Compositions and methods for sequence determination
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Abstract
A sequencing methodology is disclosed that allows a single DNA or RNA molecule or portion thereof to be sequenced directly and in substantially real time. The methodology involves engineering a polymerase and/or dNTPs with atomic and/or molecular tags that have a detectable property that is monitored by a detection system.
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Citations
72 Claims
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- 10. A composition comprising a polymerizing agent including a fluorescent tag, a nucleic acid template, a primer adapted to hybridize to a complementary portion of the template to form a primer-template duplex and monomers for the polymerizing agent, where one monomer type includes a first quencher having a first quenching efficiency, where the fluorescent tag is quenched before, during and/or after the incorporation of each first quencher modified monomer in a sequence of monomer incorporations due to an interaction between the fluorescent tag and the first quencher as each first quencher modified monomer is incorporated.
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38. A composition:
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comprising a polymerizing agent including a fluorescent tag, a nucleic acid template, a primer adapted to hybridize to a complementary portion of the template to form a primer-template duplex, and monomers for the polymerizing agent, where one monomer type includes a first quencher covalently bonded to a p, γ
or terminal phosphate group of one monomer type and where the first quencher has a first quenching efficiency,where the fluorescent tag is quenched before, during and/or after each monomer incorporation of a first quencher modified monomer in a sequence of monomer incorporations due to an interaction between the fluorescent tag and the first quencher as each first quencher modified monomer is incorporated. - View Dependent Claims (39, 40, 41, 42, 43)
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44. A composition:
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comprising a polymerizing agent including a fluorescent tag, a nucleic acid template, a primer adapted to hybridize to a complementary portion of the template to form a primer-template duplex, and monomers for the polymerizing agent, where one monomer type includes a first quencher covalently bonded to a β
phosphate group of one monomer type and where the first quencher has a first quenching efficiency,where the fluorescent tag is quenched during each monomer incorporation of a first quencher modified monomer in a sequence of monomer incorporations due to an interaction between the fluorescent tag and the first quencher as each first quencher modified monomer is incorporated. - View Dependent Claims (45, 46, 47, 48, 49)
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50. A composition:
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comprising a polymerizing agent including a fluorescent tag, a nucleic acid template, a primer adapted to hybridize to a complementary portion of the template to form a primer-template duplex, and monomers for the polymerizing agent, where one monomer type includes a first quencher covalently bonded to a γ
phosphate group of one monomer type and where the first quencher has a first quenching efficiency,where the fluorescent tag is quenched during each monomer incorporation of a first quencher modified monomer in a sequence of monomer incorporations due to an interaction between the fluorescent tag and the first quencher as each first quencher modified monomer is incorporated. - View Dependent Claims (51, 52, 53, 54, 55)
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56. A composition:
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comprising a polymerizing agent including a fluorescent tag, a nucleic acid template, a primer adapted to hybridize to a complementary portion of the template to form a primer-template duplex, and monomers for the polymerizing agent, where one monomer type includes a first quencher covalently bonded to a terminal phosphate group of one monomer type and where the first quencher has a first quenching efficiency, where the fluorescent tag is quenched during each monomer incorporation of a first quencher modified monomer in a sequence of monomer incorporations due to an interaction between the fluorescent tag and the first quencher as each first quencher modified monomer is incorporated. - View Dependent Claims (57, 58, 59, 60, 61)
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- 62. A composition comprising a polymerizing agent including a fluorescent tag associated with the polymerizing agent or covalently bonded to a site on the polymerase and monomer types of the polymerizing agent, where one monomer type includes a molecular and/or atomic tag that reduces fluorescence from the polymerizing agent fluorescent tag before, during and/or after incorporation of the one monomer type due to the interaction between the fluorescent polymerizing agent tag and the monomer tag.
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64. A composition:
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comprising a polymerizing agent including a fluorescent polymerizing agent tag, a nucleic acid template, a primer adapted to hybridize to a complementary portion of the template to form a primer-template duplex, at least one monomer type includes a quencher covalently bonded thereto, and at least one monomer type includes a fluorescent monomer tag covalently bonded thereto, where the quencher reduces a fluorescent intensity of the fluorescent polymerizing agent tag before, during and/or after each incorporation of a quencher modified monomer in a sequence of monomer incorporations or where a fluorescent property of the fluorescent polymerizing agent and/or the fluorescent monomer tag changes before, during and/or after each incorporation of a fluorescent tagged monomer in the sequence of monomer incorporations. - View Dependent Claims (65)
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66. The composition of claim 661, wherein the polymerase is selected from the group consisting of Tag DNA polymerase I, T7 DNA polymerase, Sequenase, and the Klenow fragment from E. coli DNA polymerase I and wherein the reverse transcriptase comprises HIV-1 reverse transcriptase.
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67. A composition:
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comprising a polymerizing agent including a fluorescent tag, a nucleic acid template, a primer adapted to hybridize to a complementary portion of the template to form a primer-template duplex, monomer types for the polymerizing agent, where each monomer type includes a quencher or a fluorophore covalently bonded thereto, where the quenchers are the same or different and the fluorophores are the same or different, and where the quenchers reduce a fluorescent intensity of the fluorescent tag before, during and/or after each incorporation of a quencher modified monomer in a sequence of monomer incorporations or where a fluorescent property of the fluorescent tag and/or the fluorophore changes before, during and/or after each incorporation of a fluorophore modified monomer in the sequence of monomer incorporations. - View Dependent Claims (68, 69)
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70. A method comprising the steps of:
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providing a composition comprising a polymerizing agent including a fluorescent tag, a nucleic acid template, a primer adapted to hybridize to a complementary portion of the template to form a primer-template duplex, monomer types for the polymerizing agent, where each monomer type includes a quencher or a fluorophore covalently bonded thereto, where the quenchers are the same or different and the fluorophores are the same or different, detecting a reduction in fluorescent intensity due to the quenchers interacting with the fluorescent tag before, during and/or after each incorporation of a quencher modified monomer in a sequence of monomer incorporations or detecting a change in a fluorescent property of the fluorescent tag and/or the fluorophore before, during and/or after each incorporation of a fluorophore modified monomer in the sequence of monomer incorporations, and converting the reductions or changes in an identity of monomer incorporations corresponding to a complementary identity of nucleotides of the template. - View Dependent Claims (71, 72)
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Specification