Comprehensive in vitro reporting of cleavage events by sequencing (CIRCLE-seq)
First Claim
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1. A method of preparing a library of covalently closed circular double-stranded DNA (dsDNA) fragments from a subject'"'"'s genomic DNA, the method comprising:
- providing a sample comprising the subject'"'"'s genomic DNA (gDNA);
randomly shearing the gDNA to a defined average length to provide a population of dsDNA fragments;
preparing the fragments for end-ligation;
ligating to the ends of the fragments a stem-loop adapter comprising a single deoxyuridine adjacent to or within a single-stranded loop sequence comprising a palindromic sequence for intramolecular ligation, to prepare a population of ligated linear dsDNA fragments;
contacting the population of ligated linear dsDNA fragments with an exonuclease to degrade any remaining linear fragments with unligated ends, to produce a purified population of ligated linear dsDNA fragments,contacting the purified population of ligated linear dsDNA fragments with enzymes that nick the ligated dsDNA fragments at the deoxyuridine and remove a 3′
terminal phosphate;
incubating the nicked linear dsDNA fragments under conditions sufficient to promote intramolecular ligation and formation of circular dsDNA fragments;
purifying the ligated circular dsDNA fragments using an exonuclease to degrade unligated noncircular fragments, thereby preparing a library of covalently closed fully circular dsDNA fragments from the subject'"'"'s gDNA.
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Abstract
Sensitive, unbiased methods for genome-wide detection of potential CRISPR-Cas9 off-target cleavage sites from cell type-specific genomic DNA samples.
65 Citations
20 Claims
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1. A method of preparing a library of covalently closed circular double-stranded DNA (dsDNA) fragments from a subject'"'"'s genomic DNA, the method comprising:
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providing a sample comprising the subject'"'"'s genomic DNA (gDNA); randomly shearing the gDNA to a defined average length to provide a population of dsDNA fragments; preparing the fragments for end-ligation; ligating to the ends of the fragments a stem-loop adapter comprising a single deoxyuridine adjacent to or within a single-stranded loop sequence comprising a palindromic sequence for intramolecular ligation, to prepare a population of ligated linear dsDNA fragments; contacting the population of ligated linear dsDNA fragments with an exonuclease to degrade any remaining linear fragments with unligated ends, to produce a purified population of ligated linear dsDNA fragments, contacting the purified population of ligated linear dsDNA fragments with enzymes that nick the ligated dsDNA fragments at the deoxyuridine and remove a 3′
terminal phosphate;incubating the nicked linear dsDNA fragments under conditions sufficient to promote intramolecular ligation and formation of circular dsDNA fragments; purifying the ligated circular dsDNA fragments using an exonuclease to degrade unligated noncircular fragments, thereby preparing a library of covalently closed fully circular dsDNA fragments from the subject'"'"'s gDNA. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18)
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19. A method of preparing a library of fragments comprising sites of engineered nuclease-induced double stranded breaks in double-stranded DNA (dsDNA) molecules from a subject'"'"'s genomic DNA (gDNA), the method comprising:
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providing dsDNA, wherein the dsDNA comprises a subject'"'"'s gDNA; randomly shearing the dsDNA to a defined average length; end-repairing and/or A-tailing the sheared dsDNA; ligating a stem-loop adapter comprising; a first region; a second region that forms one or more loops and comprises a single deoxyuridine nucleotide adjacent to a palindromic sequence for intramolecular ligation; and a third region that is complementary to the first region with one additional nucleotide; contacting the library enzymes that nick the dsDNA at the deoxyuridine and remove a terminal 3′
phosphateincubating the nicked dsDNA under conditions sufficient to promote intramolecular ligation and formation of a sample comprising circular dsDNA molecules; contacting the sample with one or more exonucleases sufficient to degrade any DNA molecules that are not circular; treating the sample with an engineered nuclease to induce site-specific cleavage; optionally end-repairing and then A-tailing resulting ends; ligating a sequencing adapter comprising; a first region; a second region that forms one or more hairpin loops and comprises a primer site compatible for use in PCR priming and/or sequencing; a third region that is complementary to the first region with one additional nucleotide; and a single deoxyuridine nucleotide between the second and third regions, to create a population wherein the DNA fragments that were cleaved by the nuclease have a sequencing adapter ligated to each end; thereby preparing a library enriched for nuclease-cleaved adapter-ligated fragments. - View Dependent Claims (20)
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Specification