Cloned DNA polymerases from thermotoga and mutants thereof
First Claim
1. A method of sequencing a DNA molecule comprising:
- (a) hybridizing a primer to a first DNA molecule;
(b) contacting said first DNA molecule with deoxyribonucleoside triphosphates, a Thermotoga neapolitana DNA polymerase, and a terminator molecule to form a mixture;
(c) incubating said mixture under conditions sufficient to synthesize a random population of DNA molecules complementary to 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 portion of the nucleotide sequence of said first DNA molecule can be determined;
wherein;
said Thermotoga neapolitana DNA polymerase is selected from the group consisting of a mutant Thermotoga neapolitana DNA polymerase and a fragment of said mutant Thermotoga neapolitana DNA polymerase, wherein said fragment has DNA polymerase activity; and
further wherein;
said mutant Thermologa neapolitana DNA polymerase has at least one mutation selected from the group consisting of;
(1) a first mutation that reduces, substantially reduces or eliminates 3'"'"'-5'"'"' exonuclease activity of said DNA polymerase, wherein said first mutation is in the 3'"'"'-5'"'"' exonuclease domain of said polymerase;
(2) a second mutation that reduces, substantially reduces or eliminates 5'"'"'-3'"'"' exonuclease activity of said DNA polymerase, wherein said second mutation is in the 5'"'"'-3'"'"' exonuclease domain of said polymerase; and
(3) a third mutation in the O-helix of said DNA polymerase, wherein said third mutation results in said DNA polymerase becoming non-discriminating against dideoxynucleotides.
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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'"'"'→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.
64 Citations
55 Claims
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1. A method of sequencing a DNA molecule comprising:
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(a) hybridizing a primer to a first DNA molecule; (b) contacting said first DNA molecule with deoxyribonucleoside triphosphates, a Thermotoga neapolitana DNA polymerase, and a terminator molecule to form a mixture; (c) incubating said mixture under conditions sufficient to synthesize a random population of DNA molecules complementary to 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 portion of the nucleotide sequence of said first DNA molecule can be determined;
wherein;said Thermotoga neapolitana DNA polymerase is selected from the group consisting of a mutant Thermotoga neapolitana DNA polymerase and a fragment of said mutant Thermotoga neapolitana DNA polymerase, wherein said fragment has DNA polymerase activity; and further wherein; said mutant Thermologa neapolitana DNA polymerase has at least one mutation selected from the group consisting of; (1) a first mutation that reduces, substantially reduces or eliminates 3'"'"'-5'"'"' exonuclease activity of said DNA polymerase, wherein said first mutation is in the 3'"'"'-5'"'"' exonuclease domain of said polymerase; (2) a second mutation that reduces, substantially reduces or eliminates 5'"'"'-3'"'"' exonuclease activity of said DNA polymerase, wherein said second mutation is in the 5'"'"'-3'"'"' exonuclease domain of said polymerase; and (3) a third mutation in the O-helix of said DNA polymerase, wherein said third mutation results in said DNA polymerase becoming non-discriminating against dideoxynucleotides. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10)
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11. A method of amplifying a double-stranded DNA molecule comprising:
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(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 primer to said first strand and said second primer to said second strand in the presence of a Thermotoga neapolitana DNA polymerase, 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;
wherein;said Thermotoga neapolitana DNA polymerase is selected from the group consisting of a mutant Thermotoga neapolitana DNA polymerase and a fragment of said mutant Thermotoga neapolitana DNA polymerase, wherein said fragment has DNA polymerase activity; and
further wherein;said mutant Thermotoga neapolitana DNA polymerase has at least one mutation selected from the group consisting of; (1) a first mutation that reduces, substantially reduces or eliminates 3'"'"'-5'"'"' exonuclease activity of said DNA polymerase, wherein said first mutation is in the 3'"'"'-5'"'"' exonuclease domain of said polymerase; (2) a second mutation that reduces, substantially reduces or eliminates 5'"'"'-3'"'"' exonuclease activity of said DNA polymerase, wherein said second mutation is in the 5'"'"'-3'"'"' exonuclease domain of said polymerase; and (3) a third mutation in the O-helix of said DNA polymerase, wherein said third mutation results in said DNA polymerase becoming non-discriminating against dideoxynucleotides. - View Dependent Claims (12, 13, 14, 15, 16, 17, 18)
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19. A kit for sequencing a DNA molecule comprising:
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(a) a first container comprising a Thermotoga neapolitana DNA polymerase; (b) a second container comprising one or more dideoxyribonucleoside triphosphates; and (c) a third container comprising one or more deoxyribonucleoside triphosphates;
wherein;said Thermotoga neapolitana DNA polymerase is selected from the group consisting of a mutant Thermotoga neapolitana DNA polymerase and a fragment of said mutant Thermotoga neapolitana DNA polymerase, wherein said fragment has DNA polymerase activity; and
further wherein;said mutant Thermotoga neapolitana DNA polymerase has at least one mutation selected from the group consisting of; (1) a first mutation that reduces, substantially reduces or eliminates 3'"'"'-5'"'"' exonuclease activity of said DNA polymerase, wherein said first mutation is in the 3'"'"'-5'"'"' exonuclease domain of said polymerase; (2) a second mutation that reduces, substantially reduces or eliminates 5'"'"'-3'"'"' exonuclease activity of said DNA polymerase, wherein said second mutation is in the 5'"'"'-3'"'"' exonuclease domain of said polymerase; and (3) a third mutation in the O-helix of said DNA polymerase, wherein said third mutation results in said DNA polymerase becoming non-discriminating against dideoxynucleotides. - View Dependent Claims (20, 21, 22, 23, 24, 25, 26)
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27. A kit for amplifying a DNA molecule, comprising:
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(a) a first container comprising a Thermotoga neapolitana DNA polymerase; and (b) a second container comprising one or more deoxyribonucleoside triphosphates; wherein; said Thermotoga neapolitana DNA polymerase is selected from the group consisting of a mutant Thermotoga neapolitana DNA polymerase and a fragment of said mutant Thermotoga neapolitana DNA polymerase, wherein said fragment has DNA polymerase activity; and further wherein; said mutant Thermotoga neapolitana DNA polymerase has at least one mutation selected from the group consisting of; (1) a first mutation that reduces, substantially reduces or eliminates 3'"'"'-5'"'"' exonuclease activity of said DNA polymerase, wherein said first mutation is in the 3'"'"'-5'"'"' exonuclease domain of said polymerase; (2) a second mutation that reduces, substantially reduces or eliminates 5'"'"'-3'"'"' exonuclease activity of said DNA polymerase, wherein said second mutation is in the 5'"'"'-3'"'"' exonuclease domain of said polymerase; and (3) a third mutation in the O-helix of said DNA polymerase, wherein said third mutation results in said DNA polymerase becoming non-discriminating against dideoxynucleotides. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34)
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35. A method for synthesizing a DNA molecule comprising:
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(a) hybridizing a primer to a first DNA molecule; and (b) incubating said DNA molecule in the presence of a Thermotoga neapolitana DNA polymerase 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; and wherein; said Thermotoga neapolitana DNA polymerase is selected from the group consisting of a mutant Thermotoga neapolitana DNA polymerase and a fragment of said mutant Thermotoga neapolitana DNA polymerase, wherein said fragment has DNA polymerase activity; and further wherein; said mutant Thermotoga neapolitana DNA polymerase has at least one mutation selected from the group consisting of; (1) a first mutation that reduces, substantially reduces or eliminates 3'"'"'-5'"'"' exonuclease activity of said DNA polymerase, wherein said first mutation is in the 3'"'"'-5'"'"' exonuclease domain of said polymerase; (2) a second mutation that reduces, substantially reduces or eliminates 5'"'"'-3'"'"' exonuclease activity of said DNA polymerase, wherein said second mutation is in the 5'"'"'→
3'"'"' exonuclease domain of said polymerase; and(3) a third mutation in the O-helix of said DNA polymerase, wherein said third mutation results in said DNA polymerase becoming non-discriminating against dideoxynucleotides. - View Dependent Claims (36, 37, 38)
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- 39. A mutant Thermotoga neapolitana DNA polymerase, wherein said mutation is a substitution of Arg at position 722 of said DNA polymerase with an amino acids selected from the group consisting of Asp, Glu, Ala, Val, Leu, Ile, Pro, Met, Phe, Trp, Gly, Ser, Thr, Cys, Tyr, Gln, Asn, Lys, and His.
Specification