Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field.

ABSTRACT: In addition to the well-characterized B-form of DNA, duplex DNA can adopt various conformations, such as A or Z-DNA. Though less common, these structures can be induced biologically through protein or ligand interactions or experimentally with niche environmental conditions, such as high salt concentrations or in mixed water-ethanol. Reproducing these alternate structures through molecular dynamics simulations in recent years has been quite challenging with the currently available force fields, simulation techniques, and time scales. In this study, the Drude polarizable force field is tested for its ability to facilitate transitions between A-DNA and B-DNA or maintain A-DNA. Though transitions away from B-DNA were observed in high concentrations of ethanol, the resulting structures had hyb

SUBMITTER: Winkler L 

PROVIDER: S-EPMC10720382 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature