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Enhancement of DNA Hybridization Kinetics by DC Electrokinetic Mixing in Microchannels

Jean-Roland Pascault and Hong Susan Zhou. Chemical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609

Gene chips, capable of detecting specific DNA sequences in a sample, have become a widely used device. The chips feature an array of high density single-stranded DNA probes that can bind to their complementary target sequence. This event is called hybridization, and can be detected, thus indicating the presence of the target in the sample. However, the existing arrays are mainly passive: the motion of DNA in the sample is only governed by diffusion, which make the DNA transport slow and limits the hybridization rate. In the literature, devices capable of creating mixing and fluid circulation through electrokinetics have been described, and are candidates to enhance the DNA hybridization kinetics. In this work, the influence of mixing on the hybridization kinetics is simulated with a finite element software package (COMSOL Multiphysics®). The focus is on DC devices, where electroosmotically driven flow is generated and DNA electrophoresis occur. Several channel geometries are investigated: open channels, closed-end channels, and channels presenting steps. Different planar electrode geometries are studied as well: electrodes placed at the extremities of the channel, and electrodes placed along the walls of the channel. Globally, it is found that the DNA hybridization kinetics is substantially enhanced. Also, these results encourage us to study AC electrokinetics, because of their ability to create more complex flow patterns and force field on DNA.