Local and global effects of strong DNA bending induced during molecular dynamics simulations |
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| Authors: | Jeremy Curuksu Martin Zacharias Richard Lavery and Krystyna Zakrzewska |
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| Institution: | 1.Computational Biology, School of Engineering and Science, Jacobs University, Campus Ring 1, D-28759 Bremen, Germany and 2.Bioinformatique et RMN structurales, Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon, 7 passage du Vercors, 69367 Lyon, France |
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| Abstract: | DNA bending plays an important role in many biological processes, but its molecular and energetic details as a function of base sequence remain to be fully understood. Using a recently developed restraint, we have studied the controlled bending of four different B-DNA oligomers using molecular dynamics simulations. Umbrella sampling with the AMBER program and the recent parmbsc0 force field yield free energy curves for bending. Bending 15-base pair oligomers by 90° requires roughly 5 | |
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