Seminars of the Focus Area Complex Systems

Prof. Dr. C. Beta, Prof. Dr. K. Dethloff, Prof. Dr. R. Engbert, Prof. Dr. M. Holschneider, Prof. Dr. W. Huisinga, Prof. Dr. Ralf Metzler, Prof. Dr. A. Pikovsky, Prof. Dr. S. Reich, Prof. Dr. M. Rosenblum, Prof. Dr. G. Rüdiger, Prof. Dr. T. Scheffer, Prof. Dr. F. Scherbaum, Prof. Dr. J. Selbig, Prof. Dr. F. Spahn


Speaker: Jaeoh Shin, Pohang University of Science and Technology, Department of Physics, South Korea, and Inst. f. Theoretische Physik, Uni Potsdam

Title: Short DNA bending and looping: Effects of bubble nucleation and tension * Colloquium on Complex and Biological Systems

Time: Fri, May 3, 2013, 10:15am

Place: bldg 28, room 0.108

Double-stranded DNA is a fairly stiff chain molecule with a persistence length of about 150 base pairs or 50 nm. In spite of this fact, highly bent DNAs are found in many biological processes such as in DNA packing into nucleolus and in loop formation. In the first part of this talk, we consider the bubble nucleation in a tightly bent DNA by using a statistical model. We find that a bending above a critical level initiates nucleation of a bubble, which can be trapped for a long time, unlike the bubble in free DNA which is either transient or unstable. The trapped bubble can easily release the high bending energy and tremendously enhance the cyclization probability, in a reasonable agreement with a recent experiment. Secondly, we consider the loop formation of DNA subject to tensions which are either static or temporally fluctuating far away from equilibrium. By using Brownian dynamics simulations combined with an analytical theory, we find that a minute tension can dramatically changes the looping time, especially for long chains. Considering a dichtomically flipping tension as a simple example of the non-equilibrium fluctuation, we find that the resonant activation phenomena, where the looping time has a minimum at an optimal flipping time. We discuss our results in connection with recent experiments.

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Udo Schwarz, Zentrum für Dynamik komplexer Systeme,
Universität Potsdam, Campus Golm Karl-Liebknecht-Str. 24, 14476 Potsdam, building 28, room 2.107
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