title: Trapping electrophoresis and ratchets: a theoretical study for DNA-protein complexes.
abstract: 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.
authors.affiliation: Department of Biology, University of Ottawa, Ontario, Canada.
authors.forename: C
authors.initials: C
authors.lastname: Desruisseaux
authors.forename: G W
authors.initials: GW
authors.lastname: Slater
authors.forename: T B
authors.initials: TB
authors.lastname: Kist
mesh_terms: D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification*; D004586:Electrophoresis / Q000379:methods*; D046911:Macromolecular Substances; D008962:Models, Theoretical; D011506:Proteins / Q000737:chemistry / Q000302:isolation & purification*; D055672:Static Electricity
chemical_list: D046911:Macromolecular Substances; D011506:Proteins; D004247:DNA