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AKB: Biologische Physik

AKB 30: Poster Session I

AKB 30.12: Poster

Montag, 27. März 2006, 15:30–18:00, P1

Diffusive target-site search on a dynamic polymer — •Thomas Schötz and Ulrich Gerland — Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for Nanoscience (CeNS), LMU München

During the biophysical search process of DNA-binding proteins for their specific functional target sites, the DNA conformation is typically neither frozen nor completely equilibrated. We study the interplay of the DNA polymer dynamics and the protein search dynamics within a simple toy model on a lattice. In this model, the DNA conformation evolves according to the generalized Verdier-Stockmayer kinetic Monte Carlo scheme, while the proteins search their target sites using a combination of three-dimensional diffusion through the solvent, inter-segment transfer at places where loops in the DNA conformation are spontaneously formed, and one-dimensional sliding along the DNA. We study explicitly the breakdown of correlations in the search dynamics as a function of the relative rate for DNA and protein movement. The observed behaviour can be understood with the help of a dynamic scaling argument.