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Nucleic Acids Research Advance Access published online on May 3, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn173
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Bology

Spatial effects on the speed and reliability of protein–DNA search

Zeba Wunderlich1,* and Leonid A. Mirny2,3

1Biophysics Program, Harvard University, Cambridge, MA, 02138, 2Harvard–MIT Division of Health Sciences and Technology, and 3Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

*To whom correspondence should be addressed. Tel: +1 617 452 4075; Fax: +1 617 253 7498; Email: wunderl{at}fas.harvard.edu

Received December 1, 2007. Revised March 7, 2008. Accepted March 25, 2008.

Strong experimental and theoretical evidence shows that transcription factors (TFs) and other specific DNA-binding proteins find their sites using a two-mode search: alternating between three-dimensional (3D) diffusion through the cell and one-dimensional (1D) sliding along the DNA. We show that, due to the 1D component of the search process, the search time of a TF can depend on the initial position of the TF. We formalize this effect by discriminating between two types of searches: global and local. Using analytical calculations and simulations, we estimate how close a TF and binding site need to be to make a local search likely. We then use our model to interpret the wide range of experimental measurements of this parameter. We also show that local and global searches differ significantly in average search time and the variability of search time. These results lead to a number of biological implications, including suggestions of how prokaryotes achieve rapid gene regulation and the relationship between the search mechanism and noise in gene expression. Lastly, we propose a number of experiments to verify the existence and quantify the extent of spatial effects on the TF search process in prokaryotes.


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