method according to claim 45, wherein the first and second oligonucleotide sets are in molar excess of the first and second nucleotide sequences.

53. A method according to claim 45, wherein the ligase is isolated from Thermus aquaticus.

54. A method according to claim 53, wherein the ligase has a sequence corresponding to SEQ.ID.No.2.

55. A method according to claim 45, wherein at least one of said detecting steps comprises:

capturing a hook attached to at least one of the oligonucleotides of the first or second oligonucleotide sets.

56. A method according to claim 55, wherein the hook is selected from the group consisting of antigens, biotin, and DNA binding proteins.

57. A method according to claim 45, wherein at least one of said detecting steps comprises:

detecting a label attached to at least one of the oligonucleotides of the first or second oligonucleotide sets.

58. A method according to claim 57, wherein the label is selected from the group consisting of chromophores, fluorescent moieties, enzymes, antigens, chemiluminescent moieties, and electrochemical detecting moieties.

59. A method according to claim 55, wherein at least one of said detecting steps comprises:

separating products of said subjecting by size.

60. A method according to claim 45, wherein the oligonucleotides of the first and second oligonucleotide sets are deoxyribonucleic acids.

61. A method according to claim 45, wherein the oligonucleotides of the first and second oligonucleotide sets each have a hybridization temperature of about 66°

to 70°

C.

62. A method according to claim 45, wherein at least one of the amplification mixtures further includes a carrier DNA.

63. A method according to claim 62, wherein the carrier DNA is salmon sperm DNA.

64. A method according to claim 45, wherein the thermal hybridization step discriminates between the first nucleotide sequence and the second nucleotide sequence based on a distinguishing nucleotide at the first ligation junction.

65. A method according to claim 64, wherein the difference between the first and second nucleotide sequences is a single nucleic acid base pair change.

66. A method according to claim 64, wherein the difference between the first and second nucleotide sequences is a nucleic acid deletion.

67. A method according to claim 64, wherein the difference between the first and second nucleotide sequences is a nucleic acid insertion.

68. A method according to claim 64, wherein A:

A mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 0.4 to <

1.0%.

69. A method according to claim 64, wherein T:

T mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 0.7 to 1.0%.

70. A method according to claim 64, wherein G:

T mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 1.0 to 1.5%.

71. A method according to claim 64, wherein C:

T mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 0.4 to <

1.0%.

72. A method according to claim 64, wherein G:

A mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 0.4 to <

1.0%.

73. A method according to claim 64, wherein C:

A mismatches at the distinguishing nucleotide have a mismatched/complementary percentage of 0.4 to <

1.0%.

74. A method according to claim 45, further comprising:

amplifying the first nucleotide sequence and the second nucleotide sequence in the sample prior to said blending by subjecting the sample to a polymerase chain reaction process.

75. A method according to claim 64, wherein the distinguishing nucleotide is complementary to the oligonucleotide of the first oligonucleotide set having its 3'"'"' end at the first ligation junction.

76. A method according to claim 45, wherein the first nucleotide sequence is present as a first strand of a first double stranded DNA molecule, while the second nucleotide sequence is present as a first strand of a second double stranded DNA molecule.

77. A method according to claim 76 further comprising:

providing a third oligonucleotide set of at least two oligonucleotides suitable for ligation together at a third ligation junction and for hybridization without mismatch at the third ligation junction to a third nucleotide sequence, the third nucleotide sequence being complementary to the first nucleotide sequence and present in the second strand of the first DNA molecule;

providing a fourth oligonucleotide set of at least two oligonucleotides suitable for ligation together at a fourth ligation junction and for hybridization without mismatch at the fourth ligation junction to a fourth nucleotide sequence, the fourth nucleotide sequence being complementary to the second nucleotide sequence and present in the second strand of the second DNA molecule;

blending the third oligonucleotide set with the first amplification mixture;

blending the fourth oligonucleotide set with the second amplification mixture, whereby said subjecting exponentially amplifies the first, second, third, and fourth nucleotide sequences;

detecting the presence of the third nucleotide sequence in the sample by detection of the presence of ligated oligonucleotides of the third oligonucleotide set; and

detecting the presence of the fourth nucleotide sequence in the sample by detection of the presence of the ligated oligonucleotides of the fourth oligonucleotide set.

78. A method according to claim 77, wherein the thermal hybridization step discriminates between the first nucleotide sequence and the second nucleotide sequence based on distinguishing nucleotides at the first ligation junction and the second ligation junction and between the third nucleotide sequence and the fourth nucleotide sequence based on distinguishing nucleotides at the third ligation junction and the fourth ligation junction.

79. A method according to claim 78, wherein the difference between the first and second nucleotide sequences and between the third and fourth nucleotide sequences is a single nucleic acid base pair change.

80. A method according to claim 78, wherein the difference between the first and second nucleotide sequences and between the third and fourth nucleotide sequences is a nucleic acid deletion.

81. A method according to claim 78, wherein the difference between the first and second nucleotide sequences and between the third and fourth nucleotide sequences is a nucleic acid insertion.

82. A method according to claim 78, wherein A:

A and T;

T mismatches at the distinguishing nucleotides have a mismatched/complementary percentage of 0.6 to 1.3%.

83. A method according to claim 78, wherein T:

T and A;

A mismatches at the distinguishing nucleotides have a mismatched/complementary percentage of <

0.2%.

84. A method according to claim 78, wherein G:

T and C;

A mismatches at the distinguishing nucleotides have a mismatched/complementary percentage of 0.6 to 1.3%.

85. A method according to claim 78, wherein G:

A and C;

T mismatches at the distinguishing nucleotides have a mismatched/complementary percentage of <

0.2%.

86. A method according to claim 77, wherein said subjecting is repeated for up to 40 cycles.

87. A method according to claim 77, wherein the first nucleotide sequence and the first complementary nucleotide sequence can be detected in the sample at a concentration of 0.001 to 100 attomoles.

88. A method according to claim 77, wherein the ligase is isolated from Thermus aquaticus.

89. A method according to claim 88, wherein the ligase has an amino acid sequence corresponding to SEQ.ID.NO.2.