Visualized Detection of Aldehyde Dehydrogenase 2 Gene Polymorphism By Serial Invasive Reaction Coupled with Gold Nanoparticle Probe Assembling

Abstract

Conventional assays for identifying polymorphism of aldehyde dehydrogenase 2 (ALDH2) gene (rs671) are based on electrophoresis, fluorescence-labeled probes or sequencing, which are laborious and expensive. Herein, we proposed a visualized detection of ALDH2 genotype by PCR-based serial invasive reaction coupled with gold nanoparticle probe (GNP) assembling, in which target DNAs were firstly amplified by PCR, and then the alleles on the amplicons were identified by serial invasive reaction, and finally the genotyping results could be read out with naked eyes by observing the color changes caused by GNP assembling. If the allele-specific invasive probe matched the target sequence, the hairpin probe could be cleaved into two parts by Flap endonuclease 1 (FEN1). As a result, the GNPs could not be aggregated by the hairpin probe, keeping the solution red. Otherwise, the intact hairpin probe caused the aggregation of GNPs, leading to the color change from red to purple or clear. Therefore, the genotyping result could be read out with naked eyes by observing the color changes of the reaction. As low as 80 pg of genomic DNA could be accurately genotyped, and the genotyping results of 207 clinical samples were consistent with that of pyrosequencing, indicating that the proposed method has great potential in genotyping of personalized medicine-related single nucleotide polymorphism. A visualized method for detecting ALDH2 gene polymorphism site was established by coupling PCR-based serial invasive reaction coupled with gold nanoparticle probe (GNP) assembling. After reaction finished, the tube with target allele was red, and the tube without target allele was colorless.