Method and apparatus for DNA sequencing and DNA identification
First Claim
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1. A method for analyzing a target nucleic acid by hybridization, comprising the steps of:
- contacting an array of probes fixed on a substrate with the target nucleic acid under hybridization conditions discriminating between full complementarity and a one base mismatch, the fixed probes being shorter than the target nucleic acid, wherein a horizontal electrical field is applied to the array, parallel to the substrate, during at least a portion of said contacting step;
exposing the array of probes and the target nucleic acid with a labeled probe under hybridization conditions discriminating between full complementarity and a one base mismatch;
covalently joining fixed and labeled probes that hybridize contiguously to the same target nucleic acid molecule; 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.
65 Citations
32 Claims
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1. A method for analyzing a target nucleic acid by hybridization, comprising the steps of:
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contacting an array of probes fixed on a substrate with the target nucleic acid under hybridization conditions discriminating between full complementarity and a one base mismatch, the fixed probes being shorter than the target nucleic acid, wherein a horizontal electrical field is applied to the array, parallel to the substrate, during at least a portion of said contacting step;
exposing the array of probes and the target nucleic acid with a labeled probe under hybridization conditions discriminating between full complementarity and a one base mismatch;
covalently joining fixed and labeled probes that hybridize contiguously to the same target nucleic acid molecule; and
analyzing the result. - View Dependent Claims (2, 3, 13, 14, 15, 25, 29)
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4. A method for analyzing target nucleic acids by hybridization, comprising the steps of:
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contacting an array of probes fixed on a substrate with a pool of target nucleic acids under hybridization conditions discriminating between full complementarity and a one base mismatch, the fixed probes being shorter than at least one of the target nucleic acids in said pool of target nucleic acids, wherein a horizontal electrical field is applied to the array, parallel to the substrate, during at least a portion of said contacting step;
exposing the array of probes and the pool of target nucleic acids with a labeled probe, under hybridization conditions discriminating between full complementarity and a one base mismatch;
covalently joining fixed and labeled probes that hybridize contiguously to the same target nucleic acid molecule; and
analyzing the result. - View Dependent Claims (5, 6, 16, 17, 18, 26, 30)
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7. A method for analyzing a target nucleic acid by hybridization, comprising the steps of:
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contacting an array of probes fixed on a substrate with said target nucleic acid under hybridization conditions discriminating between full complementarity and a one base mismatch, the fixed probes being shorter than the target nucleic acid, wherein a horizontal electrical field is applied to the array, parallel to the substrate, during at least a portion of said contacting step;
exposing the array of probes and the target nucleic acid with a pool of labeled probes, under hybridization conditions discriminating between full complementarity and a one base mismatch;
covalently joining fixed and labeled probes that hybridize contiguously to the same target nucleic acid molecule; and
analyzing the result. - View Dependent Claims (8, 9, 19, 20, 21, 27, 31)
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10. A method for analyzing target nucleic acids by hybridization, comprising the steps of:
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contacting an array of probes fixed on a substrate with a pool of target nucleic acids under hybridization conditions discriminating between full complementarity and a one base mismatch, the fixed probes being shorter than at least one of the target nucleic acids in the pool of target nucleic acids, wherein a horizontal electrical field is applied to the array, parallel to the substrate, during at least a portion of said contacting step;
exposing the array of probes and the target nucleic acids with a pool of labeled probes, under hybridization conditions discriminating between full complementarity and a one base mismatch;
covalently joining fixed and labeled probes that hybridize contiguously to the same target nucleic acid molecule; and
analyzing the result. - View Dependent Claims (11, 12, 22, 23, 24, 28, 32)
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Specification