ZB 10 - Soft Condensed Matter (R. Holyst)

Method for the analysis of contribution of sliding and hopping to a diffusion of DNA-binding protein: Application to in vivo data

Author(s): Tabaka, Marcin and Burdzy, Krzysztof and Holyst, Robert
Title: Method for the analysis of contribution of sliding and hopping to a diffusion of DNA-binding protein: Application to in vivo data
Abstract: DNA-binding protein searches for its target, a specific site on DNA, by of diffusion. The search process consists of many recurrent steps one-dimensional diffusion (sliding) along the DNA chain and diffusion (hopping) after dissociation of a protein the DNA chain. Here we propose a computational method that allows the contribution of sliding and hopping to the search process vivo from the measurements of the kinetics of the target search by lac repressor in Escherichia coli [}P. Hammar et al., Science 336, (2012)]. The method combines lattice Monte Carlo simulations with Brownian excursion theory and includes explicitly steric constraints hopping due to the helical structure of DNA. The simulation results all experimental data reveal that the in vivo target search is by sliding. The short-range hopping to the same base pair one-dimensional sliding while long-range hopping does not significantly to the kinetics of the search of the target in vivo.
Journal: PHYSICAL REVIEW E
Volume: 92
ID: ISI:000360288500008
Year: 2015
DOI: 10.1103/PhysRevE.92.022721