Conformation and dynamics of single DNA molecules in parallel-plate slit microchannels

The conformation and diffusion of a single DNA molecule confined between two parallel plates are examined using both single molecule experiments and Brownian dynamics simulations accounting for hydrodynamic interactions. The degree of chain stretching and the diffusivity are characterized as a function of the chain confinement and the channel geometry. Good agreement is found between the simulations, experiments, and scaling theory predictions.

Figure 1

Illustrations of (A) the slit channel geometry and (B) the square microchannel.

Figure 2

BD-HI simulation results for the normalized chain stretch in the slit channel as a function of inverse normalized channel width for chain lengths of $N_{\mathrm{s}}=10$ (circles), 20 (squares), 40 (triangles), 80 (inverted triangles), and 120 (diamonds). The crosses are the simulation results for the square channel geometry from Ref. 9. The solid line is the scaling theory prediction of ${(R_{\mathrm{g},\text{bulk}}∕H)}^{1∕4}$ and the dashed line is ${(R_{\mathrm{g},\text{bulk}}∕H)}^{2∕3}$.

Figure 3

BD-HI simulation results for the normalized chain diffusivity in the slit channel as a function of inverse normalized channel width for chain lengths of $N_{\mathrm{s}}=10$ (circles), 20 (squares), 40 (triangles), 80 (inverse triangles). Experimental measurements for $\lambda$-DNA (filled circles), $2\lambda$-DNA (filled squares), and $3\lambda$-DNA (filled triangles) are shown with error bars. The crosses are the results for the square channel geometry from Ref. 9. The solid line is the scaling theory prediction of ${(R_{\mathrm{g},\text{bulk}}∕H)}^{-2∕3}$.