Journal Article

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

Marco Pasi, John H. Maddocks, David Beveridge, Thomas C. Bishop, David A. Case, Thomas Cheatham, Pablo D. Dans, B. Jayaram, Filip Lankas, Charles Laughton, Jonathan Mitchell, Roman Osman, Modesto Orozco, Alberto Pérez, Daiva Petkevičiūtė, Nada Spackova, Jiri Sponer, Krystyna Zakrzewska and Richard Lavery

in Nucleic Acids Research

Volume 42, issue 19, pages 12272-12283
Published in print October 2014 | ISSN: 0305-1048
Published online September 2014 | e-ISSN: 1362-4962 | DOI: https://dx.doi.org/10.1093/nar/gku855

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We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters.

Journal Article.  9313 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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