Multiple SNPs genotyping by ligation of universal probes on 3D DNA microarray

A novel approach for simultaneous detection of multiple SNPs genotyping by ligation of universal probes on a 3D polyacrylamide gel DNA microarray was reported in this study. In the principle experiment, synthetic single-stranded DNA (ssDNA) templates simulating 3 SNP loci modified with acrylamide group at the 5´-termial were copolymerized with the acrylamide monomer to be immobilized onto one chip and hybridized with the corresponding 3 kinds of sequencing primers designed to be complementary with the immobilized ssDNA templates, respectively. Then, enzymatic ligation reactions were performed between the 3´-hydroxyl terminus of sequencing primers and 5´-phosphorylate end of the probes labeled with different fluorescent dyes. The fluorescent signals were detected and then the 3 simulative SNP loci were accurately identified simultaneously on one microarray when the discriminating base of the probes was complementary to the point mutation or SNP locus of the templates. This new strategy is effective, simple, inexpensive and may be widely promoted in many critical researches and diagnostic applications which focus on the high specificity and sensitivity but low-cost to detect multiple SNP loci simultaneously.