Investigation of the Effect of Hydrogel Pore Morphology on DNA Migration Mechanisms in Microchip Gel Electrophoresis

Abstract

Many efforts to develop advanced medical diagnostic capabilities rely on the ability to perform size-based separations of DNA and proteins. Miniaturized formats have potential to provide rapid integrated solutions, but rational development requires an improved understanding of the physics underlying separation. This dissertation majorly focuses on the DNA transport in microchip gel electrophoresis systems. We have developed a transport model that allows us to determine the interplay between the hydrogel pore size distribution, the applied electric field strength, and DNA size in determining separation performance. This fundamental understanding makes it possible to access a unique DNA transport mode, entropic trapping, that becomes dominant when the hydrogel pore size is close that of DNA coil. Further investigation of the entropic trapping phenomena, both experimentally and computationally, shows how the inherently disordered dynamics governing macromolecular transport under nanoconfined surroundings can paradoxically be precisely controlled. This capability lays a foundation for a sensitive probe of nanoscale molecular conformation, revealing previously unseen details about DNA-protein binding interactions at size scales far below the limits of conventional techniques. A key breakthrough is that our method is the first practical application of stochastic resonance in entropic trapping transport of macromolecules (previously studied, but only theoretically), yielding a new tool to “image” nanoscale details of biomolecular conformation.