Barcoding nucleic acids
First Claim
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1. A method of making a dual barcoded nucleic acid molecule comprising:
- (a) ligating one strand of a stem-loop oligonucleotide adaptor of a population of stem-loop oligonucleotide adaptors, wherein each stem-loop oligonucleotide adaptor of the population comprises a loop and a double-stranded stem region that forms an intramolecular inverted repeat, the double-stranded stem region comprising a first stem strand and a second stem strand that comprises a unique barcode comprising a random or partially random sequence, to each end of a nucleic acid molecule to form a first barcode-coupled nucleic acid molecule;
(b) displacing the first stem strand of the stem-loop oligonucleotide adaptor from the first barcode-coupled nucleic acid molecule by strand displacement or by nick translation polymerization to form a first barcoded nucleic acid molecule that lacks the intramolecular inverted repeat and comprises the unique barcode;
(c) annealing a primer to the first barcoded nucleic acid molecule, wherein the primer comprises a first portion complementary to the first barcoded nucleic acid molecule and a second portion comprising a second barcode; and
(d) extending the annealed primer to form a dual barcoded nucleic acid molecule, the dual barcoded nucleic acid molecule comprising the second barcode, the unique barcode, and at least a portion of the nucleic acid molecule.
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Abstract
Methods of barcoding nucleic acids, such as genomic DNA, are provided herein. In some embodiments, a fragment of genomic DNA may comprise a first and a second barcode.
55 Citations
22 Claims
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1. A method of making a dual barcoded nucleic acid molecule comprising:
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(a) ligating one strand of a stem-loop oligonucleotide adaptor of a population of stem-loop oligonucleotide adaptors, wherein each stem-loop oligonucleotide adaptor of the population comprises a loop and a double-stranded stem region that forms an intramolecular inverted repeat, the double-stranded stem region comprising a first stem strand and a second stem strand that comprises a unique barcode comprising a random or partially random sequence, to each end of a nucleic acid molecule to form a first barcode-coupled nucleic acid molecule; (b) displacing the first stem strand of the stem-loop oligonucleotide adaptor from the first barcode-coupled nucleic acid molecule by strand displacement or by nick translation polymerization to form a first barcoded nucleic acid molecule that lacks the intramolecular inverted repeat and comprises the unique barcode; (c) annealing a primer to the first barcoded nucleic acid molecule, wherein the primer comprises a first portion complementary to the first barcoded nucleic acid molecule and a second portion comprising a second barcode; and (d) extending the annealed primer to form a dual barcoded nucleic acid molecule, the dual barcoded nucleic acid molecule comprising the second barcode, the unique barcode, and at least a portion of the nucleic acid molecule. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22)
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Specification