Diffusion of DNA in confinement: From nanochannels to cells

The key challenge in understanding the diffusivity of DNA in strongly confined systems is accounting for the hydrodynamic interactions between the polymer and its environment. I will present both experimental and theoretical results on the diffusion of DNA in two highly confined systems that illustrate the complexity of this problem.

In the first case, I will show how combining biased Monte Carlo simulations and confined hydrodynamics calculations leads to a complete picture for the friction of a semiflexible polymer confined to a square nanochannel. The regimes of hydrodynamic friction are closely related to those for the chain extension, including a Rouse-like regime at moderate confinement where the friction is independent of the fractional extension of the chain. Subsequent experimental measurements of DNA diffusion in the so-called “extended de Gennes” regime agree well with the model calculations.

In the second case, I will describe an experimental test of the viscoelastic Rouse model for the segmental motion of DNA within E. coli cells. When the cells are compressed under "Quake" valves, the mean-squared displacement of cytoplasmic particles slows down by over one order of magnitude but the exponent characterizing their subdiffusion is unchanged. In contrast, the corresponding exponent for the subdiffusion of segments of DNA on short time scales (~1 s) undergoes a statistically significantly change when the cells are compressed. These results suggest that factors other than the cytoplasmic viscoelasticity play a role in this non-equilibrium perturbation of the cells.