A DNA prism: physical principles for optimizing a microfabricated DNA separation device

Recently, we reported a microfabricated "DNA prism" device that continuously sorts large DNA molecules (61 kilo-base pair to 209 kb) according to size in 15 seconds. In this paper, we develop models to understand and optimize the device. The device\´s complicated characteristics are explained poorly by a simple model based on the assumption that DNA molecules are fully stretched. Assuming DNA molecules obey Hooke\´s law, a second model successfully explains the "biphasic" separation characteristics under low fields. Further, the model suggests the use of high fields combined with shorter pulse durations for more linear separation dependence on molecular weight, an advantage which is then confirmed by experiments.