Nucleic Acids Research Advance Access originally published online on February 24, 2008
Nucleic Acids Research 2008 36(7):2379-2394; doi:10.1093/nar/gkn082
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Nucleic Acids Research, 2008, Vol. 36, No. 7 2379-2394
© 2008 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 |
Towards a molecular dynamics consensus view of B-DNA flexibility
1Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, 2Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona. Barcelona 08034, 3Departament de Fisicoquímica, Facultat de Farmàcia, Avgda Diagonal sn, Barcelona 08028, Spain, 4Laboratory for Computation and Visualization in Mathematics and Mechanics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland, 5Centre for Complex Molecular Systems and Biomolecues, Institute of Organic Chemistry and Biochemistry Flemingovo nam. 2, 166 10 Praha 6, Czech Republic, 6National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5 and 7Departament de Bioquímica, Facultat de Biología, Avgda Diagonal 647, Barcelona 08028, Spain
*To whom correspondence should be addressed. Tel: +34 93 403 71 55; Fax: +34 93 403 71 57; Email: modesto{at}mmb.pcb.ub.es
Received December 3, 2007. Revised February 7, 2008. Accepted February 8, 2008.
We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility.
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