PCR-product microarray based on polyacrylic acid-modified surface for SNP genotyping

PCR-product microarray has great efficiency in SNP genotyping, mutation screening and epigenetic analyzing from a large number of samples. The current PCR-product microarray technology is mostly based on the 3-D gel microarray technologies due to its high loading capacity for PCR products, while there is little progress for PCR-product microarray on planar glass, which gives low background and convenient fabrication. In this study, we improved the PCR-product microarray on planar glass by employing a polyacrylic acid-covered slide. The raw amino-modified PCR products were simply precipitated with ethanol and directly spotted for DNA immobilization. Three detection methods of hybridization, solid-single base extension and solid-multiple bases elongation were carried out for single nucleotide variation identification on the PCR-product microarray. The experimental results showed that the high immobilization yield for raw PCR product was achieved, and the high specificity and high ratio of S/N for genotyping on the microarray were obtained. SNP genotyping of cytochrome P450 2D6 gene in 30 individuals was successfully demonstrated. This study has significantly increased the performances of PCR-product microarray, which could improve its applications in SNP genotyping and mutation screening in large number of individuals.