title: Effect of DNA conformation on facilitated diffusion.
abstract: Within a living cell, site-specific DNA-binding proteins need to search the whole genome to find a target of ~10-20 bp. That they find the target, and do so quickly, is vital for the correct functioning of the DNA, and of the cell as a whole. The current understanding is that this search is performed via facilitated diffusion, i.e. by combining three-dimensional bulk diffusion within the cytoplasm or nucleoplasm, with one-dimensional diffusion along the DNA backbone, to which the protein binds non-specifically. After reviewing the standard theory of facilitated diffusion, we discuss in the present article the still rather rare direct computer simulations of this process, focusing on the three-dimensional part of the search, and the effect of DNA looping and the general DNA conformation on its efficiency. We close by highlighting some open questions in this field.
authors.affiliation: SUPA (Scottish Universities Physics Alliance), School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, U.K. cbrackle@ph.ed.ac.uk
authors.forename: Chris A
authors.initials: CA
authors.lastname: Brackley
authors.forename: Mike E
authors.initials: ME
authors.lastname: Cates
authors.forename: Davide
authors.initials: D
authors.lastname: Marenduzzo
mesh_terms: D000818:Animals; D003198:Computer Simulation; D055459:Facilitated Diffusion; D006801:Humans; D009690:Nucleic Acid Conformation; D009716:Numerical Analysis, Computer-Assisted; D011506:Proteins / Q000378:metabolism
chemical_list: D011506:Proteins