Cloned DNA polymerases from thermotoga maritima and mutants thereof

US 5,948,614 A
Filed: 09/06/1996
Issued: 09/07/1999
Est. Priority Date: 09/08/1995
Status: Expired due to Term

First Claim

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1. A mutant Thermotoga maritima DNA polymerase, which is modified to comprise a mutation in the 3'"'"'→

5'"'"' exonuclease domain of said polymerase to substantially reduce the 3'"'"'→

5'"'"' exonuclease activity of said polymerase, and is further modified in at least one way selected from the group consisting of;

(a) a first mutation in the 5'"'"'→

3'"'"' exonuclease domain of said polymerase to substantially reduce the 5'"'"'→

3'"'"' exonuclease activity of said polymerase; and

(b) a second mutation in the O helix of said polymerase to substantially reduce discriminatory activity against a dideoxynucleotide.

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Abstract

The invention relates to a substantially pure thermostable DNA polymerase from Thermotoga (Tne and Tma) and mutants thereof. The Tne DNA polymerase has a molecular weight of about 100 kilodaltons and is more thermostable than Taq DNA polymerase. The mutant DNA polymerase has at least one mutation selected from the group consisting of (1) a first mutation that substantially reduces or eliminates 3'"'"'→5'"'"' exonuclease activity of said DNA polymerase; (2) a second mutation that substantially reduces or eliminates 5'"'"'.increment.3'"'"' exonuclease activity of said DNA polymerase; (3) a third mutation in the O helix of said DNA polymerase resulting in said DNA polymerase becoming non-discriminating against dideoxynucleotides. The present invention also relates to the cloning and expression of the wild type or mutant DNA polymerases in E. coli, to DNA molecules containing the cloned gene, and to host cells which express said genes. The DNA polymerases of the invention may be used in well-known DNA sequencing and amplification reactions.

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185 Claims

1. A mutant Thermotoga maritima DNA polymerase, which is modified to comprise a mutation in the 3'"'"'→
- 5'"'"' exonuclease domain of said polymerase to substantially reduce the 3'"'"'→
  
  5'"'"' exonuclease activity of said polymerase, and is further modified in at least one way selected from the group consisting of;
  
  (a) a first mutation in the 5'"'"'→
  
  3'"'"' exonuclease domain of said polymerase to substantially reduce the 5'"'"'→
  
  3'"'"' exonuclease activity of said polymerase; and
  
  (b) a second mutation in the O helix of said polymerase to substantially reduce discriminatory activity against a dideoxynucleotide.
- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185)
- - 2. The mutant DNA polymerase of claim 1, which is modified to comprise both said first mutation in the 5'"'"'→
    - 3'"'"' exonuclease domain and said second mutation in the O helix.
  - 3. The mutant Thermotoga maritima DNA polymerase of claim 1, which comprises a mutation in the O helix of said polymerase to substantially reduce discriminatory activity against a dideoxynucleotide.
  - 4. The mutant DNA polymerase of claim 3, wherein said O-helix is defined as RXXXKXXXFXXXYX (SEQ ID NO 1), wherein X is any amino acid.
  - 5. The mutant Thermotoga maritima DNA polymerase as claimed in claim 4, wherein said mutation is a Phe⁷³⁰ →
    - Tyr⁷³⁰ substitution.
  - 6. The mutant Thermotoga maritima DNA polymerase as claimed in claim 1, wherein said mutation in the 3'"'"'→
    - 5'"'"' exonuclease domain is a Asp³²³ -Ala³²³ substitution.
  - 7. The mutant Thermotoga maritima DNA polymerase as claimed in claim 1, wherein said mutant polymerase comprises both a Phr⁷³⁰ →
    - Tyr³⁰ substitution and a Asp³²³ →
      
      Ala³²³ substitution.
  - 8. The mutant DNA polymerase of claim 1, wherein said mutant DNA polymerase is a Thermotoga maritima DNA polymerase having substantially reduced 5'"'"'→
    - 3'"'"' exonuclease activity.
  - 9. The mutant DNA polymerase as claimed in claim 8, wherein said mutation is a deletion mutation in the N-terminal 5'"'"'→
    - 3'"'"' exonuclease domain.
  - 10. The mutant DNA polymerase as claimed in claim 9, wherein said mutant polymerase is devoid of the 219 N-terminal amino acids.
  - 11. A vector comprising a gene encoding the DNA polymerase of claim 1.
  - 12. The vector of claim 11, wherein said gene is operably linked to a promoter.
  - 13. The vector of claim 12, wherein said promoter is selected from the group consisting of a λ
    - -P_L promoter, a tac promoter, a trp promoter, and a trc promoter.
  - 14. A host cell comprising the vector of claim 11.
  - 15. A method of producing a DNA polymerase, said method comprising:
    - (a) culturing the host cell of claim 14;
      
      (b) expressing said gene; and
      
      (c) isolating said DNA polymerase from said host cell.
  - 16. The method of claim 15, wherein said host cell is E. coli.
  - 17. A method of synthesizing a double-stranded DNA molecule comprising:
    - (a) hybridizing a primer to a first DNA molecule; and
      
      (b) incubating said DNA molecule of step (a) in the presence of one or more deoxy- or dideoxyribonucleoside triphosphates and the DNA polymerase of claim 1, under conditions sufficient to synthesize a second DNA molecule complementary to all or a portion of said first DNA molecule.
  - 18. The method of claim 17, wherein said deoxy- or dideoxyribonucleoside triphosphates are selected from the group consisting of dATP, dCTP, dGTP, dTTP, dITP, 7-deaza-dGTP, dUTP, ddATP, ddCTP, ddGTP, ddlTP, ddTTP, α
    - -S!dATP, α
      
      -S!dTTP, α
      
      -S!dGTP, and α
      
      -S!dCTP.
  - 19. The method of claim 17, wherein one or more of said deoxy- or dideoxyribonucleoside triphosphates are detectably labeled.
  - 20. A method of sequencing a DNA molecule, comprising:
    - (a) hybridizing a primer to a first DNA molecule;
      
      (b) contacting said DNA molecule of step (a) with deoxyribonucleoside triphosphates, the DNA polymerase of claim 1, and a terminator nucleotide;
      
      (c) incubating the mixture of step (b) under conditions sufficient to synthesize a random population of DNA molecules complementary to said first DNA molecule, wherein said synthesized DNA molecules are shorter in length than said first DNA molecule and wherein said synthesized DNA molecules comprise a terminator nucleotide at their 5'"'"' termini; and
      
      (d) separating said synthesized DNA molecules by size so that at least a part of the nucleotide sequence of said first DNA molecule can be determined.
  - 21. The method of claim 20, wherein said deoxyribonucleoside triphosphates are selected from the group consisting of dATP, dCTP, dGTP, dTTP, dITP, 7-deaza-dGTP, dUTP, α
    - -S!dATP, α
      
      -S!dTTP, α
      
      -S!dGTP, and α
      
      -S!dCTP.
  - 22. The method of claim 20, wherein said terminator nucleotide is ddTTP, ddATP, ddGTP or ddCTP.
  - 23. The method of claim 20, wherein one or more of said deoxyribonucleoside triphosphates is detectably labeled.
  - 24. The method of claim 20, wherein one or more of said terminator nucleotides is detectably labeled.
  - 25. A method for amplifying a double stranded DNA molecule, comprising:
    - (a) providing a first and second primer, wherein said first primer is complementary to a sequence at or near the 3'"'"'-termini of the first strand of said DNA molecule and said second primer is complementary to a sequence at or near the 3'"'"'-termini of the second strand of said DNA molecule;
      
      (b) hybridizing said first primer to said first strand and said second primer to said second strand in the presence of the DNA polymerase of claim 1, under conditions such that a third DNA molecule complementary to said first strand and a fourth DNA molecule complementary to said second strand are synthesized;
      
      (c) denaturing said first and third strand, and said second and fourth strands; and
      
      (d) repeating steps (a) to (c) one or more times.
  - 26. The method of claim 25, wherein said deoxyribonucleoside triphosphates are selected from the group consisting of dATP, dCTP, dGTP, dTTP, dITP, 7-deaza-dGTP, dUTP, α
    - -S!dATP, α
      
      -S!dTTP, α
      
      -S!dGTP, and α
      
      -S!dCTP.
  - 27. A kit for sequencing a DNA molecule, comprising:
    - (a) a first container means comprising the DNA polymerase of claim 1;
      
      (b) a second container means comprising one or more dideoxyribonucleoside triphosphates; and
      
      (c) a third container means comprising one or more deoxyribonucleoside triphosphates.
  - 28. A kit for amplifying a DNA molecule, comprising:
    - (a) a first container means comprising the DNA polymerase of claim 1; and
      
      (b) a second container means comprising one or more deoxyribonucleoside triphosphates.
  - 29. The mutant Thermotoga maritima DNA polymerase as claimed in claim 1 having substantially reduced or eliminated 5'"'"'-3'"'"' exonuclease activity, wherein at least one of the amino acids corresponding to Asp⁸, Glu¹¹², Asp¹¹⁴, Asp¹¹⁵, Asp¹³⁷, Asp¹³⁹, Gly¹⁰², Gly¹⁸⁷, or Gly¹⁹⁵ of Thermotoga neapolitana DNA polymerase has been mutated.
  - 30. A vector coding for the mutant DNA polymerase of claim 29.
  - 31. A host cell comprising the vector of claim 30.
  - 32. A method of producing a mutant Thermotoga maritima DNA polymerase having substantially reduced or eliminated 5'"'"'-3'"'"' exonuclease activity, wherein at least one of the amino acids corresponding to Asp⁸, Glu¹¹², Asp¹¹⁴, Asp¹¹⁵, Asp¹³⁷, Asp¹³⁹, Gly¹⁰², Gly¹⁸⁷, or Gly¹⁹⁵ of Thermotoga neapolitana DNA polymerase has been mutated, comprising;
    - (a) culturing the host cell of claim 31;
      
      (b) expressing the mutant DNA polymerase; and
      
      (c) isolating said mutant DNA polymerase.
  - 33. A method of preparing cDNA from mRNA, comprising:
    - (a) contacting mRNA with an oligo (dT) primer or other complementary primer to form a hybrid;
      
      (b) contacting said hybrid formed in (a) with the mutant Thermotoga maritima DNA polymerase of claim 1 and one or more nucleotide triphosphates, whereby a cDNA-RNA hybrid is obtained.
  - 34. A method of preparing ds DNA from mRNA, comprising:
    - (a) contacting mRNA with an oligo (dT) primer or other complementary primer to form a hybrid;
      
      (b) contacting said hybrid formed in (a) with the mutant Thermotoga maritima DNA polymerase of claim 1 and one or more deoxyribonucleoside triphosphates, whereby a DNA-RNA hybrid is obtained; and
      
      c) contacting said cDNA-RNA hybrid with an oligonucleotide or primer which is complementary to the first strand cDNA with the mutant Thermotoga maritima DNA polymerase of claim 1 in the presence of one or more deoxyribonucleoside triphosphates whereby dsDNA is obtained.
  - 35. A method for synthesizing a fluorescently labeled DNA molecule comprising:
    - a) hybridizing a primer to a first DNA molecule; and
      
      b) incubating said DNA molecule in the presence of a Thermotoga maritima DNA polymerase of claim 1 and one or more deoxyribonucleoside triphosphates under conditions sufficient to synthesize a second DNA molecule complementary to all or a portion of said first DNA molecule,wherein said primer or one or more said deoxyribonucleoside triphosphates are fluorescently labeled.
  - 36. The method of claim 35, wherein one or more of said deoxyribonucleoside triphosphates are fluorescently labeled.
  - 37. The method of claim 35, wherein said primer is fluorescently labeled.
  - 38. A method for synthesizing a fluorescently labeled DNA molecule comprising:
    - a) hybridizing a primer to a first DNA molecule; and
      
      b) incubating said DNA molecule in the presence of a DNA polymerase of claim 1 and one or more dideoxyribonucleoside triphosphates under conditions sufficient to synthesize a second DNA molecule complementary to all or a portion of said first DNA molecule,wherein said primer or one or more of said dideoxyribonucleoside triphosphates are fluorescently labeled.
  - 39. The method of claim 38, wherein one or more said dideoxyribonucleoside triphosphates are fluorescently labeled.
  - 40. The method of claim 38, wherein said primer is fluorescently labeled.
  - 41. The method of claims 35 or 38, wherein said DNA polymerase has reduced or eliminated discriminatory activity against dideoxyribonucleoside triphosphates.
  - 42. The method of claim 41, wherein said DNA polymerase has been modified in the O-helix.
  - 43. The method of claim 42, wherein Phe at position 730 of said DNA polymerase is substituted with an amino acid selected from the group consisting of Lys, Arg, His, Asp, Glu, Ala, Val, Leu, Ile, Pro, Met, Trp, Gly, Ser, Tyr, Cys, Thr, Asn, and Gln.
  - 44. The method of claim 43, wherein Phe at position 730 of said DNA polymerase is substituted with Tyr.
  - 45. The method of claims 35 or 38, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 46. The method of claim 41, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 47. The method of claim 46, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 48. The method of claims 35 or 38, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 49. The method of claims 35 or 38, wherein said fluorescent labels comprise one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 50. The method of claim 38, wherein said dideoxyribonucleoside triphosphates are selected from the group consisting of ddATP, ddCTP, ddGTP, ddITP, and ddTTP.
  - 51. The method of claim 50, wherein said dideoxyribonucleoside triphosphates are labeled with one or more dyes selected from the group consisting of JOE, FAM, TAMRA and ROX.
  - 52. The method claims 35 or 38, wherein said incubation further comprises the presence of pyrophosphatase.
  - 53. A method for sequencing as claimed in claim 20, wherein said primer, one or more of said deoxyribonucleoside triphosphates, or one or more of the said terminator nucleotide are fluorescently labeled.
  - 54. The method of claim 53, wherein one or more of said terminator nucleotides are fluorescently labeled.
  - 55. The method of claim 53, wherein one or more of said deoxyribonucleoside triphosphates are fluorescently labeled.
  - 56. The method of claim 53, wherein said primer is fluorescently labeled.
  - 57. The method of claim 53, wherein said DNA polymerase has reduced or eliminated discriminatory activity against dideoxyribonucleoside triphosphates.
  - 58. The method of claim 57, wherein said DNA polymerase has been modified in the O-helix.
  - 59. The method of claim 58, wherein Phe at position 730 of said DNA polymerase is substituted with an amino acid selected from the group consisting of Lys, Arg, His, Asp, Glu, Ala, Val, Leu, Ile, Pro, Met, Trp, Gly, Ser, Tyr, Cys, Thr, Asn, and Gln.
  - 60. The method of claim 59, wherein Phe at position 730 of said DNA polymerase is substituted with Tyr.
  - 61. The method of claim 53, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 62. The method of claim 57, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 63. The method of claim 62, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 64. The method of claim 53, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 65. The method of claim 53, wherein said fluorescent labels comprise one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 66. The method of claim 53, wherein said terminator nucleotides comprise one or more nucleotides selected from the group consisting of ddATP, ddCTP, ddGTP, ddITP, and ddTTP.
  - 67. The method of claim 66, wherein said terminator nucleotides are labeled with one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 68. The method of claim 53, wherein said incubation further comprises the presence of pyrophosphatase.
  - 69. A kit for sequencing a DNA molecule comprising a Thermotoga maritima DNA polymerase of claim 1, one or more fluorescently labeled dideoxynucleotide triphosphates, and one or more container means.
  - 70. The kit of claim 69, said kit further comprising one or more deoxyribonucleoside triphosphates.
  - 71. The kit of claim 69, said kit further comprising a pyrophosphatase.
  - 72. The kit of claim 69, said kit further comprising one or more primers.
  - 73. The kit of claim 69, wherein said fluorescently labeled dideoxynucleotide triphosphates comprise one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 74. The kit of claim 69, wherein said dideoxyribonucleoside triphosphates are selected from the group consisting of ddATP, ddCTP, ddGTP, ddITP, and ddTTP.
  - 75. The kit of claim 74, wherein said dideoxyribonucleoside triphosphates are labeled with one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 76. A kit for sequencing a DNA molecule comprising a Thermotoga maritima DNA polymerase of claim 1, one or more fluorescently labeled deoxyribonucleoside triphosphates, and one or more container means.
  - 77. The kit of claim 76, said kit further comprising one or more dideoxyribonucleoside triphosphates.
  - 78. The kit of claim 76, said kit further comprising a pyrophosphatase.
  - 79. The kit of claim 76, said kit further comprising one or more primers.
  - 80. The kit of claim 76, wherein said fluorescently labeled deoxyribonucleoside triphosphates comprise one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 81. The kit of claim 76, wherein said deoxyribonucleoside triphosphates are selected from the group consisting of dATP, dCTP, dGTP, dITP, 7-deaza-dCTP, 7-deaza-dATP, and dTTP.
  - 82. The kit of claim 81, wherein said deoxyribonucleoside triphosphates are labeled with one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 83. A kit for sequencing a DNA molecule comprising a Thermotoga maritima DNA polymerase of claim 1, one or more fluorescently labeled primers, and one or more container means.
  - 84. The kit of claim 83, said kit further comprising one or more deoxyribonucleoside triphosphates.
  - 85. The kit of claim 83, said kit further comprising one or more dideoxyribonucleoside triphosphates.
  - 86. The kit of claim 83, wherein said fluorescently labeled primers comprise one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 87. The kit of claim 85, wherein said dideoxyribonucleoside triphosphates are selected from the group consisting of ddATP, ddCTP, ddGTP, ddITP, and ddTTP.
  - 88. The kit of claim 87, wherein said primers are labeled with one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 89. The kit of any one of claims 69, 76 or 83, wherein said Tma DNA polymerase has reduced or eliminated discriminatory activity against deoxyribonucleoside triphosphates.
  - 90. The kit of claim 89, wherein said DNA polymerase has been modified in the O-helix.
  - 91. The kit of claim 90, wherein Phe at position 730 of said DNA polymerase is substituted with an amino acid selected from the group consisting of Lys, Arg, His, Asp, Glu, Ala, Val, Leu, Ile, Pro, Met, Trp, Gly, Ser, Tyr, Cys, Thr, Asn, and Gln.
  - 92. The kit of claim 91, wherein Phe at position 730 of said DNA polymerase is substituted with Tyr.
  - 93. The kit of any one of claims 69, 76 or 83, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 94. The kit of claim 89, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 95. The kit of claim 94, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 96. The kit of any one of claims 69, 76 or 83, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 97. A sequencing composition comprising a Thermotoga maritima DNA polymerase of claim 1 and one or more fluorescently labeled dideoxyribonucleoside triphosphates.
  - 98. The composition of claim 97, further comprising a DNA molecule to be sequenced.
  - 99. The composition of claim 97, further comprising a pyrophosphatase.
  - 100. The composition of claim 97, further comprising one or more primers.
  - 101. The composition of claim 97, further comprising one or more deoxyribonucleoside triphosphates.
  - 102. A sequencing composition comprising a Thermotoga maritima DNA polymerase of claim 1 and one or more fluorescently labeled deoxyribonucleoside triphosphates.
  - 103. The composition of claim 102, further comprising a DNA molecule to be sequenced.
  - 104. The composition of claim 102, further comprising a pyrophosphatase.
  - 105. The composition of claim 102, further comprising one or more primers.
  - 106. The composition of claim 102, further comprising one or more dideoxyribonucleoside triphosphates.
  - 107. A sequencing composition comprising a Thermotoga maritima DNA polymerase of claim 1 and one or more fluorescently labeled primers.
  - 108. The composition of claim 107, further comprising a DNA molecule to be sequenced.
  - 109. The composition of claim 107, further comprising a pyrophosphatase.
  - 110. The composition of claim 107, further comprising one or more dideoxyribonucleoside triphosphates.
  - 111. The composition of claim 107, further comprising one or more deoxyribonucleoside triphosphates.
  - 112. The composition of any one of claims 97, 102 or 107, wherein said fluorescent labels comprise one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 113. The composition of any one of claims 97, 102 or 107, wherein said DNA polymerase has reduced or eliminated discriminatory activity against deoxyribonucleoside triphosphates.
  - 114. The composition of claim 113, wherein said Tma DNA polymerase has been modified in the O-helix.
  - 115. The composition of claim 114, wherein Phe at position 730 of said DNA polymerase is substituted with an amino acid selected from the group consisting of Lys, Arg, His, Asp, Glu, Ala, Val, Leu, Ile, Pro, Met, Trp, Gly, Ser, Tyr, Cys, Thr, Asn, and Gln.
  - 116. The composition of claim 115, wherein Phe at position 730 of said DNA polymerase is substituted with Tyr.
  - 117. The composition of any one of claims 97, 102 or 107, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 118. The composition of claim 113, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 119. The composition of claim 118 wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 120. The composition of any one of claims 97, 102 or 107, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 121. The mutant Thermotoga maritima DNA polymerase of claim 1, wherein said polymerase provides greater evenness of peak heights compared to ampliTaqFS DNA polymerase in automated fluorescent sequencing.
  - 122. A method for synthesizing a DNA molecule comprising:
    - a) hybridizing a primer to a first DNA molecule; and
      
      b) incubating said DNA molecule in the presence of a Thermotoga maritima DNA polymerase of claim 1 and one or more deoxyribonucleoside triphosphates under conditions sufficient to synthesize a second DNA molecule complementary to all or a portion of said first DNA molecule,wherein said one or more deoxyribonucleoside triphosphates are α
      
      S nucleotides.
  - 123. The method of claim 122, wherein said α
    - S nucleotides comprise radioactive isotopes.
  - 124. The method of claim 123, wherein said α
    - S nucleotides are α
      
      ³⁵ S nucleotides.
  - 125. The method of claim 122, wherein said α
    - S nucleotides are fluorescently labeled.
  - 126. The method of claim 122, wherein said DNA polymerase has reduced or eliminated discriminatory activity against dideoxyribonucleoside triphosphates.
  - 127. The method of claim 126, wherein said DNA polymerase has been modified in the O-helix.
  - 128. The method of claim 127, wherein Phe at position of 730 of said DNA polymerase is substituted with an amino acid selected from the group consisting of Lys, Arg, His, Asp, Glu, Ala, Val, Leu, Ile, Pro, Met, Trp, Gly, Ser, Tyr, Cys, Thr, Asn, and Gln.
  - 129. The method of claim 128, wherein Phe at position 730 of said DNA polymerase is substituted with Tyr.
  - 130. The method of claim 122, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 131. The method of claim 126, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 132. The method of claim 131, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 133. The method of claim 122, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 134. The method of claim 125, wherein said fluorescent labels comprise one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 135. The method of claim 122, wherein said incubation further comprises the presence of a pyrophosphatase.
  - 136. A method for sequencing a DNA molecule comprising:
    - a) hybridizing a primer to a first DNA molecule;
      
      b) contacting said DNA molecule with one or more deoxyribonucleoside triphosphates, a Thermotoga maritima DNA polymerase of claim 1, and one or more terminator nucleotides;
      
      c) incubating said mixture under conditions sufficient to synthesize a random population of DNA molecules complementary to said first DNA molecule, wherein said synthesized DNA molecule are shorter in length than said first DNA molecule and wherein said synthesized DNA molecules comprised a terminator nucleotide at their 5'"'"' termini; and
      
      d) separating said synthesized DNA molecules by size so that at least a part of the nucleotide sequence of said DNA molecule can be determined,wherein said one or more deoxyribonucleoside triphosphates are α
      
      S nucleotides.
  - 137. The method of claim 136, wherein said α
    - S nucleotides comprise radioactive isotopes.
  - 138. The method of claim 136, wherein said α
    - S nucleotides are α
      
      ³⁵ S nucleotides.
  - 139. The method of claim 136, wherein said α
    - S nucleotides are fluorescently labeled.
  - 140. The method of claim 136, wherein said DNA polymerase has reduced or eliminated discriminatory activity against dideoxyribonucleoside triphosphates.
  - 141. The method of claim 140, wherein said DNA polymerase has been modified in the O-helix.
  - 142. The method of claim 141, wherein Phe at position of 730 of said DNA polymerase is substituted with an amino acid selected from the group consisting of Lys, Arg, His, Asp, Glu, Ala, Val, Leu, Ile, Pro, Met, Trp, Gly, Ser, Tyr, Cys, Thr, Asn, and Gln.
  - 143. The method of claim 142, wherein Phe at position 730 of said DNA polymerase is substituted with Tyr.
  - 144. The method of claim 136, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 145. The method of claim 140, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 146. The method of claim 145, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 147. The method of claim 136, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 148. The method of claim 139, wherein said fluorescent labels comprise one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 149. The method of claim 136, wherein said terminator nucleotides are selected from the group consisting of ddATP, ddCTP, ddGTP, ddITP, and ddTTP.
  - 150. The method of claim 136, wherein said incubation further comprises the presence of a pyrophoshatase.
  - 151. A kit for sequencing a DNA molecule comprising a Thermotoga maritima DNA polymerase of claim 1, one or more α
    - S nucleotides, and one or more container means.
  - 152. The kit of claim 151, said kit further comprising one or more dideoxyribonucleoside triphosphates.
  - 153. The kit of claim 151, said kit further comprising a pyrophosphatase.
  - 154. The kit of claim 151, said kit fuirther comprising one or more primers.
  - 155. The kit of claim 151, wherein said α
    - S nucleotides comprise radioactive isotopes.
  - 156. The kit of claim 155, wherein said α
    - S nucleotides are α
      
      ³⁵ S nucleotides.
  - 157. The kit of claim 151, wherein said α
    - S nucleotides are fluorescently labeled.
  - 158. The kit of claim 157, wherein said fluorescent labels comprise one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 159. The kit of claim 151, wherein said DNA polymerase has reduced or eliminated discriminatory activity against dideoxyribonucleoside triphosphates.
  - 160. The kit of claim 159, wherein said DNA polymerase has been modified in the O-helix.
  - 161. The kit of claim 160, wherein Phe at position of 730 of said DNA polymerase is substituted with an amino acid selected from the group consisting of Lys, Arg, His, Asp, Glu, Ala, Val, Leu, Ile, Pro, Met, Trp, Gly, Ser, Tyr, Cys, Thr, Asn, and Gln.
  - 162. The kit of claim 161, wherein Phe at position 730 of said DNA polymerase is substituted with Tyr.
  - 163. The kit of claim 151, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 164. The kit of claim 159, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 165. The kit of claim 164, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 166. The kit of claim 151, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 167. A sequencing composition comprising a Thermotoga maritima DNA polymerase of claim 1 and one or more α
    - S nucleotides.
  - 168. The composition of claim 167, further comprising a DNA molecule to be sequenced.
  - 169. The composition of claim 167, further comprising a pyrophosphatase.
  - 170. The composition of claim 167, further comprising one or more primers.
  - 171. The composition of claim 167, further comprising one or more dideoxyribonucleoside triphosphates.
  - 172. The composition of claim 167, wherein said α
    - S nucleotides comprise radioactive labels.
  - 173. The composition of claim 172, wherein said α
    - S nucleotides are α
      
      ³⁵ S nucleotides.
  - 174. The composition of claim 167, wherein said α
    - S nucleotides are fluorescently labeled.
  - 175. The composition of claim 174, wherein said fluorescent labels comprise one or more dyes selected from the group consisting of JOE, FAM, TAMRA, and ROX.
  - 176. The composition of claim 167, wherein said DNA polymerase has reduced or eliminated discriminatory activity against ideoxyribonucleoside triphosphates.
  - 177. The composition of claim 176, wherein said DNA polymerase has been modified in the O-helix.
  - 178. The composition of claim 177, wherein Phe at position of 730 of said DNA polymerase is substituted with an amino acid selected from the group consisting of Lys, Arg, His, Asp, Glu, Ala, Val, Leu, Ile, Pro, Met, Trp, Gly, Ser, Tyr, Cys, Thr, Asn and Gln.
  - 179. The composition of claim 178, wherein Phe at position 730 of said DNA polymerase is substituted with Tyr.
  - 180. The composition of claim 167, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease activity.
  - 181. The composition of claim 176, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 182. The composition of claim 181, wherein said DNA polymerase has eliminated 3'"'"' to 5'"'"' exonuclease acitivity.
  - 183. The composition of claim 167, wherein said DNA polymerase has reduced or eliminated 5'"'"' to 3'"'"' exonuclease activity.
  - 184. The mutant Thermotoga maritima DNA polymerase of claim 3, wherein said mutant polymerase further comprises a mutation in the 5'"'"'→
    - 3'"'"' exonuclease domain of said polymerase to substantially reduce the 5'"'"'→
      
      3'"'"' exonuclease activity of said polymerase.
  - 185. The mutant Thermotoga maritima DNA polymerase of claim 7, wherein said mutant polymerase further comprises a mutation in the 5'"'"'→
    - 3'"'"' exonuclease domain of said polymerase to substantially reduce the 5'"'"'→
      
      3'"'"' exonuclease activity of said polymerase.

Specification

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Litigation Campaign Assessment

Current Assignee
Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
Original Assignee
Life Technologies Incorporated (Thermo Fisher Scientific Incorporated)
Inventors
Chatterjee, Deb K.
Primary Examiner(s)
Hendricks, Keith D.

Application Number

US08/706,702
Time in Patent Office

1,096 Days
Field of Search

435/6, 435/194, 435/196, 435/252.3, 435/252.33, 435/320.1, 435/91.1, 435/91.2, 536/23.2
US Class Current

435/6.12
CPC Class Codes

C12N 9/1252 DNA-directed DNA polymerase...

Cloned DNA polymerases from thermotoga maritima and mutants thereof

First Claim

6 Assignments

0 Petitions

Accused Products

Abstract

110 Citations

185 Claims

Specification

Solutions

Use Cases

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Cloned DNA polymerases from thermotoga maritima and mutants thereof

First Claim

6 Assignments

Subscription Required

Subscription Required

0 Petitions

Subscription Required

Accused Products

Subscription Required

Abstract

110 Citations

185 Claims

Specification

Subscription Required

Solutions

Use Cases

Quick Links