C. Desruisseaux et al., TRAPPING ELECTROPHORESIS AND RATCHETS - A THEORETICAL-STUDY FOR DNA-PROTEIN COMPLEXES, Biophysical journal, 75(3), 1998, pp. 1228-1236
Recently, Griess and Serwer (1998. Biophys. J. 74:A71) showed that it
was possible to use trapping electrophoresis and unbiased but asymmetr
ical electric field pulses to build a correlation ratchet that would a
llow the efficient separation of naked DNAs from identical DNAs that f
orm a complex with a bulky object such as a protein. Here we present a
theoretical investigation of this novel macromolecular separation pro
cess. We start by looking at the general features of this electrophore
tic 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 experime
ntal regimes that can provide good resolution for specific application
s.