help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
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 Klenin, K. V.
Right arrow Articles by Langowski, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Klenin, K. V.
Right arrow Articles by Langowski, J.

Biophys J, January 2001, p. 69-74, Vol. 80, No. 1

Diffusion-Controlled Intrachain Reactions of Supercoiled DNA: Brownian Dynamics Simulations

Konstantin V. Klenin and Jörg Langowski

Division of Biophysics of Macromolecules, German Cancer Research Center, D-69120, Heidelberg, Germany

The Brownian Dynamics technique was used to model a diffusion-controlled intramolecular reaction of supercoiled DNA (2500 basepairs) in 0.1 M sodium chloride solution. The distance between the reactive groups along the DNA contour was 470 basepairs. The reaction radius was varied from 6 to 20 nm. The results are presented in terms of the probability distribution PF(t) of the first collision time. The general form of the function PF(t) could be correctly predicted by a simple analytical model of one-dimensional diffusion of the superhelix ends along the DNA contour. The distribution PF(t) is essentially non-exponential: within a large initial time interval, it scales as PF(t) ~ t-1/2, which is typical for one-dimensional diffusion. However, the mean time of the first collision is inversely proportional to the reaction radius, as in three dimensions. A visual inspection of the simulated conformations showed that a considerable part of the collisions is caused by the bending of the superhelix axis in the regions of the end loops, where the axis is most flexible. This fact explains why the distribution PF(t) combines the features of one- and three-dimensional diffusion. The simulations were repeated for a DNA chain with a permanent bend of 100° in the middle position between the reactive groups along the DNA contour. The permanent bend changes dramatically the form of the distribution PF(t) and reduces the mean time of the first collision by approximately one order of magnitude.

Biophys J, January 2001, p. 69-74, Vol. 80, No. 1
© 2001 by the Biophysical Society   0006-3495/01/01/69/06  $2.00


This article has been cited by other articles:


Home page
 Biophys. JHome page
Y. S. Polikanov, V. A. Bondarenko, V. Tchernaenko, Y. I. Jiang, L. C. Lutter, A. Vologodskii, and V. M. Studitsky
Probability of the Site Juxtaposition Determines the Rate of Protein-Mediated DNA Looping
Biophys. J., October 15, 2007; 93(8): 2726 - 2731.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2001 by the Biophysical Society.