Nucleic Acids Research Advance Access originally published online on August 30, 2007
Nucleic Acids Research 2007 35(18):6063-6074; doi:10.1093/nar/gkm627
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Nucleic Acids Research, 2007, Vol. 35, No. 18 6063-6074
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Sequence-dependent DNA deformability studied using molecular dynamics simulations
1Department of Bioscience and Bioinformatics, Kyushu Institute of Technology (KIT) 680-4 Kawazu, Iizuka, Fukuoka 820-8502, 2Advanced Technology Institute, Inc. (ATI), 2-3-13-103 Tate, Shiki, Saitama 353-0006, 3Computational Biology Group, Neutron Biology Research Center, Quantum Beam Science Directorate, Japan Atomic Energy Agency 8-1 Umemidai, Kizu, Souraku, Kyoto, 619-0215, 4PRESTO, Japan Science and Technology Agency (JST) 4-1-8, Hon-cho, Kawaguchi, Saitama 332-0012 and 5Department of Materials Science, Faculty of Engineering Kyushu Institute of Technology (KIT), 1-1 Sensui, Tobata, Kita-kyushu, Fukuoka 804-8550 Japan
*To whom correspondence should be addressed. Tel: + 81-774-71-3465; Fax: + 81-774-71-3460; Email: kono.hidetoshi{at}jaea.go.jp
Received April 23, 2007. Revised July 31, 2007. Accepted July 31, 2007.
Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein–DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein–DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.
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