BIOPOLYMER SEQUENCING BY HYBRIDIZATION OF PROBES TO FORM TERNARY COMPLEXES AND VARIABLE RANGE ALIGNMENT
First Claim
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1. A method for determining a whole or partial sequence of a target biopolymer, the method comprising the steps of:
- providing a double-stranded biopolymer target molecule;
contacting said target molecule or fragment thereof with a first probe having specificity for one or more first recognition sites of said target molecule, thereby forming one or more first local ternary complexes along said double-stranded biopolymer target molecule or fragment thereof, said one or more first recognition sites each having a first known sequence;
detecting at least a subset of said one or more first local ternary complexes along said double-stranded biopolymer target molecule or fragment thereof to determine a first probe map; and
determining said whole or partial sequence of said target biopolymer using at least said first probe map.
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Abstract
Methods for sequencing a biopolymer by forming local ternary complexes along the length of the double-stranded biopolymer target molecule using one or more probes and obtaining information about the location of the probe(s) using a detector. These methods offer particular advantage when implemented with nanopore (including micropore) detection systems.
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Citations
18 Claims
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1. A method for determining a whole or partial sequence of a target biopolymer, the method comprising the steps of:
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providing a double-stranded biopolymer target molecule; contacting said target molecule or fragment thereof with a first probe having specificity for one or more first recognition sites of said target molecule, thereby forming one or more first local ternary complexes along said double-stranded biopolymer target molecule or fragment thereof, said one or more first recognition sites each having a first known sequence; detecting at least a subset of said one or more first local ternary complexes along said double-stranded biopolymer target molecule or fragment thereof to determine a first probe map; and determining said whole or partial sequence of said target biopolymer using at least said first probe map. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
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16. A method for determining a whole or partial sequence of a target biopolymer, the method comprising the steps of:
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providing a double-stranded biopolymer target molecule; contacting said target molecule or fragment thereof with a plurality of n probes each having specificity for one or more recognition sites of said target molecule, thereby forming local ternary complexes along said double-stranded biopolymer target molecule or fragment thereof, each of said recognition sites having a known sequence; detecting at least a subset of said local ternary complexes along said double-stranded biopolymer target molecule or fragment thereof to determine one or more probe maps; and determining said whole or partial sequence of said target biopolymer using at least said one or more probe maps. - View Dependent Claims (17, 18)
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Specification