(141c) Microchip-Based Investigation of the Interplay Between the Nanoporous Gel Morphology and the Onset of Entropic Trapping in DNA Gel Electrophoresis

The design of miniaturized DNA electrophoresis systems imposes demanding requirements that are challenging our knowledge about how the nanoscale pore morphology of the sieving matrix influences the physical mechanism of DNA migration through the gel. But a detailed understanding of this interplay is limited by a general lack of experiments probing fundamental parameters like mobility and diffusion coefficients that are key descriptors of electrophoretic migration. We have recently developed an innovative way to address this need through the use of a microfluidic platform that allows continuous whole channel scanning of DNA separation progress so that the size dependence of these parameters can be quickly and accurately measured. When combined with material characterization methods we have developed that enable both the mean pore size and pore size distribution of the gel to be quantified, we are able to establish a direct link between sieving matrix morphology and DNA migration in photopolymerized crosslinked polyacrylamide gels cast under different UV intensities and concentrations.

We have applied this approach is applied to examine electrophoresis of double-stranded DNA with lengths ranging from 0.1 to 1 kb in these gels, and have discovered that varying the rate of photopolymerization appears to induce a corresponding change in the physical mechanism of DNA migration between reptation and entropic trapping. Furthermore, we have identified a range of conditions where a favorable interplay exists between these migration mechanisms that results in improved separation performance. These counterintuitive results have led us to reconsider the applicability of some scaling relationships and theories widely used to describe electrophoretic migration of DNA, and we present our progress toward developing modifications that can enable them to account for the influence of the gel pore size and pore size distribution. This will allow us to better predict separation performance in different sieving gels and operating conditions, and ultimately provide new insights that can help enable rational selection of optimal matrix materials and polymerization conditions that deliver enhanced separation performance.