Identification of nucleic acid template-linked barcodes comprising nucleic acid modifications
First Claim
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1. A method of identifying a barcode, the method comprising:
- a) providing a sequencing template comprising a nucleic acid linked to a barcode, wherein the barcode consists of a nucleotide sequence comprising a base modification;
b) subjecting the sequencing template to a single-molecule sequencing reaction;
c) collecting reaction data in real time during the single-molecule sequencing reaction, wherein said reaction data comprises a sequence read for the sequencing template, and wherein the reaction data further comprises a kinetic change in the single-molecule sequencing reaction, wherein the kinetic change is indicative of the base modification in the nucleotide sequence of the barcode; and
d) analyzing both the sequence read and the kinetic change in the reaction data to detect the nucleotide sequence of the barcode, thereby identifying the barcode in the sequencing template.
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Abstract
Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
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16 Claims
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1. A method of identifying a barcode, the method comprising:
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a) providing a sequencing template comprising a nucleic acid linked to a barcode, wherein the barcode consists of a nucleotide sequence comprising a base modification; b) subjecting the sequencing template to a single-molecule sequencing reaction; c) collecting reaction data in real time during the single-molecule sequencing reaction, wherein said reaction data comprises a sequence read for the sequencing template, and wherein the reaction data further comprises a kinetic change in the single-molecule sequencing reaction, wherein the kinetic change is indicative of the base modification in the nucleotide sequence of the barcode; and d) analyzing both the sequence read and the kinetic change in the reaction data to detect the nucleotide sequence of the barcode, thereby identifying the barcode in the sequencing template. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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Specification