Testing Primer Sequence Variations Using AS-PCR to Diagnose the V232D-CFTR Mutation

Abstract

There are over 1,700 mutations of the CFTR gene that lead to the autosomal recessive disease cystic fibrosis (CF). Of these, the V232D mutation is a rare condition caused by a single nucleotide polymorphism at the 232nd codon. At the mutation site, a T→A nucleotide change causes GTC (valine), to become GAC (aspartic acid). This promotes the formation of non-native hydrogen bonds, which lead to a misfolding of the CFTR protein. To increase the specificity of detecting the V232D mutation of CFTR, an array of allele specific polymerase chain reaction (AS-PCR) strategies were tested. Preliminary control experiments were conducted by analyzing commercially purified genomes and human genomic DNA isolated from somatic buccal cells using chelex resin. Primers were developed to compare amplification stability versus nucleotide sequence. Applying the Yaku group's strategy, we hypothesized that a primer designed with the V232D SNP nucleotide mismatch at the second base from the 3' end would be more effective at diagnosing the V232D mutation of CFTR than a primer with a mismatch at the third base from the 3' end due to steric strain principle limiting false positive results. Final analysis yielded data to support the function of our mutant seeking primers on mutant DNA. Yet further studies are needed to investigate mismatched nucleotide placement versus annealing and polymerization.