title: Target search on a dynamic DNA molecule.
abstract: We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein "jumps" between sites distant along the DNA contour but close in three-dimensional space. A strongly binding protein that searches by one-dimensional sliding and jumping alone explores the search space less redundantly when the DNA dynamics is fast on the time scale of protein jumps than in the opposite "frozen DNA" limit. We characterize the crossover between these limits using simulations and scaling theory. We also rationalize the slow exploration in the frozen limit as a subtle interplay between long jumps and long trapping times of the protein in "islands" within random DNA configurations in solution.
authors.affiliation: Arnold Sommerfeld Center for Theoretical Physics and Center for Nano Science, University of Munich, München, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schötz
authors.forename: Richard A
authors.initials: RA
authors.lastname: Neher
authors.forename: Ulrich
authors.initials: U
authors.lastname: Gerland
mesh_terms: D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004058:Diffusion; D008954:Models, Biological; D011485:Protein Binding; D013997:Time Factors
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA