Microfabricated Linear Hydrogel Microarray for Single-Nucleotide Polymorphism Detection

A platform is developed for rapid, multiplexed detection of single-nucleotide polymorphisms using gels copolymerized with oligonucleotide capture probes in a linear microchannel array. DNA samples are analyzed by electrophoresis through the linear array of gels, each containing 20–40 μM of a unique oligonucleotide capture probe. Electrophoresis of target DNA through the capture sites and the high concentration of capture probes within the gels enables significantly shorter incubation times than standard surface DNA microarrays. These factors also result in a significant concentration of target within the gels, enabling precise analysis of as little as 0.6 femtomoles of DNA target. Differential melting of perfectly matched and mismatched targets from capture probes as a function of electric field and temperature enables rapid, unambiguous identification of single-nucleotide polymorphisms.