Searching DNA by Brownian Motion of Transcription Factors

POSTER

Abstract

Transcription factor proteins are able to locate their DNA operator binding site by slide-skip motion along DNA without getting trapped by the large binding energy fluctuations associated with partial recognition. Mirny and Slutsky proposed that this can be avoided by assuming that partial recognition involves increased strain energy of the protein. We present an analytical model for such a search in the form of a 2D random walk with DNA arc-length and an internal configurational parameter as coordinates. This leads to a relation between the nature of the DNA randomness and the optimal choice for the internal energy spectrum.

Authors

  • Robijn Bruinsma

    • UCLA
    • Department of Physics and Astronomy, University of California, Los Angeles
    • Department of Physics and Astronomy, UCLA

  • Alexander Grosberg

    • New York University
    • Department of Physics, New York University, New York, NY
    • New York University, Center for Soft Matter Research and Department of Physics
    • Center for Soft Matter Research, New York University
    • Theoretical Biophysics, New York University
    • Professor