Allele-specific holliday junction formation: A new mechanism of allelic discrimination for SNP scoring

Qinghong Yang, Alla Lishanski, Wendy Yang, Sandra Hatcher, Henrietta Seet, Jeffrey Gregg

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

We report here a new mechanism for allelic discrimination - allele-specific Holliday Junction formation. The Holliday Junction (HJ) is a unique DNA structure that can be formed in a sequence-nonspecific manner by routine PCR. To cause the PCR-based HJ formation to occur in an allele-specific manner, the PCR primers are manipulated such that an extra mismatch next to a SNP of interest is introduced between a target and a reference amplicon and a GC-clamp is added. Based on this new mechanism, novel SNP genotyping methods were developed, including a homogeneous fluorescence polarization (FP) competition assay that requires neither labeled primers/probes nor expensive enzymes/substrates. Using this novel genotyping technology, we were able to convert >95% of SNP sequences into genotyping assays that work well under a universal set of assay conditions and achieved 100% accuracy in clinical samples.

Original languageEnglish (US)
Pages (from-to)1754-1764
Number of pages11
JournalGenome Research
Volume13
Issue number7
DOIs
StatePublished - Jul 1 2003

ASJC Scopus subject areas

  • Genetics

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