Trapping electrophoresis and ratchets: a theoretical study for DNA-protein complexes

Recently, Griess and Serwer (1998. Biophys. J. 74:A71) showed that it was possible to use trapping electrophoresis and unbiased but asymmetrical electric field pulses to build a correlation ratchet that would allow the efficient separation of naked DNAs from identical DNAs that form a complex with a bulky object such as a protein. Here we present a theoretical investigation of this novel macromolecular separation process. We start by looking at the general features of this electrophoretic ratchet mechanism in the zero-frequency limit. We then examine the effects of finite frequencies on velocity and diffusion. Finally, we use the biased reptation model and computer simulations to understand the band-broadening processes. Our study establishes the main experimental regimes that can provide good resolution for specific applications.