File(s) not publicly available
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(C(p)G) steps.
journal contribution
posted on 2023-06-08, 05:35 authored by David L Beveridge, Gabriela Barreiro, K Suzie Byun, David A Case, Thomas E Cheatham, Surjit B Dixit, Emmanuel Giudice, Filip Lankas, Richard Lavery, John H Maddocks, Roman Osman, Eleanore Seibert, Heinz Sklenar, Gautier Stoll, Kelly M Thayer, Peter Varnai, Matthew A YoungWe 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 similar to0.6 mus of simulation for systems containing similar to24,000 atoms. The resulting trajectories involve 600,000 coordinate sets and represent similar to400 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.
History
Publication status
- Published
Journal
Biophysical JournalISSN
0006-3495Publisher
Cell PressExternal DOI
Issue
6Volume
87Page range
3799-3813Department affiliated with
- Chemistry Publications
Full text available
- No
Peer reviewed?
- Yes
Legacy Posted Date
2012-02-06Usage metrics
Categories
No categories selectedKeywords
Licence
Exports
RefWorks
BibTeX
Ref. manager
Endnote
DataCite
NLM
DC