The conformational dynamics of λ-DNA in the anti-Brownian electrokinetic trap: Brownian dynamics and Monte Carlo simulation

Abstract

In this work, we examine the conformational dynamics of long polymer molecules under confinement, as in the recently developed anti-Brownian electrokinetic (ABEL) trap [A. Cohen and W. Moerner, Proc. Natl. Acad. Sci. USA. 103, 4362 (2006)]. We analyze polymer motion using Brownian dynamics simulations (bead-spring and bead-rod models) and via Monte Carlo methods. We first verify Cohen and Moerner's (2007) single molecule observations regarding the existence of short time correlations [Phys. Rev. Lett. 98, 116001 (2007)] in the motion of a polymer's center of mass, which arise due to fluctuating hydrodynamic interactions. Thereafter, following Cohen and Moerner, we use principal component analysis to extract the principal modes governing polymer conformation and find that confinement and backbone bending only affect small polymers and should not play a significant role in the dynamics of long polymers such as lambda-DNA. We find excellent agreement between our principal component analysis modes and those measured by Cohen and Moerner [Proc. Natl. Acad. Sci. U.S.A. 104, 12622 (2007)]. Finally, to explore the effect of excluded volume, in particular, the effect of the excluded volume parameter (z), we use image-image correlations to examine its relation to polymer dynamics. Image-image correlation measurements performed on lambda-DNA in the ABEL trap did not display a simple exponential-type behavior and motivated the use of stretched exponential functions to determine the characteristic timescale (tau) governing conformational dynamics. We show that tau scales with polymer length as N(2) and decreases with increasing z. Furthermore, we can collapse a variety of data when tauN(-2) is plotted with respect to N/z(m) (m=0.14 for freespace and 0.366 for walls).