Methods for detecting nucleic acid analyte
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Abstract
The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.
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Citations
125 Claims
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1-61. -61. (canceled)
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62. A method of detecting an analyte comprising the steps of:
- (a) anchoring said analyte to a nucleic acid template;
(b) conducting a nucleic acid polymerase reaction to produce labeled polyphosphate, said reaction comprising the reaction of said template, a primer, at least one terminal phosphate-labeled nucleotide, and a nucleic acid polymerase; and
(c) analyzing said labeled polyphosphate. - View Dependent Claims (63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 91, 92, 93, 94, 95, 97, 98)
- (a) anchoring said analyte to a nucleic acid template;
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87. A method of detecting and characterizing multiple analytes in a sample, comprising the steps of:
- (a) anchoring to each analyte a specific template nucleic acid sequence with a unique base at the site opposite to the complementary nucleotide being added;
(b) conducting a DNA polymerase reaction to produce uniquely labeled polyphosphates;
said reaction comprising the reaction of said templates, nuclease resistant primers complementary to said specific target sequence of each of said multiple analytes, two or more terminal phosphate-labeled nucleotides having 2 or more phosphate groups in the polyphosphate chain and each bearing a different label, a DNA polymerase and an enzyme having 3′
-5′
exonuclease activity; and
(c) detecting the labeled polyphosphates. - View Dependent Claims (88, 89, 90)
- (a) anchoring to each analyte a specific template nucleic acid sequence with a unique base at the site opposite to the complementary nucleotide being added;
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96. The method of 62, wherein one or more additional detection reagents are added in said polymerase reaction of said conducting step, and said additional detection reagents are capable of a response that is detectably different from said labeled polyphosphate.
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99. A method of detecting and characterizing multiple analytes in a reaction compartment, comprising the steps of:
- (a) anchoring a unique template nucleic acid sequence to each of said analytes;
(b) anchoring said analytes to the surface of said reaction compartment;
(c) conducting a DNA polymerase reaction to produce labeled polyphosphate;
said reaction comprising the reaction of the unique template sequence of one of said analytes, a nuclease resistant primer complementary to said unique template sequence, at least one terminal phosphate-labeled nucleotides having 2 or more phosphate groups in the polyphosphate chain, a DNA polymerase and an enzyme having 3′
-5′
exonuclease activity;
(d) detecting said labeled polyphosphate;
(e) washing off the unanchored components; and
(f) repeating steps (a) to (d) with a nuclease resistant primer complementary to another unique template sequence of a different analyte until all the analytes are analyzed. - View Dependent Claims (100, 101)
- (a) anchoring a unique template nucleic acid sequence to each of said analytes;
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102. A method of detecting and characterizing multiple analytes in a sample, comprising the steps of:
- (a) anchoring to each analyte a specific template nucleic acid sequence with a unique base at the site opposite to the complementary nucleotide being added;
(b) conducting a DNA polymerase reaction to produce labeled polyphosphates, said reaction comprising the reaction of said templates, primers complementary to said specific template sequence, two or more terminal phosphate-labeled nucleotides with different labels, a DNA polymerase and an enzyme having 3′
-5′
exonuclease activity;
(c) permitting said labeled polyphosphates to react with one or more additional enzymes to produce detectable species unique to each of said analytes; and
(d) detecting said detectable species.
- (a) anchoring to each analyte a specific template nucleic acid sequence with a unique base at the site opposite to the complementary nucleotide being added;
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103. A method of sequencing a target nucleic acid, comprising:
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providing a reaction mixture comprising the target nucleic acid, a primer, a polymerase enzyme, and one or more labeled nucleotides or nucleotide analogs, wherein the target nucleic acid and/or the primer is immobilized upon a substrate;
sequentially optically detecting incorporation of at least first and second labeled nucleotides or nucleotide analogs in a nascent nucleic acid strand by an individual polymerase enzyme; and
identifying the first and second nucleotides or nucleotide analogs incorporated into the nascent nucleic acid strand. - View Dependent Claims (105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116)
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104. A method of sequencing a target nucleic acid, comprising:
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providing a reaction mixture comprising the target nucleic acid, a primer, a polymerase enzyme, and one or more labeled nucleotides or nucleotide analogs, wherein the target nucleic acid and/or the primer is immobilized upon a substrate;
sequentially optically detecting incorporation of at least first and second labeled nucleotides or nucleotide analogs into an individual nascent nucleic acid strand by the polymerase enzyme; and
identifying the first and second nucleotides or nucleotide analogs incorporated into the nascent nucleic acid strand.
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- 117. A method of sequencing a target nucleic acid, comprising optically detecting sequential incorporation of nucleotides or nucleotide analogs into a nascent nucleic acid strand by an individual polymerase enzyme complexed with the template polynucleotide, wherein the template polynucleotide is coupled to a substrate.
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119. A method for sequencing a target nucleic acid, comprising:
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(a) providing a complex comprising a polymerase and a target nucleic acid such that said polymerase is capable of incorporating a nucleotide or nucleotide analog complementary to a nucleotide on the target nucleic acid, wherein the complex is immobilized on a substrate;
(b) providing a plurality of labeled nucleotides or nucleotide analogs to the complex to effect incorporation of a labeled nucleotide or analog into a nascent strand that is complementary to the target nucleic acid;
(c) optically detecting the incorporated nucleotide or analog by sensing its detectable label, wherein said detecting is performed by applying radiation through the complex at a spatial location of the complex where said label is expected to occur;
(d) repeating, with the complex immobilized on the substrate, steps (b) through (c) so that a plurality of nucleotides incorporated is identified and, as a result, a sequence of the target nucleic acid is determined. - View Dependent Claims (120, 121, 122, 123, 124, 125)
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Specification