Method for the direct, exponential amplification and sequencing of DNA molecules and its application
First Claim
1. A method for sequencing at least a portion of a RNA involving converting said RNA into a DNA and simultaneously amplifying said DNA and generating truncated copies of said DNA for sequencing, comprising the steps of(a) subjecting a mixture A to conversion of said RNA to said DNA and, in a single step, to DNA amplification and generation of truncated copies of said DNA by subjecting the mixture A to a thermocycling reaction, the thermocycling reaction comprises heat denaturation, annealing and synthesis, wherein said mixture A comprises said RNA, a first primer which is able to hybridize with a strand of said DNA, a second primer which is able to hybridize with a strand of DNA complementary to the strand with which the first primer is able to hybridize, wherein at least one of the first and second primers is labelled, a reaction buffer, deoxynucleotides or deoxynucleotide derivatives, wherein said deoxynucleotide derivatives are able to be incorporated by a thermostable DNA polymerase into growing DNA molecules in place of one of dATP, dGTP, dTTP or dCTP, at least one dideoxynucleotide or another terminating nucleotide, and a thermostable DNA polymerase having a reduced, compared to wild-type Taq DNA polymerase, discrimination against the incorporation of dideoxynucleotides relative to deoxynucleotides, wherein said thermostable DNA polymerase has (1) a Tabor-Richardson mutation, or a functional derivative thereof, and (2) reverse transcriptase activity, to simultaneously make full-length and truncated copies of said DNA, wherein the full-length copies have a length equal to that of at least a portion of said DNA spanning the binding sites of the first and second primers;
- (b) separating at least the truncated copies of said DNA to obtain a sequence ladder; and
thereafter (c) reading the sequence ladder to obtain the sequence of said at least a portion of said RNA.
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Abstract
A method is described for the direct, exponential amplification and sequencing (“DEXAS”) of a DNA molecule from a complex mixture of nucleic acids, wherein truncated DNA molecules as well as DNA molecules of full length are synthesized simultaneously and exponentially between two positions on the said DNA molecule, which initially contains a DNA molecule in a thermocycling reaction, a first primer, a second primer, a reaction buffer, a thermostable DNA polymerase, a thermostable pyrophosphatase (optionally), deoxynucleotides or derivatives thereof and a dideoxynucleotide or derivatives thereof. In a preferred embodiment of the method of the invention, direct sequencing of RNA can be performed using one polymerase having a Tabor-Richardson mutation, or a functional derivative thereof, and reverse transcriptase activity. In a more preferred embodiment of the method of the invention, direct sequencing of RNA can be performed in one step, in one vessel.
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Citations
87 Claims
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1. A method for sequencing at least a portion of a RNA involving converting said RNA into a DNA and simultaneously amplifying said DNA and generating truncated copies of said DNA for sequencing, comprising the steps of
(a) subjecting a mixture A to conversion of said RNA to said DNA and, in a single step, to DNA amplification and generation of truncated copies of said DNA by subjecting the mixture A to a thermocycling reaction, the thermocycling reaction comprises heat denaturation, annealing and synthesis, wherein said mixture A comprises said RNA, a first primer which is able to hybridize with a strand of said DNA, a second primer which is able to hybridize with a strand of DNA complementary to the strand with which the first primer is able to hybridize, wherein at least one of the first and second primers is labelled, a reaction buffer, deoxynucleotides or deoxynucleotide derivatives, wherein said deoxynucleotide derivatives are able to be incorporated by a thermostable DNA polymerase into growing DNA molecules in place of one of dATP, dGTP, dTTP or dCTP, at least one dideoxynucleotide or another terminating nucleotide, and a thermostable DNA polymerase having a reduced, compared to wild-type Taq DNA polymerase, discrimination against the incorporation of dideoxynucleotides relative to deoxynucleotides, wherein said thermostable DNA polymerase has (1) a Tabor-Richardson mutation, or a functional derivative thereof, and (2) reverse transcriptase activity, to simultaneously make full-length and truncated copies of said DNA, wherein the full-length copies have a length equal to that of at least a portion of said DNA spanning the binding sites of the first and second primers; -
(b) separating at least the truncated copies of said DNA to obtain a sequence ladder; and
thereafter(c) reading the sequence ladder to obtain the sequence of said at least a portion of said RNA. - 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, 87)
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34. A method for sequencing at least a portion of a DNA involving simultaneously amplifying said DNA and generating truncated copies of said DNA for sequencing, comprising the steps of
(a) subjecting a mixture, in a single step, to DNA amplification and generation of truncated copies of said DNA by subjecting the mixture to a thermocycling reaction, the thermocycling reaction comprises heat denaturation, annealing and synthesis, wherein said mixture comprises said DNA, a first primer which is able to hybridize with a strand of said DNA, a second primer which is able to hybridize with a strand of DNA complementary to the strand with which the first primer is able to hybridize, wherein at least one of the first and second primers is labelled, a reaction buffer, deoxynucleotides or deoxynucleotide derivatives, wherein said deoxynucleotide derivatives are able to be incorporated by a thermostable DNA polymerase into growing DNA molecule, in place of one of dATP, dGTP, dTTP or dCTP, m at least one dideoxynucleotide or another terminating nucleotide a thermostable DNA polymerase having a reduced, compared to wild-type Taq DNA polymerase, discrimination against the incorporation of dideoxynucleotides relative to deoxynucleotides, and at least one polymerase-inhibiting agent against said thermostable DNA polymerase, which polymerase-inhibiting agent loses inhibitory ability, thereby allowing said thermostable DNA polymerase to be active, at a temperature which is at least the temperature at which unspecifically hydridized primers separate from a DNA molecule, to simultaneously make full-length and truncated copies of said DNA, wherein the full-length copies have a length equal to that of at least a portion of said DNA spanning the binding sites of the first and second primers; -
(b) separating at least the truncated copies of said DNA to obtain a sequence ladder; and
thereafter(c) reading the sequence ladder to obtain the sequence of said at least a portion of said DNA. - View Dependent Claims (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, 85, 86)
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64. A kit for sequencing at least a portion of a DNA comprising deoxynucleotides or deoxynucleotide derivatives, which deoxynucleotide derivatives are able to be incorporated by a thermostable DNA polymerase into growing DNA molecules in place of one of dATP, dGTP, dTTP or dCTP;
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at least one dideoxynucleotide or another terminating nucleotide;
a thermostable DNA polymerase having a reduced, compared with wild-type Taq polymerase, discrimination against the incorporation of dideoxynucleotides relative to deoxynucleotides, and at least one polymerase-inhibiting agent against said thermostable DNA polymerase, which polymerase-inhibiting agent loses inhibitory ability, thereby allowing said thermostable DNA polymerase to be active, at a temperature which is at least the temperature at which unspecifically hydridized primers separate from a DNA molecule. - View Dependent Claims (65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84)
(1) said first primer is able to hybridize with a strand of a DNA to be sequenced, and (2) said second primer is able to hybridize with a strand of a DNA complementary to the strand with which said first primer is able to hydridize, wherein at least one of the first and second primers is labelled. -
79. The kit of claim 78, wherein the molar ratio of said first primer to said second primer is different from 1:
- 1.
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80. The kit of claim 79, wherein the molar ratio of said first primer to said second primer is 2:
- 1 to 3;
1.
- 1 to 3;
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81. The kit of claim 80, wherein the molar ratio of said first primer to said second primer is 2:
- 1.
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82. The kit of claim 78, wherein the first and second primers are differently labelled.
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83. The kit of claim 78, wherein the first and second primers independently have a length of at least 16 nucleotides.
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84. The kit of claim 83, wherein the first and second primers independently have a length of at least 25 nucleotides.
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Specification