Hindered DNA coordinated motion in nanochannels

We investigate the relaxation dynamics of long DNA molecules confined in micro- and nano-channels with Brownian dynamics simulations. Prior experiment by Reisner et al. found that the stretch fluctuation correlation time ($t_{relax}$) of DNA molecules in nanochannels increases as the channel height ($H$) decreases for $H$ greater than the DNA Kuhn length ($\sigma_k$), and $t_{relax}$ decreases as $H$ decreases for $H < \sigma_k$. Our simulations capture this behavior, and quantitatively agree with the experimental results within the error bars. The scaling-law dependence of $t_{relax}$ on $H$ in different regimes is verified. Rouse mode analysis of the chain relaxation mechanism further shows that segmental relaxation on length scale longer than $\sigma_k$ are hindered and the dynamics of segments shorter than $H$ dominate the chain relaxation processes. We also find that the inclusion of intra-chain hydrodynamic interactions affect segmental relaxation. The implications for DNA translocation through nanopores and nanochannels are discussed.