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

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Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.full
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. 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. (en)
Title	muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA (en)
skos:prefLabel	muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA (en)
skos:notation	RIV/00216224:14740/14:00077975!RIV15-MSM-14740___
http://linked.open...avai/riv/aktivita	I P
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(GA14-21893S), P(GAP208/11/1822)
http://linked.open...iv/cisloPeriodika	19
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Šponer, Jiří
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	30911
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/14:00077975
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	BASE-PAIR; RECOGNITION; CONFORMATIONS; SIMULATIONS; BACKBONE; STEPS; OLIGONUCLEOTIDES; FLUCTUATIONS; FLEXIBILITY; DODECAMER (en)
http://linked.open.../riv/klicoveSlovo	BACKBONE BASE-PAIR DODECAMER STEPS OLIGONUCLEOTIDES FLEXIBILITY RECOGNITION SIMULATIONS FLUCTUATIONS CONFORMATIONS
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[61FEF51C6424]
http://linked.open...i/riv/nazevZdroje	Nucleic Acids Research
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	19 (xsd:int)
http://linked.open...vavai/riv/projekt	Central european institute of technology Structure and dynamics of DNA. Advanced computational studies. Nanomechanics of RNA and DNA structural motifs
http://linked.open...UplatneniVysledku	2014
http://linked.open...v/svazekPeriodika	42
http://linked.open...iv/tvurceVysledku	Špačková, Naďa Šponer, Jiří Lankaš, Filip Orozco, Modesto Jayaram, B. Beveridge, David Bishop, Thomas C. Case, David A. Cheatham III., Thomas Dans, Pablo D. Laughton, Charles Lavery, Richard Maddocks, John H. Mitchell, Jonathan Osman, Roman Pasi, Marco Petkevičiüté, Daiva Pérez, Alberto Zakrzewska, Krystyna
http://linked.open...ain/vavai/riv/wos	000347689500044
issn	0305-1048
number of pages	12 (xsd:int)
http://bibframe.org/vocab/doi	10.1093/nar/gku855
http://localhost/t...ganizacniJednotka	14740

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