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

@inproceedings{Noy2007TheoreticalSO,
  title={Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water},
  author={Agnes Noy and Alberto P{\'e}rez and Charles A. Laughton and Modesto Orozco},
  booktitle={Nucleic acids research},
  year={2007}
}
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… CONTINUE READING