Detection of single nucleotide polymorphism by measuring extension kinetics with T7 exonuclease mediated isothermal amplification

Abstract

In this work, we measured the primer extension kinetics of the Klenow fragment (exo-) to achieve rapid detection of single nucleotide polymorphism (SNP). Both the matching and the single-base mismatching targets were used as the primer in the kinetic measurements to identify the single nucleotide polymorphism. By coupling with the T7 exonuclease-assisted target cycling process, we decreased the detection limit but still maintained a high discrimination factor. After the demonstration of a good discrimination ability with synthetic DNA strands, we applied the method to detect low abundance of epidermal growth factor receptor (EGFR) mutation in human genomic DNA, which was a biomarker of non-small cell lung cancer. The kinetics based SNP detection was performed at room temperature and was robust against photobleaching and other optical interferences for the detection of low abundance of point mutations in human genomic DNA. The detection method is adaptable to a microarray platform for high-throughput and point-of-care detection.