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The Stretched Intermediate Model of B-Z DNA Transition

Department of Physics, Faculty of Science, National University of Singapore, Singapore 117542

Correspondence: Address reprint requests to Wilber Lim, E-mail: choonsiang.lim{at}yale.edu.

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 overstretch during the transition. The overstretching of DNA is then understood from the Zhou, Zhang, and Ou-Yang 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 nonlinear 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.

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				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]