Experimental Validation of a DNA Pre-Conditioning Strategy Developed Using Brownian Dynamics Simulations

We have developed a new pre-conditioning strategy to improve DNA stretching by electrokinetic flow in a microfluidic device using Brownian dynamics simulations. The core of the strategy is to “pre-stretch” DNA in the direction orthogonal to its final stretching direction. This allows DNA to be pre-stretched while requires no additional strain to be provided. Although we have shown in simulations that this strategy can improve the degree of DNA extension considerably even at medium Deborah number, an experimental validation is yet to be performed. In this study, experiments on the newly developed pre-conditioning strategy and some of its variation are performed. We compare in details the predictions and experimental results in the averaged maximum DNA extension, its distribution and the mechanism causing the preconditioning effect. It is found that the new strategy provides moderate improvement on the degree of DNA extension. The cause of the discrepancy between simulations and experiments will be discussed.