Towards a molecular dynamics consensus view of B-DNA flexibility.

TitleTowards a molecular dynamics consensus view of B-DNA flexibility.
Publication TypeJournal Article
Year of Publication2008
AuthorsPérez, Alberto, Lankaš Filip, F Luque Javier, and Orozco Modesto
JournalNucleic Acids Res
Date Published2008 Apr
KeywordsBase Sequence, Computer Simulation, DNA, Models, Molecular, Nucleic Acid Conformation, Software

We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility.