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Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides

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Item Type:Article
Title:Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides
Creators Name:Beveridge, D.L. and Barreiro, G. and Byun, S.K. and Case, D.A. and Cheatham, T.E. and Dixit, S.B. and Giudice, E. and Lankas, F. and Lavery, R. and Maddocks, J.H. and Osman, R. and Seibert, E. and Sklenar, H. and Stoll, G. and Thayer, K.M. and Varnai, P. and Young, M.A.
Abstract:We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base sequences. This initiative was undertaken by an international collaborative effort involving nine research groups, the "Ascona B-DNA Consortium" (ABC). Calculations were carried out on the 136 cases imbedded in 39 DNA oligomers with repeating tetranucleotide sequences, capped on both ends by GC pairs and each having a total length of 15 nucleotide pairs. All MD simulations were carried out using a well-defined protocol, the AMBER suite of programs, and the parm94 force field. Phase I of the ABC project involves a total of approximately 0.6 mus of simulation for systems containing approximately 24,000 atoms. The resulting trajectories involve 600,000 coordinate sets and represent approximately 400 gigabytes of data. In this article, the research design, details of the simulation protocol, informatics issues, and the organization of the results into a web-accessible database are described. Preliminary results from 15-ns MD trajectories are presented for the d(CpG) step in its 10 unique sequence contexts, and issues of stability and convergence, the extent of quasiergodic problems, and the possibility of long-lived conformational substates are discussed.
Keywords:Base Sequence, Computer Simulation, DNA, Kinetics, Molecular Sequence Data, Motion, Nucleic Acid Conformation, Oligodeoxyribonucleotides, Structure-Activity Relationship
Source:Biophysical Journal
ISSN:0006-3495
Publisher:Biophysical Society (U.S.A.)
Volume:87
Number:6
Page Range:3799-3813
Date:December 2004
Official Publication:https://doi.org/10.1529/biophysj.104.045252
PubMed:View item in PubMed

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