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Nucleic Acids Research Advance Access originally published online on April 25, 2007
Nucleic Acids Research 2007 35(10):3330-3338; doi:10.1093/nar/gkl1135
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Nucleic Acids Research, 2007, Vol. 35, No. 10 3330-3338
© 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

Theoretical study of large conformational transitions in DNA: the B{leftrightarrow}A conformational change in water and ethanol/water

Agnes Noy1, Alberto Pérez1, Charles A. Laughton2 and Modesto Orozco1,3,4,*

1Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica & Instituto Nacional de Bioinformática, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, 2School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK, 3Departament de Bioquímica i Biologia Molecular. Facultat de Biología. Universitat de Barcelona. Avgda Diagonal 645, Barcelona 08028, Spain and 4Computational Biology Program, Barcelona Supercomputer Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain

*To whom Correspondence should be addressed: Tel: +34 934037155; Fax: +34 934037157; Email: modesto{at}mmb.pcb.ub.es

We explore here the possibility of determining theoretically the free energy change associated with large conformational transitions in DNA, like the solvent-induced B{Leftrightarrow}A conformational change. We find that a combination of targeted molecular dynamics (tMD) and the weighted histogram analysis method (WHAM) can be used to trace this transition in both water and ethanol/water mixture. The pathway of the transition in the A->B direction mirrors the B->A pathway, and is dominated by two processes that occur somewhat independently: local changes in sugar puckering and global rearrangements (particularly twist and roll) in the structure. The B->A transition is found to be a quasi-harmonic process, which follows closely the first spontaneous deformation mode of B-DNA, showing that a physiologically-relevant deformation is in coded in the flexibility pattern of DNA.


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