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Journal of Biological Physics

, Volume 31, Issue 3–4, pp 365–373 | Cite as

Diffusion of DNA Molecules in Gel at High Electric Fields

  • P. Pasciak
  • M. J. Krawczyk
  • E. Gudowska-Nowak
  • K. KulakowskiEmail author
Article

Abstract

Problems related to the gel electrophoretic migration of polymers can be investigated by models based on a Brownian-type ratchet where a particle can undergo a net transport on a potential energy surface that is externally driven to fluctuate between several distinct states. Here we describe the method of polymer transport and separation by means of the cellular automata technique. Numerical simulations of the polymer reptation in the model system allow us to understand the band-broadening processes in the gel electrophoresis experiments. They indicate also possible ways of fine-tuning the parameters in designing desired resolution of the experiments.

Key words

transport coefficients ratchet systems reptation model 

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References

  1. Smoluchowski, M.: Experimentell nachweisbare, der üblichen Thermodynamik widersprechende Molekularphänomene, Physik Z. 13 (1912), 1069–1078.zbMATHGoogle Scholar
  2. Feynman, R.P., Leighton, R.B. and Sands, M.: Feynman Lectures in Physics, Addison-Wesley, Reading, MA, Vol. 1, Chap. 46, 1966.Google Scholar
  3. Reimann, P.: Brownian Motors: Noisy Transport far from Equilibrium, Phys. Rep. 361 (2002), 57–265.CrossRefADSzbMATHMathSciNetGoogle Scholar
  4. Astumian, R.D. and Bier, M.: Fluctuation Driven Ratchets: Molecular Motors, M. Phys. Rev. Lett. 72 (1993), 1766–1769.ADSGoogle Scholar
  5. Astumian, R.D. and Hänggi, P.: Brownian Motors, Physics Today 55 (11) (2002), 33–39.Google Scholar
  6. Wolfe, S.L.: Molecular and Cellular Biology, Wadsworth Publ. Comp., Belmont, 1993.Google Scholar
  7. Viovy, J.-L.: Electrophoresis of DNA and other Polyelectolytes: Physical Mechanism, Rev. Mod. Phys. 72 (2000), 813–872.CrossRefADSGoogle Scholar
  8. Wolfram, S.: Cellular Automata and Complexity, Addison-Wesley Publ. Comp., Reading, MA, 1994.Google Scholar
  9. Newman, M.E.J. and Barkema, G.T.: Monte Carlo Methods in Statistical Physics, Chap. 19, Clarendon Press, Oxford, 1999.Google Scholar
  10. Krawczyk, M.J., Dulak, J., Pasciak, P. and Kulakowski, K.: Diffusion Constant in Gel Electrophoresis at High Fields, Electrophoresis 25 (2004), 785–789.CrossRefGoogle Scholar
  11. Slater, G.W., Desruisseaux, C., Hubert, S.J., Mercier, J.-F., Labrie, J., Boileau, J., Tessier, F. and Pepin, M.P.: Theory of DNA Electrophoresis: A Look at Some Current Challenges, Electrophoresis 21 (2000), 3873–3887.CrossRefGoogle Scholar
  12. Slater, G.W., Guillouzic, S., Gautier, M.G., Mercier, J.-F., Kenward, M., McCormick, L.C. and Tessier, F.: Theory of DNA Electrophoresis (1999–2002), Electrophoresis 23 (2002), 3791–3816.Google Scholar
  13. Slater G.W., Guo, H.L., Nixon, G.L.: Bidirectional Transport of Polyelectrolytes Using Self-Modulating Entropic Ratchets, Phys. Rev. Lett. 78 (1997), 1170–1174.CrossRefADSGoogle Scholar
  14. Yarmola, E. and Chrambach, A.: Band Width Measurement in Automated Gel Electrophoresis Apparatus: DNA Dispersion in a Discontinuous System and in a Single Buffer, Electrophoresis 16 (1995), 345–349.Google Scholar
  15. Gardiner, C.W.: Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences, Springer-Verlag, Berlin, 1997.Google Scholar
  16. Popelka, S., Kabatek, Z., Viovy, J.-L. and Gas, B.: Peak Dispersion due to Geometration Motion in Gel Electrophoresis of Macromolecules, J. Chromatogr. A 838 (1999), 45–53.CrossRefGoogle Scholar
  17. Deutsch, J. M.: Science 240 (1988), 922–924.Google Scholar
  18. Magnusdottir, S., Akerman, B. and Jonsson, M.: DNA Electrophresis in Agarose Gels: Three Regimes of DNA Migration Identified and Characterized by the Electrophoretic Orientational Behaviour of the DNA, J. Phys. Chem. 98 (1994), 2624–2633.CrossRefGoogle Scholar
  19. Slater, G.W. and Noolandi, J.: Electric Field Gradients and Band Sharpening in DNA Gel Electrophoresis, Electrophoresis 9 (1988), 643–646.CrossRefGoogle Scholar
  20. Kobayashi, T., Doi, M., Makino, Y. and Ogawa, M.: Mobility Minima in Field Inversion Gel Electrophoresis, Macromolecules 23 (1990), 4480–4481.Google Scholar
  21. Bader, J.S., Hammond, R.W., Henck, S.A., Deem, M.W., McDermott, G.A., Bustillo, J.M., Simpson, J.W., Mulhern, G.T. and Rothberg, J.M.: DNA Transport by a Micromachined Brownian Ratchet Device, Proc. Nat. Acad. Sci. of USA, 96 (1999), 13165–13169.ADSGoogle Scholar

Copyright information

© Springer Science + Business Media, Inc. 2005

Authors and Affiliations

  • P. Pasciak
    • 1
  • M. J. Krawczyk
    • 1
  • E. Gudowska-Nowak
    • 2
  • K. Kulakowski
    • 1
    Email author
  1. 1.Faculty of Physics and Applied Computer ScienceAGH University of Science and TechnologyKrakówPoland
  2. 2.Faculty of Physics, Astronomy and Applied Computer ScienceJagiellonian UniversityKrakówPoland

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