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Biophys J, September 1998, p. 1228-1236, Vol. 75, No. 3

Trapping Electrophoresis and Ratchets: A Theoretical Study for DNA-Protein Complexes

Claude Desruisseaux,*# Gary W. Slater,# and Tarso B. L. Kist#§

 *Department of Biology and  #Department of Physics, University of Ottawa, Ottawa, Ontario, Canada, and  §Departamento de Biofísica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil

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.

Biophys J, September 1998, p. 1228-1236, Vol. 75, No. 3
© 1998 by the Biophysical Society   0006-3495/98/09/1228/09  $2.00




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Copyright © 1998 by the Biophysical Society.