DNA Electrophoresis in Colloidal Self-Assembled Arrays

This thesis investigates electrophoretic separation of DNA molecules in different types of separation media formed by silica nanoparticles. Particle arrays within microfluidic chips are fabricated using evaporation induced colloidal self-assembly. Methods to adjust pore size and the order of the particle lattice were developed, in order to probe the effect of lattice structure and size on separation of DNA.;A stepwise packing procedure was developed to fabricate structures with stepwise gradient in pore size. Monodisperse packed structures yield pore sizes from a few nanometers to a few hundred nanometers according to the particle size being used, but the electrophoresis can only be optimized for a certain range of DNA sizes. By packing separation zones with two different pore sizes, optimal separation can be achieved for larger and smaller DNA size range, by taking advantages from both larger and smaller pore sizes within one device. The separation accomplished in the upstream region is retained as DNA moves across the zone boundary, even when the separated DNA has the same deflection angle in the downstream region. Small DNA not separated in the larger pore size is then separated in the smaller, downstream pore size. The peak capacity is improved by employment of this stepwise pore gradient.;Colloidal arrays with two different sized nanoparticles mixed in various proportions are prepared, yielding structures with different degrees of disorder. The roles of order within a separation matrix on DNA separation in both asymmetric pulsed field angular separation and capillary zone electrophoresis are studied systematically. Radial distribution functions and orientational order parameters are determined to characterize the scale of disorder.;In pulsed field electrophoresis, the DNA separation resolution is quantified for each structure, showing a strong dependence on order within the structure. Ordered structures give better separation resolution than highly disordered structures. However, the variation of separation performance with order is not monotonic, showing a small, but statistically significant improvement in structures with short range order compared to those with long range order.;In capillary zone electrophoresis, regression analysis is conducted for the electrophoretic mobility and the dispersion coefficient. Both parameters exhibit a weak monotonic dependence on matrix order, complementary to the effect of DNA size and pore size. Higher degree of matrix order is favored by higher mobility and lower dispersion coefficient.