Development of a MATLAB Error-Prone PCR Simulator for Random Mutation of Target Gene

Abstract

Error-prone polymerase chain reaction (ep-PCR) is useful for generating mutational variant of target genes in exploring the sequence space that could be correlated with enhanced protein or enzyme function and activity. However, screening the resulting library is often expensive and tedious. This software development work aims to develop a MATLAB based error-prone PCR simulator that could be used to simulate the process of randomly generating mutations in the gene sequence of a target gene. Specifically, the software picks a random nucleotide in the gene sequence for random mutation into another or the same nucleotide. Application of the software to the 16S rRNA gene of Helicobacter pylori found that just 12 cycles of error-prone PCR would result in a 16S rRNA gene sequence that is only 99% similar to the original gene sequence. This meant that evolution of 16S rRNA gene may be intrinsically fast, which is a phenomenon that needs confirmation for a larger variety of microbial species. Given the phylogenetic importance of 16S rRNA gene for confirming the identity of microbial species, the error-prone PCR software may offer a facile method to investigate the issue of how fast 16S rRNA gene evolves, and how does this impact on microbial identification.

Keywords: Helicobacter pylori, 16S rRNA gene, random mutagenesis, error-prone PCR, sequence space