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|
|Keywords||A-Form, Computer Simulation, DNA, Ethanol, Models, Molecular, Nucleic Acid Conformation, Solvents, Water|
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.