(162i) When Is DNA Flexible and Non-Draining?

The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion in the literature in various geometries including slits, channels and even the dilute unconfined case. In order to elaborate on many of these details, we have directly computed the polymer size and diffusivity for unconfined, slit-confined and channel-confined wormlike chains near these limits. To do so, we use a chain-growth Monte Carlo algorithm, the pruned-enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties (using a rigid-body approximation for the chain hydrodynamics) of wormlike chains over an extremely large dynamic range. For instance, we can accurately predict the diffusivity of an unconfined molecule of double-stranded DNA from about 100 bp up to several hundred kilobase pairs. From our calculations, we find that very large chains are required to reach the universal, flexible regimes including the de Gennes regime in slits and channels and the swollen coil regime for unconfined wormlike chains. Furthermore, our results indicate that the dynamic properties (i.e. the chain diffusivity) converge less quickly to universal, non-draining behavior than do the static properties. Accordingly, for the case of unconfined DNA in a high-ionic strength buffer, we predict that the chain becomes flexible and non-draining for contour lengths near 1 megabase pair. Qualitatively similar results are also obtained for DNA confined in slits and channels. This suggests that the flexible, non-draining limit is rarely (if ever) applicable to double-stranded DNA in situations commonly encountered in nanofluidic devices.