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Nucleic acid detection combining amplification with fragmentation

  • US 9,783,854 B2
  • Filed: 04/06/2015
  • Issued: 10/10/2017
  • Est. Priority Date: 04/27/2007
  • Status: Active Grant
First Claim
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1. A method for detecting the presence or absence of a target nucleic acid by testing a sample containing unamplified nucleic acids that potentially contains the target nucleic acid in the presence of non-target nucleic acid, said method comprising:

  • a) fragmenting the unamplified nucleic acids under conditions such that the non-target nucleic acid is preferentially fragmented relative to the target nucleic acid, wherein the target nucleic acid and the non-target nucleic acid are at least 50% identical at aligned nucleotide positions and the non-target nucleic acid comprises at least one fragmentation site not present in the target nucleic acid;

    b) combining the unamplified nucleic acids of step a) with a polymerase chain reaction (PCR) mixture comprising a pair of primers specific for the target nucleic acid, wherein one primer of the pair spans or overlaps the at least one fragmentation site present in the non-target nucleotide sequence but absent from the target nucleotide sequence, and wherein fragmentation of the non-target nucleotide sequence in part a) prevents hybridization of said primer to the non-target nucleic acid;

    c) amplifying the target nucleic acid from the unamplified nucleic acids combined with the PCR mixture in step b); and

    d) detecting presence or absence of an amplification product from step c), which indicates the presence or absence of the target nucleic acid in the sample, wherein the non-target nucleic acid comprises a wild-type nucleotide sequence and the target nucleic acid comprises a mutant version of the wild-type nucleotide sequence, and wherein step a) is performed prior to step b).

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