Informace o publikaci

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

Autoři	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
Rok publikování	2014
Druh	Článek v odborném periodiku
Časopis / Zdroj	Nucleic Acids Research
Fakulta / Pracoviště MU	Středoevropský technologický institut
Citace
www	http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.full
Doi	http://dx.doi.org/10.1093/nar/gku855
Obor	Fyzikální chemie a teoretická chemie
Klíčová slova	BASE-PAIR; RECOGNITION; CONFORMATIONS; SIMULATIONS; BACKBONE; STEPS; OLIGONUCLEOTIDES; FLUCTUATIONS; FLEXIBILITY; DODECAMER
Popis	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.
Související projekty:	CEITEC - středoevropský technologický institut