Paired end sequencing
First Claim
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1. A method for obtaining a DNA construct comprising two end regions of a target nucleic acid comprising the steps of:
- (a) fragmenting a large nucleic acid molecule to produce a target nucleic acid;
(b) ligating a hairpin adaptor to each end of said target nucleic acids from step (a), digesting with exonuclease to remove nucleic acids with exposed 5′
or 3′
ends and cleaving said hairpin adaptors to create sticky ends for circularization;
(c) ligating a signature tag to said sticky ends to form a circular nucleic acid molecule;
(d) digesting said circular nucleic acid with a restriction endonucleases which cuts said target nucleic acid but which does not cut said hairpin adaptor or said signature tag to produce said DNA construct comprising two end regions of a target nucleic acid;
(e) ligating a PCR primer to each end of said DNA construct; and
(f) amplifying said DNA construct by PCR.
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Abstract
The present invention provides for a method of preparing a target nucleic acid fragments to produce a smaller nucleic acid which comprises the two ends of the target nucleic acid. Specifically, the invention provides cloning and DNA manipulation strategies to isolate the two ends of a large target nucleic acid into a single small DNA construct for rapid cloning, sequencing, or amplification.
63 Citations
53 Claims
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1. A method for obtaining a DNA construct comprising two end regions of a target nucleic acid comprising the steps of:
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(a) fragmenting a large nucleic acid molecule to produce a target nucleic acid; (b) ligating a hairpin adaptor to each end of said target nucleic acids from step (a), digesting with exonuclease to remove nucleic acids with exposed 5′
or 3′
ends and cleaving said hairpin adaptors to create sticky ends for circularization;(c) ligating a signature tag to said sticky ends to form a circular nucleic acid molecule; (d) digesting said circular nucleic acid with a restriction endonucleases which cuts said target nucleic acid but which does not cut said hairpin adaptor or said signature tag to produce said DNA construct comprising two end regions of a target nucleic acid; (e) ligating a PCR primer to each end of said DNA construct; and (f) amplifying said DNA construct by PCR. - View Dependent Claims (2, 3, 4, 5, 6, 7, 44, 45, 46, 47)
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8. A method for obtaining a DNA construct comprising two end regions of a target nucleic acid comprising the steps of:
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(a) fragmenting a large nucleic acid molecule to produce a target nucleic acid; (b) ligating a first hairpin adaptor to one end of said target nucleic acid and a second hairpin adaptor to a second end of said target nucleic acid to form an adaptor tagged target nucleic acid, wherein the first and second hairpin adaptors comprise a hairpin element and at least one hairpin adaptor is biotinylated; (c) cleaving the hairpin element from the first and second hairpin adaptors of the adaptor tagged nucleic acid producing a cleaved end on the first and second hairpin adaptor; (d) circularizing said adaptor tagged target nucleic acid by ligating the cleaved end of said first hairpin adaptor to the cleaved end of said second hairpin adaptor to form a circular nucleic acid molecule comprising a target nucleic acid region and an adaptor region; (e) fragmenting said circular nucleic acid molecule to produce at least one said DNA construct comprising two end regions of a target nucleic acid with a ligated adaptor region therebetween; and (f) enriching for said DNA construct by affinity purification with an avidin or streptavidin coated solid support. - View Dependent Claims (9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 43, 48)
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27. A method for obtaining a DNA construct comprising two end regions of a target nucleic acid comprising the steps of:
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(a) fragmenting a large nucleic acid molecule to produce a target nucleic acid; (b) ligating a hairpin adaptor to each end of said target nucleic acids from step (a), digesting with exonuclease to remove nucleic acids with exposed 5′
or 3′
ends and cleaving said hairpin adaptors to create sticky ends for circularization;(c) ligating a capture element to said target nucleic acid to form a circular nucleic acid molecule, wherein said capture element is a nucleic acid comprising one member of a binding pair; (d) digesting said circular nucleic acid with a restriction endonuclease which cuts said target nucleic acid but which does not cut said capture element to produce said DNA construct comprising two end regions of a target nucleic acid separated by said capture element; and (e) enriching for said DNA construct by affinity purification using a solid support comprising a second member of said binding pair. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42)
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49. A method for obtaining a DNA construct comprising two end regions of a target nucleic acid comprising the steps of:
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(a) fragmenting a large nucleic acid molecule to produce a target nucleic acid, wherein said large nucleic acid or said target nucleic acid is methylated with a methylase; (b) ligating a first adaptor comprising a hairpin to one end of said target nucleic acid and a second adaptor comprising a hairpin to a second end of said target nucleic acid to form an adaptor tagged target nucleic acid; (b1) treating said adaptor tagged target nucleic acid with an exonuclease to digest any target nucleic acids not ligated to the hairpin adaptors at both ends; (b2) removing said exonuclease from said adaptor tagged target nucleic acid; (b3) digesting said adaptor tagged target nucleic acid with a restriction endonuclease which cleaves the hairpins from said first and second adaptors and which does not cleave said target nucleic acid to generate an adaptor tagged target nucleic acid with cleaved adaptors at both ends; (c) circularizing said adaptor tagged target nucleic acid by ligating said first adaptor to said second adaptor to form a circular nucleic acid molecule comprising a target nucleic acid region and an adaptor region; and (d) fragmenting said circular nucleic acid molecule at the target nucleic acid region to produce said DNA construct comprising two end regions of a target nucleic acid. - View Dependent Claims (50, 51, 52, 53)
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Specification