Methods and apparatus for DNA sequencing and DNA identification
First Claim
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1. A method of analyzing nucleic acids by hybridization, comprising the steps of:
- contacting a first plurality of different nucleic acid segments disposed on a first sector of a substrate with a first hybridization oligonucleotide, wherein said first plurality of nucleic acids is arranged on said first sector in a spatially identifiable array, under conditions that discriminate between a perfect match and a single base mismatch in the hybridization of a member of said first array of nucleic acid segments to the informational portion of said first hybridization oligonucleotide;
contacting a second plurality of different nucleic acid segments disposed on a second sector of the substrate with a second hybridization oligonucleotide, wherein said second plurality of nucleic acids is arranged on said second sector in a spatially identifiable array, under conditions that discriminate between a perfect match and a single base mismatch in this hybridization of a member of said second array of nucleic acid segments to the informational portion of said second hybridization oligonucleotide, wherein said second hybridization oligonucleotide differs in sequence from said first hybridization oligonucleotide;
wherein said first plurality of nucleic acid segments is not contacted with said second hybridization oligonucleotide;
detecting hybridization of a hybridization oligonucleotide to a nucleic acid segment; and
analyzing the result.
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Abstract
Sequencing by Hybridization (SBH) methods and apparatus employing subdivided filters for discrete multiple probe analysis of multiple samples may be used for DNA identification and for DNA sequencing. Partitioned filters are prepared. Samples are affixed to sections of partitioned filters and each sector is probed with a single probe or a multiplexed probe for hybridization scoring. Hybridization data is analyzed for probe complementarity, partial sequencing by SBH or complete sequencing by SBH.
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37 Claims
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1. A method of analyzing nucleic acids by hybridization, comprising the steps of:
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contacting a first plurality of different nucleic acid segments disposed on a first sector of a substrate with a first hybridization oligonucleotide, wherein said first plurality of nucleic acids is arranged on said first sector in a spatially identifiable array, under conditions that discriminate between a perfect match and a single base mismatch in the hybridization of a member of said first array of nucleic acid segments to the informational portion of said first hybridization oligonucleotide;
contacting a second plurality of different nucleic acid segments disposed on a second sector of the substrate with a second hybridization oligonucleotide, wherein said second plurality of nucleic acids is arranged on said second sector in a spatially identifiable array, under conditions that discriminate between a perfect match and a single base mismatch in this hybridization of a member of said second array of nucleic acid segments to the informational portion of said second hybridization oligonucleotide, wherein said second hybridization oligonucleotide differs in sequence from said first hybridization oligonucleotide;
wherein said first plurality of nucleic acid segments is not contacted with said second hybridization oligonucleotide;
detecting hybridization of a hybridization oligonucleotide to a nucleic acid segment; and
analyzing the result.- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 37)
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15. A method for analyzing a plurality of nucleic acids from a plurality of subjects, comprising the steps of:
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providing a substrate comprising the nucleic acids, wherein the nucleic acids are disposed on a plurality of sectors on the substrate, and wherein different nucleic acids are arranged on each sector in a spatially identifiable array;
contacting the nucleic acids with a plurality of oligonucleotide probes under conditions that discriminate between a perfect match and a single base mismatch in the hybridization of a member of said plurality of nucleic acid segments to the informational portion of a member of said plurality of oligonucleotides, wherein the different nucleic acids on a first sector are contacted with a first probe and the nucleic acids on a different second sector are contacted with a second probe, wherein the second probe differs in sequence from the first probe and the first sector is not contacted with the second probe; and
determining which probes bind to the nucleic acids, thereby identifying single nucleotide polymorphisms among the plurality of samples. - View Dependent Claims (16, 17, 18, 19, 20, 21, 22)
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23. A method for analyzing a nucleic acid, comprising the steps of:
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providing a substrate comprising the nucleic acid, wherein the nucleic acid is disposed on a plurality of sectors on the substrate, and wherein each sector comprises a spatially identifiable array of immobilized nucleic acids;
contacting the nucleic acid with a plurality of oligonucleotides under conditions that discriminate between a perfect match and a single base mismatch in the hybridization of the nucleic acid to the informational portion of a member of said plurality of oligonucleotides, wherein the nucleic acid in a first sector of the substrate is contacted with a first oligonucleotide and the nucleic acid in a second sector of the substrate is contacted with a second oligonucleotide, wherein the second oligonucleotide differs in sequence from the first oligonucleotide and the first sector is not contacted with the second oligonucleotide; and
determining which oligonucleotides bind to the nucleic acid. - View Dependent Claims (24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36)
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Specification