(250r) DNA Gel Electrophoresis via Entropic Trapping: Insights From Monte Carlo Simulations

The ability to precisely manipulate transport of charged macromolecules (DNA, proteins) in nanoporous surroundings plays a critical role in the design of microfluidic electrophoresis systems. Reptation is the predominant transport mechanism in most hydrogel-based separation matrices, where the characteristic macromolecular size scale is larger than that of the surrounding pores. DNA electrophoresis in the reptation regime yields a scaling of mobility with the inverse of macromolecular size. Alternatively, when the characteristic macromolecular size is the same as that of the surrounding pores, transport occurs via an entropic trapping mechanism. In contrast to reptation, transport in this regime occurs via discrete hops between larger pores joined by narrow interconnecting spaces, leading to a stronger size dependence of electrophoretic mobility that is desirable for enhanced separation performance.

We have previously shown how application of a time varying electric field driving force can enable the activated hopping process to become synchronized, leading to a resonance state that can be exploited both to obtain improved separation performance and to extract nanoscale physical parameters of the macromolecules (contour length, persistence length). In these initial studies, our transport model was focused on the activated process by which molecules enter the narrow space between adjacent large pores (activation time), but assumed a simplified representation of transit through the confined interconnecting region (migration time). Specifically, migration was described in terms of a simple function of the macromolecule’s radius of gyration and the applied electric field. Although this representation is consistent with previous frameworks that have been developed to describe electrophoretic entropic trapping, it does not realistically capture the hydrodynamic forces and conformational changes that occur during migration through the confined interconnecting pore spaces.

Here we apply a more realistic representation of migration through the nano-confined interconnecting spaces linking adjacent large pores. Our starting point is a model is based on a Monte Carlo algorithm developed by Slater, et. al. that directly incorporates frictional and entropic forces. The portion of the macromolecule located outside of the pore space experiences frictional interactions with the surrounding fluid, while the portion inside the pore experiences drag due to spatial confinement in the narrow interconnecting space. Entropic forces are related to conformation differences between the portion of the macromolecule at the entrance and exit of the pore space. Embedding each of these effects into our model enables the size dependence of electrophoretic mobility to be computed by integration over the pore size distribution of the hydrogel matrix. The resulting predictions are validated by comparison with experimental data. These new insights can suggest optimal operating conditions (electric field amplitude and frequency) and nanoporous gel matrix architectures (pore size distribution) to deliver enhanced separations in microfluidic electrophoresis systems.