Conformational preconditioning by electrophoresis of DNA through a finite obstacle array

We investigate the effectiveness of DNA conformational preconditioning by electrophoresis through an obstacle array on the later stretching of molecules in a microchannel contraction. The control, reproducibility, and ability to compare with the well-Studied single postcollision problem make this a model system for conformational preconditioning studies. We find that the obstacle array increases the average deformation applied to the DNA in the contraction through elimination of slower stretching DNA conformations. In the current device, a dramatic change in the resulting polymer behavior occurs at a predeformation in the obstacle array of about 20% relative extension. We show that the hooking probability in the array is geometrically limited at large electric fields and that modification of the geometrical parameters shows promise for optimization of a second-generation device.