Chris A Brackley, Mike E Cates, Davide Marenduzzo
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
Biochemical Society transactions 2013 AprWithin 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.
Chris A Brackley, Mike E Cates, Davide Marenduzzo. Effect of DNA conformation on facilitated diffusion. Biochemical Society transactions. 2013 Apr;41(2):582-8
PMID: 23514158
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