(142ac) Simulation Guided Design and Experimental Validation of Microfluidic Devices for Stretching DNA Using Electrophoresis and Pressure-Driven Flow

We have used computational fluid dynamics and Brownian dynamics simulations to design a microfluidic device for stretching DNA. The device is an implementation of a new conformation pre-conditioning strategy. The key of the strategy is to “pre-stretch” DNA in the direction orthogonal to its final stretching direction. This microfluidic device is predicted by the simulations to yield substantial improvement on DNA stretch at given Deborah number and contraction geometry. To test our design, we have performed DNA stretching experiments using either electrophoresis or pressure-driven flow as the stretching force. The pre-conditioning strategy is found working only for the case using the pressure-driven flow. We have analyzed the evolution of DNA conformation, the maximum DNA extension and its distribution. The simulations and experimental results are in reasonably good agreement for DNA driven by pressure-driven flow but are qualitatively different for DNA driven by electrophoresis. We will discuss the causes of the discrepancy between simulations and experiments.