Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water |
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Authors: | Noy Agnes Pérez Alberto Laughton Charles A Orozco Modesto |
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Affiliation: | Agnes Noy, Alberto Pérez, Charles A. Laughton, and Modesto Orozco |
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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. |
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