High throughput genome sequencing on DNA arrays
First Claim
1. A method of identifying a nucleotide sequence of a target nucleic acid, said method comprising:
- (a) providing a plurality of constructs disposed on a surface of a substrate, wherein each of said plurality of constructs comprises multiple copies of a monomer and each monomer comprises a first adaptor, a second adaptor, and fragments of the target nucleic acid and has been formed by a process that comprises;
(i) forming a first circular DNA comprising a fragment of said target nucleic acid and a first adaptor, wherein the first adaptor comprises a binding site for a restriction enzyme that cleaves DNA at a cleavage site separated from said binding site by at least six nucleotides;
(ii) forming a linearized DNA by a process that comprises cleaving the first circular DNA at a site that is internal to the fragment of the target nucleic acid using a restriction enzyme that binds to said binding site; and
(iii) forming a second circular DNA comprising said linearized DNA and a second adaptor thereby forming said monomer;
then(b) identifying a nucleotide sequence on either side of the second adaptor in a plurality of the constructs in the array.
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Abstract
The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.
184 Citations
27 Claims
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1. A method of identifying a nucleotide sequence of a target nucleic acid, said method comprising:
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(a) providing a plurality of constructs disposed on a surface of a substrate, wherein each of said plurality of constructs comprises multiple copies of a monomer and each monomer comprises a first adaptor, a second adaptor, and fragments of the target nucleic acid and has been formed by a process that comprises; (i) forming a first circular DNA comprising a fragment of said target nucleic acid and a first adaptor, wherein the first adaptor comprises a binding site for a restriction enzyme that cleaves DNA at a cleavage site separated from said binding site by at least six nucleotides; (ii) forming a linearized DNA by a process that comprises cleaving the first circular DNA at a site that is internal to the fragment of the target nucleic acid using a restriction enzyme that binds to said binding site; and (iii) forming a second circular DNA comprising said linearized DNA and a second adaptor thereby forming said monomer;
then(b) identifying a nucleotide sequence on either side of the second adaptor in a plurality of the constructs in the array. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27)
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12. A method of identifying a nucleotide sequence of a target nucleic acid, said method comprising:
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(a) providing a substrate comprising a plurality of immobilized concatemers, wherein said substrate comprises a plurality of discrete regions, and wherein said concatemers are randomly disposed on said discrete regions, wherein each concatemer is formed by replication of a monomer such that said concatemer comprises multiple copies of said monomer, and wherein said monomer comprises a first adaptor, a second adaptor, and fragments of the target nucleic acid and has been formed by a process comprising; (i) forming a first circular DNA comprising a fragment of said target nucleic acid and a first adaptor, wherein the first adaptor comprises a binding site for a restriction enzyme that cleaves DNA at a cleavage site separated from said binding site by at least six nucleotides; (ii) forming a linearized DNA by a process that comprises cleaving the first circular DNA at a site that is internal to the fragment of the target nucleic acid using a restriction enzyme that binds to said binding site; (iii) forming a second circular DNA comprising said linearized DNA and a second adaptor thereby forming said monomer; and (iv) replicating the second circular DNA to form said concatemer;
then(b) determining nucleotide sequence of the target nucleic acid both upstream and downstream from the second adaptor in a plurality of the constructs in the array. - View Dependent Claims (13, 14, 18, 19, 21)
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Specification