Design and numerical simulation of a DNA electrophoretic stretching device

Abstract

DNA stretching is now a key technology in emerging DNA mapping devices such as direct linear analysis (DLA), though DNA stretching in a high throughput manner is still a challenging problem. In this work, we present a new microfluidic channel design to enhance DNA stretching using kinematic analysis and Brownian dynamics-finite element method (BD-FEM). Our group recently showed in experiments that the extensional electrophoretic field arising from a hyperbolic microcontraction can be utilized to stretch T4-DNA. We demonstrate the reliability of our BD-FEM model for the present problem by showing that the numerical predictions are consistent with the experimental data for the hyperbolic channel. We then investigate DNA stretching for four different funnel shapes. Surprisingly the maximum mean DNA stretch is quite similar in all four designs. Finally, we propose a new design with a side-feeding branch to enhance stretching based on a kinematic analysis along different feeding locations. Our numerical simulation predicted that DNA stretching can be dramatically enhanced using side-feeding.