Preparations, compositions, and methods for nucleic acid sequencing
First Claim
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1. A method of sequencing nucleic acids, comprising;
- a) providing a sample comprising target nucleic acids;
b) adding a set of primers to said sample, wherein the set comprises primers having different nucleotide compositions;
c) contacting the target nucleic acids in the sample with the set of primers under conditions that promote hybridization to generate a set of target-primer complexes;
d) using a polymerase enzyme, pre-extending primers in the target-primer complexes to generate pre-extended target-primer complexes that further comprise the polymerase enzyme;
e) confining each of the pre-extended target-primer complexes to a separate reaction site on a substrate comprising a plurality of reaction sites;
f) initiating template-directed synthesis of nascent nucleic acid strands from each of the pre-extended target-primer complexes, wherein the nascent nucleic acid strands are complementary to the target nucleic acids, and wherein the template-directed synthesis is performed by the polymerase enzyme;
g) detecting processive incorporation of nucleotides into each of the nascent nucleic acid strands with no intervening buffer exchange during the template-directed synthesis, wherein the detecting further identifies nucleotide sequence reads for the nascent nucleic acid strands; and
h) based upon the results of step f, determining a nucleotide sequence of the target nucleic acids.
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Abstract
Preparations, compositions and methods of sequencing nucleic acids are provided. The preparations, methods and compositions employ multiple priming sites on a target nucleic acid and typically utilize single molecule sequencing processes to identify sequence portions of the target which are then assembled to obtain the sequence of the target.
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Citations
28 Claims
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1. A method of sequencing nucleic acids, comprising;
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a) providing a sample comprising target nucleic acids; b) adding a set of primers to said sample, wherein the set comprises primers having different nucleotide compositions; c) contacting the target nucleic acids in the sample with the set of primers under conditions that promote hybridization to generate a set of target-primer complexes; d) using a polymerase enzyme, pre-extending primers in the target-primer complexes to generate pre-extended target-primer complexes that further comprise the polymerase enzyme; e) confining each of the pre-extended target-primer complexes to a separate reaction site on a substrate comprising a plurality of reaction sites; f) initiating template-directed synthesis of nascent nucleic acid strands from each of the pre-extended target-primer complexes, wherein the nascent nucleic acid strands are complementary to the target nucleic acids, and wherein the template-directed synthesis is performed by the polymerase enzyme; g) detecting processive incorporation of nucleotides into each of the nascent nucleic acid strands with no intervening buffer exchange during the template-directed synthesis, wherein the detecting further identifies nucleotide sequence reads for the nascent nucleic acid strands; and h) based upon the results of step f, determining a nucleotide sequence of the target nucleic acids. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 27)
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21. A method of generating sequence information for a target nucleic acid, comprising:
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a) providing a plurality of nucleic acid templates corresponding to the target nucleic acid; b) providing multiple primers that anneal to the nucleic acid templates; c) annealing the multiple primers to multiple locations on the nucleic acid templates; d) contacting the nucleic acid templates with single polymerase enzymes that bind at single primers annealed to the nucleic acid templates to generate primer-template-polymerase complexes; e) using the polymerase enzymes, pre-extending primers in the primer-template-polymerase complexes to generate pre-extended primer-template-polymerase complexes; f) confining each of the pre-extended primer-template-polymerase complexes to separate reaction sites on a substrate comprising a plurality of reaction sites; g) performing sequence-by-synthesis reactions to determine nucleotide sequences of the nucleic acid templates within the pre-extended primer-template-polymerase complexes, wherein the performing comprises identifying bases complementary to the nucleic acid templates by detecting labels that are released from said bases upon incorporation of said bases into nascent strands complementary to the nucleic acid templates; and h) assembling an overall nucleotide sequence of the target nucleic acid from the nucleotide sequences of the nucleic acid templates. - View Dependent Claims (22, 23, 24, 26, 28)
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Specification