Ontology highlight
ABSTRACT:
SUBMITTER: Noy A
PROVIDER: S-EPMC1904281 | biostudies-literature | 2007
REPOSITORIES: biostudies-literature
Nucleic acids research 20070425 10
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 processe ...[more]