Selective DNA screening in microfluidic channels by electrophoresis through hydrogel matrices

Advances in microchip design, coupled with novel bioassays have led to advances in the field of genetic diagnostics. Microfluidic devices offer analytical advantages for samples of low concentration and small sample volume due to directed, efficient mass transport of analytes through microfluidic networks. Although significant advances have been made in genetic assays using micro-arrays, there exists a need for a high throughput, DNA detection system for use with microfluidic platforms. One such strategy is to incorporate a selective DNA screening element into a microfluidic device that takes advantage of the aforementioned attributes. We describe here a method for immobilizing single-strand DNA (ss-DNA) probe molecules in polyacrylamide hydrogels within plastic microfluidic channels. Fluorescenttagged ss-DNA targets are electrophoretically driven through the hydrogel plugs, and hybridize with complementary ss-DNA probes covalently bound in the hydrogel. Here we present results that establish: the reproducibility of the hybridization assay; the effect of base pair mismatches within the target-probe duplex on the amount of target ss-DNA retained by the probe modified hydrogel matrix; and the efficiency of hybridization of target ss-DNA with complementary immobilized probe ss-DNA within the hydrogel plug.