Influence of the PCR artifacts on the genotyping efficiency by the microsatellite loci using native polyacrylamide gel electrophoresis

Abstract

Formation of different types of artifacts during amplification has been studied using different classes of molecular-genetic markers (Indel and SSR). It has been shown that DNA heteroduplexes are formed during amplification of heterozygous samples as fragments of both target genes and microsatellite loci. Electrophoresis of the amplification products of homozygous samples by microsatellite loci in native polyacrylamide gel has revealed specific additional fragments that do not belong to the class of heteroduplex DNA. It has been supposed that the additional fragments belong to a special type of homoduplex DNA—nonlinear homoduplexes. The analysis has revealed that the formation of nonlinear homoduplex DNA takes place on the 20–25 cycle of the PCR at the amplification of both experimental samples and individual DNA fragments cut from the gel.