Ontology highlight
ABSTRACT:
SUBMITTER: Galindo-Murillo R
PROVIDER: S-EPMC9466961 | biostudies-literature | 2022 Jul
REPOSITORIES: biostudies-literature
Galindo-Murillo Rodrigo R Cheatham Thomas E TE
The journal of physical chemistry letters 20220701 27
Duplex DNA is modeled as canonical B-DNA displaying the characteristic Watson-Crick base pairs. A less common and short-lived pairing of the nucleobases is the Hoogsteen (HG) conformation. The low population of the HG base pairs (<1%) necessitates extended sampling times in order to analyze through unbiased molecular dynamics (MD) simulations. We have discovered that with extended sampling times using multiple independent copies of an 18-mer sequence, the MD trajectories reproduce the expected a ...[more]