(462a) Simulation of DNA Conformation Pre-Conditioning for Electrophoretic Stretching in a Microcontraction

We use Brownian dynamics-finite element method (BD-FEM) to examine new approaches to improve DNA stretching by electrokinetic flow in a microfluidic device. The device is based on the design of Kim and Doyle[1] that stretches DNA by passing them through a hyperbolic contraction. To further enhance DNA stretching, we propose two strategies that pre-condition DNA before they enter the contraction. For the first approach, we pre-stretch DNA in the direction perpendicular to the funnel axis with a cross-slot-like geometry. The partially stretched chains are then turned to align with the axial of the funnel, and experience the second stretching. As a result, DNA chains adapt more extended configurations before going into the funnel, and therefore achieve a higher degree of extension. For the second approach, we pre-condition DNA conformation using an oscillating extensional flow that has been shown to effectively reducing the population of folded DNA at ideal condition. However, this approach shows insignificant effect on DNA stretching. Detailed comparison for the evolution of DNA configuration will be analyzed to provide the guidance for further optimization of our design.

References [1]. Kim, J. M. and P. S. Doyle (2007). "Design and numerical simulation of a DNA electrophoretic stretching device." Lab on a Chip 7(2): 213-225.