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.
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Conference Article|
March 21 2013
Effect of DNA conformation on facilitated diffusion
Chris A. Brackley;
Chris A. Brackley
1
1SUPA (Scottish Universities Physics Alliance), School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, U.K.
1To whom correspondence should be addressed (emailcbrackle@ph.ed.ac.uk).
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Mike E. Cates;
Mike E. Cates
1SUPA (Scottish Universities Physics Alliance), School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, U.K.
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Davide Marenduzzo
Davide Marenduzzo
1SUPA (Scottish Universities Physics Alliance), School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, U.K.
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Publisher: Portland Press Ltd
Received:
September 10 2012
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© The Authors Journal compilation © 2013 Biochemical Society
2013
Biochem Soc Trans (2013) 41 (2): 582–588.
Article history
Received:
September 10 2012
Citation
Chris A. Brackley, Mike E. Cates, Davide Marenduzzo; Effect of DNA conformation on facilitated diffusion. Biochem Soc Trans 1 April 2013; 41 (2): 582–588. doi: https://doi.org/10.1042/BST20120234
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