help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
Biophys. J. BioFAST: First Published December 30, 2004. doi:10.1529/biophysj.104.052027
© 2004 by the Biophysical Society.

A more recent version of this article appeared on March 1, 2005.
This Article
Right arrow Full Text (Rapid PDF)
Right arrow All Versions of this Article:
biophysj.104.052027v1
88/3/1593    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 Lim, W.
Right arrow Articles by Feng, Y. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lim, W.
Right arrow Articles by Feng, Y. P.

BIOPHYSICAL THEORY AND MODELING

The Stretched Intermediate Model of B-Z DNA Transition

Wilber Lim 1* and Yuan Ping Feng 2

1 Yale University
2 National University of Singapore

* To whom correspondence should be addressed. E-mail: choonsiang.lim{at}yale.edu.

Submitted on August 30, 2004
Revised on October 22, 2004
Accepted on 9 December 2004


  Abstract
There have been numerous attempts to describe the mechanism of B-Z transition. Our simulations based on the stochastic difference equation with length algorithm show that a short DNA oligomer will tend to unwind and over-stretch during the transition. The over-stretching of DNA is then understood from the ZZO model. Unlike the Harvey model, the stretched intermediate model does not pose any steric dilemma; we are able to show that the chain sense reversal progresses spontaneously using the stretched intermediate model. A non-linear DNA model is used to describe the origins and mechanism of base rotation in the stretched intermediate state of DNA. We also propose an experiment that can verify the existence of a stretched intermediate state during B-Z transition, thus opening up fresh grounds for experimentation in this field.

Key Words: ZZO model, conformational transition, nonlinear DNA model




This article has been cited by other articles:


Home page
 Biophys. JHome page
M. A. Kastenholz, T. U. Schwartz, and P. H. Hunenberger
The Transition between the B and Z Conformations of DNA Investigated by Targeted Molecular Dynamics Simulations with Explicit Solvation
Biophys. J., October 15, 2006; 91(8): 2976 - 2990.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
Copyright © 2004 by the Biophysical Society.