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Biopolymer sequencing by hybridization of probes to form ternary complexes and variable range alignment

  • US 8,278,047 B2
  • Filed: 10/01/2008
  • Issued: 10/02/2012
  • Est. Priority Date: 10/01/2007
  • Status: Active Grant
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, wherein the first probe is a member selected from the group consisting of an oligonucleotide, a peptide, and a polyamide;

    contacting said target molecule or fragment thereof with a second probe having specificity for one or more second recognition sites of said target molecule, thereby forming one or more second local ternary complexes along said double-stranded biopolymer target molecule or fragment thereof, said one or more second recognition sites each having a second known sequence;

    passing said double-stranded biopolymer target molecule or fragment thereof through a nanopore or channel;

    detecting an electrical signal indicative of one or more locations of 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;

    detecting an electrical signal indicative of one or more locations of at least a subset of said one or more second local ternary complexes along said double-stranded biopolymer target molecule or fragment thereof to determine a second probe map; and

    determining said whole or partial sequence of said target biopolymer using at least said first probe map and said second probe map.

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