Theoretical study of large conformational transitions in DNA: the B<–>A conformational change in water and ethanol/water.
Title | Theoretical study of large conformational transitions in DNA: the B<–>A conformational change in water and ethanol/water. |
Publication Type | Journal Article |
Year of Publication | 2007 |
Authors | Noy, Agnes, Pérez Alberto, Laughton Charles A., and Orozco Modesto |
Journal | Nucleic Acids Res |
Volume | 35 |
Pagination | 3330-8 |
Date Published | 2007 |
ISSN | 1362-4962 |
Keywords | A-Form, Computer Simulation, DNA, Ethanol, Models, Molecular, Nucleic Acid Conformation, Solvents, Water |
Abstract | We explore here the possibility of determining theoretically the free energy change associated with large conformational transitions in DNA, like the solvent-induced BA 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. |
DOI | 10.1093/nar/gkl1135 |