help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Originally published as Biophys J. BioFAST on February 3, 2006.
doi:10.1529/biophysj.105.078162
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow All Versions of this Article:
biophysj.105.078162v1
90/8/2731    most recent
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Hu, T.
Right arrow Articles by Shklovskii, B. I.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hu, T.
Right arrow Articles by Shklovskii, B. I.
Biophysical Journal 90:2731-2744 (2006)
© 2006 The Biophysical Society

How Proteins Search for Their Specific Sites on DNA: The Role of DNA Conformation

Tao Hu *, A. Yu. Grosberg * and B. I. Shklovskii * {dagger}

* Department of Physics, and {dagger} William I. Fine Theoretical Physics Institute, University of Minnesota, Minneapolis, Minnesota

Correspondence: Address reprint requests to A. Yu. Grosberg, E-mail: grosberg{at}physics.umn.edu.

It is known since the early days of molecular biology that proteins locate their specific targets on DNA up to two orders-of-magnitude faster than the Smoluchowski three-dimensional diffusion rate. An accepted explanation of this fact is that proteins are nonspecifically adsorbed on DNA, and sliding along DNA provides for the faster one-dimensional search. Surprisingly, the role of DNA conformation was never considered in this context. In this article, we explicitly address the relative role of three-dimensional diffusion and one-dimensional sliding along coiled or globular DNA and the possibility of correlated readsorption of desorbed proteins. We have identified a wealth of new different scaling regimes. We also found the maximal possible acceleration of the reaction due to sliding. We found that the maximum on the rate-versus-ionic strength curve is asymmetric, and that sliding can lead not only to acceleration, but also in some regimes to dramatic deceleration of the reaction.




This article has been cited by other articles:


Home page
 Biophys. JHome page
L. Hu, A. Y. Grosberg, and R. Bruinsma
Are DNA Transcription Factor Proteins Maxwellian Demons?
Biophys. J., August 1, 2008; 95(3): 1151 - 1156.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Bonnet, A. Biebricher, P.-L. Porte, C. Loverdo, O. Benichou, R. Voituriez, C. Escude, W. Wende, A. Pingoud, and P. Desbiolles
Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA
Nucleic Acids Res., July 1, 2008; 36(12): 4118 - 4127.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. Wunderlich and L. A. Mirny
Spatial effects on the speed and reliability of protein-DNA search
Nucleic Acids Res., June 1, 2008; 36(11): 3570 - 3578.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
C. Lou, X. Yang, X. Liu, B. He, and Q. Ouyang
A Quantitative Study of {lambda}-Phage SWITCH and Its Components
Biophys. J., April 15, 2007; 92(8): 2685 - 2693.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. S. van Zon, M. J. Morelli, S. Tanase-Nicola, and P. R. ten Wolde
Diffusion of Transcription Factors Can Drastically Enhance the Noise in Gene Expression
Biophys. J., December 15, 2006; 91(12): 4350 - 4367.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2006 by the Biophysical Society.