Microsecond time-scale molecular dynamics simulations of the ABC oligomers

The collaborative effort of the ABC laboratories allowed the collection of microsecond scale molecular dynamics simulations on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences, using the Amber forcefield (parm99bsc0). The full MD dataset contains more than 35 million conformational snapshots of B-DNA in physiological salt conditions.

Observations include highly sequence-dependent occupancies of backbone BI/BII states, that are related to the sequence dependent multimodality of the three helical parameters shift, slide and twist.

M. Pasi, J.H. Maddocks, D. Beveridge, T.C. Bishop, D.A. Case, T. Cheatham III, P.D. Dans, B. Jayaram, F. Lankas, C. Laughton, J. Mitchell, R. Osman, M. Orozco, A. Perez, D. Petkevičiūtė, N. Spackova, J. Sponer, K. Zakrzewska, R. Lavery. µABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research 2014; doi: 10.1093/nar/gku855.