NUCLEIC ACID SEQUENCE ANALYSIS
First Claim
1. A method of generating redundant sequence information from a single template nucleic acid molecule using multiple sequencing enzymes, the method comprising:
- attaching the single template nucleic acid molecule to a solid surface;
sequencing a polynucleotide region of the single template nucleic acid molecule with a first single sequencing enzyme to obtain a first polynucleotide sequence read of the polynucleotide region;
exchanging the first single sequencing enzyme with a second single sequencing enzyme, wherein the first single sequencing enzyme is a first type of polymerase enzyme and the second single sequencing enzymes is a second type of polymerase enzyme; and
sequencing the polynucleotide region of the single template nucleic acid molecule with the second single sequencing, enzyme to obtain a second polynucleotide sequence read of the polynucleotide region, wherein the first and second sequence reads comprise redundant sequence information for the polynucleotide region, thereby generating redundant sequence information from a single template nucleic acid molecule.
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Accused Products
Abstract
Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.
105 Citations
62 Claims
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1. A method of generating redundant sequence information from a single template nucleic acid molecule using multiple sequencing enzymes, the method comprising:
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attaching the single template nucleic acid molecule to a solid surface; sequencing a polynucleotide region of the single template nucleic acid molecule with a first single sequencing enzyme to obtain a first polynucleotide sequence read of the polynucleotide region; exchanging the first single sequencing enzyme with a second single sequencing enzyme, wherein the first single sequencing enzyme is a first type of polymerase enzyme and the second single sequencing enzymes is a second type of polymerase enzyme; and sequencing the polynucleotide region of the single template nucleic acid molecule with the second single sequencing, enzyme to obtain a second polynucleotide sequence read of the polynucleotide region, wherein the first and second sequence reads comprise redundant sequence information for the polynucleotide region, thereby generating redundant sequence information from a single template nucleic acid molecule. - View Dependent Claims (2, 4, 6, 8, 9, 10, 11, 14)
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3. (canceled)
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5. (canceled)
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7. (canceled)
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12-13. -13. (canceled)
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15-32. -32. (canceled)
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33. A reaction mixture, comprising:
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a single template nucleic acid molecule attached to a solid surface in a single molecule reaction region; a first type of polymerase; a second type of polymerase; a set of different nucleotide analogs of the invention, at least one nucleotide analog of which comprises a detectable moiety linked to a phosphate moiety that is released upon incorporation of said one nucleotide analog into a complementary copy of the single template nucleic acid molecule; and multiple polynucleotide complements of the single template nucleic acid molecule, wherein some of the polynucleotide complements were synthesized by a single one of the first type of polymerase and others of the polynucleotide complements were synthesized by a single one of the second type of polymerase. - View Dependent Claims (37, 38, 41)
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34-36. -36. (canceled)
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39-40. -40. (canceled)
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42. (canceled)
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43. A method of sequencing a single template nucleic acid molecule, the method comprising:
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a) attaching the single template nucleic acid molecule to a solid surface; b) annealing an oligonucleotide primer to the template nucleic acid; c) using a first single polymerase to perform template-directed nascent strand synthesis using a polynucleotide region of the single template nucleic acid molecule to generate a first polynucleotide complement of the polynucleotide region, where the first single polymerase is a first type of polymerase that is not immobilized to the solid surface; d) detecting a first set of incorporations to generate a first temporal sequence of incorporations into the first polynucleotide complement, the first temporal sequence of incorporations comprising each nucleotide base incorporated during the template-directed nascent strand synthesis of step c; e) using a second single polymerase to perform template-directed nascent strand synthesis using the polynucleotide region of the single template nucleic acid molecule to generate a second polynucleotide complement of the polynucleotide region, where the second single polymerase is a second type of polymerase that is not immobilized to the solid surface; f) detecting a second set of incorporations to generate a second temporal sequence of incorporations into the second polynucleotide complement, the second temporal sequence of incorporations comprising each nucleotide base incorporated during the template-directed nascent strand synthesis of step e; and g) analyzing the first temporal sequence and the second temporal sequence to determine a consensus sequence for the polynucleotide region of the single template nucleic acid molecule. - View Dependent Claims (44, 47)
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45-46. -46. (canceled)
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48-55. -55. (canceled)
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56. A method of sequencing a plurality of identical template nucleic acids, the method comprising:
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attaching single molecules of the identical template nucleic acids to different single molecule reaction regions on a solid surface; exposing the solid surface to a reaction mixture comprising at least two different types of polymerases; forming a plurality of complexes at the single molecule reaction regions, the complexes comprising a single one of the molecules of identical template nucleic acids and a single polymerase selected from the at least two different types of polymerases; within each complex, using the single polymerase to synthesize a polynucleotide strand complementary to the single molecule of template nucleic acid; detecting a set of incorporations of nucleotide bases into the polynucleotide strand synthesized in each of the complexes, thereby generating a plurality of sequence reads for the identical template nucleic acids, wherein some of the sequence reads were generated by a first of the different types of polymerases and others of the sequence reads were generated by a second of the different types of polymerases; and subjecting the plurality of sequence reads to statistical analysis to determine a consensus sequence for the identical template nucleic acids. - View Dependent Claims (58, 59, 61)
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57. (canceled)
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60. (canceled)
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62. (canceled)
Specification