DNA adsorption and separation on flat and patterned surfaces

Electrophoretic methods have become the primary means of separating and sequencing DNA. Yet, despite the advances made in the design of electrophoretic separation media, like polymer solutions, they still can only apply to short DNA fragments and narrow size range.; We propose a new approach to performing electrophoresis of large and wide size range of DNA. We show that it is possible to exploit the conformational entropy of an adsorbed DNA molecule such that a perfectly flat surface can separate DNA fragments under an applied electric field in the plane of the surface. The critical factor that controls the fractionation of DNA on a flat surface is the local friction between the adsorbed DNA segments and the surface. The mobility was found to follow a power law with the field intensity beyond a certain threshold. The detected DNA peak width was shown to be constant with migration distance, which implies that there is no diffusion of DNA during migrating on surface.; In addition, we demonstrate that electrophoresis on a flat Si substrate is an effective method in separation of DNA with different configurations, e. g. linear, supercoiled and relaxed. The surface separation arises from the different number of contacts due to the conformational differences between adsorbed DNA chains. Imposing a Au nanopattern on the Si surface further improves the separation effect. The simulation of electric field on this patterned surface by the finite element method shows that An nanodots act as local pinning points for DNA segments due to dielectrophoretic force. The results of molecular dynamics simulation show that the conformational differences between adsorbed polymer chains are amplified on the attractive patterned surface and therefore enhanced separations are achieved.; We also study the surface migration of DNA chains driven by a DC electric field across periodic and localized dielectrophoretic traps. By adjusting the length scale of the trap array, separation of a selected band of DNA was accomplished with a dispersion coefficient similar to that obtained in capillary electrophoresis. We then provide a model, in good agreement with experiment, which predicts the trapping and extension of DNA chains at a dielectrophoretic trap responsible for the surface mobility and dispersion.