Eur. Phys. J. Special Topics 223, 3179–3200 (2014)
https://doi.org/10.1140/epjst/e2014-02326-4

Review

Hydrodynamics of DNA confined in nanoslits and nanochannels

¹ Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, USA
² Materials Research Laboratory, University of California – Santa Barbara, Santa Barbara, CA 93106, USA

^a e-mail: dorfman@umn.edu

Received: 17 October 2014
Revised: 5 November 2014
Published online: 15 December 2014

Abstract

Modeling the dynamics of a confined, semiflexible polymer is a challenging problem, owing to the complicated interplay between the configurations of the chain, which are strongly affected by the length scale for the confinement relative to the persistence length of the chain, and the polymer-wall hydrodynamic interactions. At the same time, understanding these dynamics are crucial to the advancement of emerging genomic technologies that use confinement to stretch out DNA and “read” a genomic signature. In this mini-review, we begin by considering what is known experimentally and theoretically about the friction of a wormlike chain such as DNA confined in a slit or a channel. We then discuss how to estimate the friction coefficient of such a chain, either with dynamic simulations or via Monte Carlo sampling and the Kirkwood pre-averaging approximation. We then review our recent work on computing the diffusivity of DNA in nanoslits and nanochannels, and conclude with some promising avenues for future work and caveats about our approach.