Methods and compositions for large-scale analysis of nucleic acids using DNA deletions
First Claim
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1. A method for forming a polynucleotide comprising a deletion mate pair, the method comprising:
- (a) providing a first linear construct, wherein the linear construct comprises a first adaptor interposed between a first target polynucleotide fragment and a second target polynucleotide fragment, and wherein the first target polynucleotide fragment and the second target polynucleotide fragment comprise contiguous nucleic acid sequences within a genome or target polynucleotide;
(b) ligating a deletion adaptor to the first linear construct to form a second linear construct, wherein the deletion adaptor comprises a recognition site for a restriction endonuclease, and wherein the restriction endonuclease cleaves at a known distance from said recognition site;
(c) cleaving the second linear construct with the restriction endonuclease to form a third linear construct comprising the first adaptor;
(d) circularizing the third linear construct to form a first circularized construct comprising the first adaptor,thereby forming the polynucleotide comprising a deletion mate pair, wherein the deletion mate pair comprises a first target sequence and a second target sequence that are separated by Y bases within the genome or target polynucleotide from which the first and second target sequences are derived, but which are contiguous in the first circularized construct, wherein Y is less than 100 bases.
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Abstract
The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are constructs that include pairs of target sequences which are separated by a known distance in the polynucleotide from which they are derived.
184 Citations
15 Claims
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1. A method for forming a polynucleotide comprising a deletion mate pair, the method comprising:
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(a) providing a first linear construct, wherein the linear construct comprises a first adaptor interposed between a first target polynucleotide fragment and a second target polynucleotide fragment, and wherein the first target polynucleotide fragment and the second target polynucleotide fragment comprise contiguous nucleic acid sequences within a genome or target polynucleotide; (b) ligating a deletion adaptor to the first linear construct to form a second linear construct, wherein the deletion adaptor comprises a recognition site for a restriction endonuclease, and wherein the restriction endonuclease cleaves at a known distance from said recognition site; (c) cleaving the second linear construct with the restriction endonuclease to form a third linear construct comprising the first adaptor; (d) circularizing the third linear construct to form a first circularized construct comprising the first adaptor, thereby forming the polynucleotide comprising a deletion mate pair, wherein the deletion mate pair comprises a first target sequence and a second target sequence that are separated by Y bases within the genome or target polynucleotide from which the first and second target sequences are derived, but which are contiguous in the first circularized construct, wherein Y is less than 100 bases. - View Dependent Claims (2, 3, 4, 5, 6)
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7. A method for forming a polynucleotide comprising a deletion mate pair, the method comprising:
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(a) providing a first circular construct, wherein the construct comprises a first adaptor and a target polynucleotide, wherein the first adaptor comprises a recognition site for a first restriction endonuclease that cleaves at a known distance from the recognition site and a recognition site for a second restriction endonuclease that cleaves within the first adaptor; (b) cleaving the first circular construct with the first restriction endonuclease to form a first linear construct; (c) cleaving the first linear construct with the second restriction endonuclease to form a second linear construct comprising a fragment of the first adaptor; and (d) circularizing the second linear construct to create a second circular construct comprising the fragment of the first adaptor; thereby forming the polynucleotide comprising a deletion mate pair, wherein the deletion mate pair comprises a first target sequence and a second target sequence that are separated by Y bases within the genome or target polynucleotide from which the first and second target sequences are derived, but which would be contiguous in the second circular construct if the fragment of the first adaptor were removed, wherein Y is less than 300. - View Dependent Claims (8, 9, 10, 11)
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12. A method for forming a polynucleotide comprising a deletion mate pair, the method comprising:
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(a) providing a first linear construct comprising a target polynucleotide and a first adaptor, wherein the first adaptor is attached to one end of the target polynucleotide; (b) ligating a deletion adaptor to the end of the first linear construct opposite the first adaptor, wherein the deletion adaptor comprises a recognition site for a restriction endonuclease that cleaves at a known distance from the recognition site; and (c) cleaving the first linear construct with the restriction endonuclease to form a second linear construct; (d) circularizing the second linear construct to form a first circularized construct, thereby forming the polynucleotide comprising a deletion mate pair, wherein the deletion mate pair comprises a first target sequence and a second target sequence separated by Y bases within the genome or polynucleotide molecule from which the first and second target sequence are derived, wherein Y is less than 100. - View Dependent Claims (13, 14, 15)
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Specification