Tagged extendable primers and extension products
DC CAFCFirst Claim
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1. A duplex comprising an oligonucleotide primer and a template, wherein the primer is covalently coupled to a chromophore or fluorophore so as to allow chain extension by a polymerase.
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Abstract
This invention provides a duplex comprising an oligonucleotide primer and a template, wherein the primer is coupled chemically to a chromophore or fluorophore so as to allow chain extension by a polymerase. In one embodiment, the primer is extended by a polymerase to generate the complement of the template. In a further embodiment, the extended primer is separated from the template for use in a number of methods, including sequencing reactions. Methods of generating these compositions of matter are further provided.
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Citations
158 Claims
- 1. A duplex comprising an oligonucleotide primer and a template, wherein the primer is covalently coupled to a chromophore or fluorophore so as to allow chain extension by a polymerase.
- 7. A set of reagents comprising oligonucleotide primers covalently coupled to one or more chromophores or fluorophores so as to allow chain extension by a polymerase, and a polymerase.
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8. A single-stranded labeled polynucleotide comprising a first portion and a second portion,
wherein the first portion comprises an oligonucleotide primer covalently coupled to a chromophore or fluorophore; - and
wherein the second portion is produced by extension of the first portion along a complementary template. - View Dependent Claims (9, 10)
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49. A duplex comprising an oligonucleotide primer and a template, wherein the primer hybridizes to a specific region of the template and wherein the primer is covalently coupled to a chromophore or fluorophore so as to allow chain extension by a polymerase.
- 50. A plurality of identical oligonucleotide primers of defined length and base sequences wherein each primer is covalently coupled to a fluorophore or chromophore so as to allow chain extension by a polymerase.
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57. A set of reagents comprising two or more pluralities of oligonucleotide primers of claim SO wherein each plurality has a different emission spectra.
- 62. A method of nucleic acid sequence analysis, comprising extending an oligonucleotide along a complementary strand of DNA of a duplex by a polymerase to produce a labeled extension product, wherein the duplex comprises the oligonucleotide specifically hybridized to the complementary strand of DNA, and wherein the oligonucleotide is covalently coupled to a fluorophore so as to allow chain extension by the polymerase.
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64. A DNA sequencing method, comprising
extending oligonucleotides of a set of duplexes along hybridized complementary strands of DNA by a polymerase to produce a set of labeled extension products, wherein the set of labeled extension products comprises two or more extension products, wherein an extension product comprises an extended oligonucleotide specifically hybridized to a complementary strand of DNA, thereby producing four sets of labeled extension products, wherein the extension products of each set are distinguishably labeled with a different type of fluorophore from the extension products of the other sets.
- 66. A mixture comprising a polymerase and a duplex, wherein the duplex comprises an oligonucleotide specifically hybridized to a complementary strand of DNA, wherein the oligonucleotide is covalently coupled to a fluorophore so as to allow chain extension by the polymerase.
- 67. A composition comprising four sets of oligonucleotides, wherein oligonucleotides of each of the four sets are distinguishably labeled with a different type of fluorophore from the oligonucleotides of the other three sets.
Specification