Polyacrylamide micro-pillar based DNA microarray and its application for genetic variation analysis.

To improve diffusive capabilities and target accessibility with a gel-based microarray, a novel `pads within a pad' approach was developed. Using a soft lithography technique, an array of `waffle'-like micro-pillars embedded on the surface of the glass slide substratum was fabricated. The micro-pillar based microarray showed more than a 3-fold increase in the effective surface area available for probe immobilization. As a result, a fivefold increase was observed in the hybridization rate and intensity of the `waffle' pad as compared to an unmodified gel pad. The functionality of the `waffle' pad was demonstrated by the accurate genotyping of two sets of SNPs (SNP_ 1236 and SNP_2677) based on the dissociation curve, dissociation temperature, Td and the difference of Td between the perfect match duplex with that of the mismatch (DeltaTd)