Publication details

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

Authors	PASI Marco MADDOCKS John H. BEVERIDGE David BISHOP Thomas C. CASE David A. CHEATHAM III. Thomas DANS Pablo D. JAYARAM B. LANKAŠ Filip LAUGHTON Charles MITCHELL Jonathan OSMAN Roman OROZCO Modesto PÉREZ Alberto PETKEVIČIÜTÉ Daiva ŠPAČKOVÁ Naďa ŠPONER Jiří ZAKRZEWSKA Krystyna LAVERY Richard
Year of publication	2014
Type	Article in Periodical
Magazine / Source	Nucleic Acids Research
MU Faculty or unit	Central European Institute of Technology
Citation
Web	http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.full
Doi	http://dx.doi.org/10.1093/nar/gku855
Field	Physical chemistry and theoretical chemistry
Keywords	BASE-PAIR; RECOGNITION; CONFORMATIONS; SIMULATIONS; BACKBONE; STEPS; OLIGONUCLEOTIDES; FLUCTUATIONS; FLEXIBILITY; DODECAMER
Description	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.
Related projects:	CEITEC - Central European Institute of Technology