Genetic Algorithm for the Design of Confronting Two-Pair Primers

Many single nucleotide polymorphisms (SNPs) genotyping techniques have been developed but most of them are expensive. Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) is a restriction enzyme-free and economic genotyping but its primer design is still computationally challenged. Here, we introduced a genetic algorithm (GA)-based PCR-CTPP primer design method. Thirty SNPs of the Janus kinase 2 gene with their SNP flanking length for 500 bps were tested. These GA-based designing CTPP primers were characterized with close values for melting temperature (Tm) and specificity, and their corresponding PCR products were provided with the optimal length. In conclusion, this novel PCR-CTPP primer designing method provides the computation for the primer information of cost- and time-effective enzyme-free SNP genotyping.