Theoretical study of large conformational transitions in DNA: The B↔A conformational change in water and ethanol/water

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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 B↔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. © 2007 The Author(s).

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Noy, A., Pérez, A., Laughton, C. A., & Orozco, M. (2007). Theoretical study of large conformational transitions in DNA: The B↔A conformational change in water and ethanol/water. Nucleic Acids Research, 35(10), 3330–3338. https://doi.org/10.1093/nar/gkl1135

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