SINGLE MOLECULE SEQUENCING WITH TWO DISTINCT CHEMISTRY STEPS
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Abstract
Methods, Compositions, and Systems are provided for nucleic acid sequencing where the sequential incorporation of nucleotides uses two distinct chemical steps. A plurality of nucleotide analogs, each having a labeled leaving group at its 3′ hydroxyl can be sequentially added to a growing strand in the presence of a selective cleaving activity that cleaves the 3′ hydroxyl leaving group preferentially after it has been incorporated. The selective cleaving agent can comprise an exonuclease activity, and the exonuclease activity can be a polymerase-associated exonuclease activity. Nucleotide analogs having labels on both a cleavable polyphosphate portion and on a 3′ hydroxyl leaving group can provide signals characteristic of nucleotide analog incorporation. Systems having illumination optics, collection optics, and substrates observe signals from the labels as they are being incorporated into a growing nucleic acid strand, allowing for the sequencing of template nucleic acids.
26 Citations
104 Claims
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1-87. -87. (canceled)
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88. A method for sequencing a nucleic acid template comprising:
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providing a sequencing mixture comprising (i) a polymerase enzyme, (ii) a template nucleic acid, (iii) a polymerase regent solution having the components for carrying out template directed synthesis of a growing nucleic acid strand including a plurality of types of nucleotide analogs;
wherein each type of nucleotide analog has a labeled leaving group that is cleavable by an exonuclease, and each type of nucleotide analog has a different label, wherein the labeled leaving group blocks further nucleotide incorporations at the 3′
hydroxyl position of the nucleotide analog once it is incorporated; and
(iv) an exonuclease activity which cleaves a labeled leaving group from an incorporated nucleotide analog;carrying out nucleic acid synthesis such that a plurality of nucleotide analogs are added sequentially whereby;
i) a nucleotide analog is incorporated, then ii) the labeled leaving group on that nucleotide analog is cleaved by the exonuclease activity, making the 3′
hydroxyl group available for a subsequent nucleotide analog addition; anddetecting light from the labels while the nucleic acid synthesis is occurring to determine a sequence of the template nucleic acid. - View Dependent Claims (89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104)
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Specification