Sequence analysis using decorated nucleic acids
First Claim
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1. A method of obtaining sequence information from a nucleic acid comprising:
- a) providing a double stranded nucleic acid that comprises single-stranded regions;
b) contacting the nucleic acid provided in step (a) with labeled probes under conditions whereby the labeled probes hybridize to single-stranded but not double stranded regions of the nucleic acid, thereby forming a decorated nucleic acid;
c) stretching said decorated nucleic acid on a substrate; and
d) detecting said labeled probes on said stretched decorated nucleic acid;
wherein the labeled probes that hybridize in step (b) comprise sequences that are complementary to the single-stranded regions to which they hybridize.
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Abstract
The present invention provides a sequence interrogation chemistry that combines the accuracy and haplotype integrity of long-read sequencing with improved methods of preparing genomic nucleic acids and analyzing sequence information generated from those nucleic acids. The present invention encompasses compositions comprising decorated nucleic acids stretched on substrates. The present invention further encompasses methods of making stretched decorated nucleic acids and methods of using decorated nucleic acids to obtain sequence information.
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Citations
36 Claims
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1. A method of obtaining sequence information from a nucleic acid comprising:
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a) providing a double stranded nucleic acid that comprises single-stranded regions; b) contacting the nucleic acid provided in step (a) with labeled probes under conditions whereby the labeled probes hybridize to single-stranded but not double stranded regions of the nucleic acid, thereby forming a decorated nucleic acid; c) stretching said decorated nucleic acid on a substrate; and d) detecting said labeled probes on said stretched decorated nucleic acid; wherein the labeled probes that hybridize in step (b) comprise sequences that are complementary to the single-stranded regions to which they hybridize. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36)
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15. A method of forming a decorated nucleic acid, said method comprising:
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a) nicking a nucleic acid to form a nicked nucleic acid; b) contacting said nicked nucleic acid with labeled probes under conditions whereby the labeled probes hybridize in a sequence-specific manner to single-stranded but not double stranded areas of the nicked nucleic acid, thereby forming said decorated nucleic acid; and c) stretching said decorated nucleic acid on a substrate; wherein said labeled probes each comprise a sequence of at least 5 nucleotides in length. - View Dependent Claims (25, 26, 27, 28, 29, 30, 31, 32)
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Specification