Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring
Open Access
- 1 July 2003
- journal article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 13 (7) , 1754-1764
- https://doi.org/10.1101/gr.997703
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.Keywords
This publication has 5 references indexed in Scilit:
- Methods for Genotyping Single Nucleotide PolymorphismsAnnual Review of Genomics and Human Genetics, 2001
- Screening for Single-Nucleotide Polymorphisms Using Branch Migration Inhibition in PCR-amplified DNAClinical Chemistry, 2000
- Branch migration inhibition in PCR-amplified DNA: homogeneous mutation detectionNucleic Acids Research, 2000
- PROCESSING OF RECOMBINATION INTERMEDIATES BY THE RuvABC PROTEINSAnnual Review of Genetics, 1997
- Formation of a Single Base Mismatch Impedes Spontaneous DNA Branch MigrationJournal of Molecular Biology, 1993