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Statements

Subject Item
n2:RIV%2F00216224%3A14740%2F14%3A00077975%21RIV15-MSM-14740___
rdf:type
skos:Concept n16:Vysledek
rdfs:seeAlso
http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.full
dcterms: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.
dcterms: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
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
skos:notation
RIV/00216224:14740/14:00077975!RIV15-MSM-14740___
n3:aktivita
n6:I n6:P
n3:aktivity
I, P(ED1.1.00/02.0068), P(GA14-21893S), P(GAP208/11/1822)
n3:cisloPeriodika
19
n3:dodaniDat
n15:2015
n3:domaciTvurceVysledku
n19:3223779
n3:druhVysledku
n5:J
n3:duvernostUdaju
n20:S
n3:entitaPredkladatele
n18:predkladatel
n3:idSjednocenehoVysledku
30911
n3:idVysledku
RIV/00216224:14740/14:00077975
n3:jazykVysledku
n11:eng
n3:klicovaSlova
BASE-PAIR; RECOGNITION; CONFORMATIONS; SIMULATIONS; BACKBONE; STEPS; OLIGONUCLEOTIDES; FLUCTUATIONS; FLEXIBILITY; DODECAMER
n3:klicoveSlovo
n4:BACKBONE n4:BASE-PAIR n4:OLIGONUCLEOTIDES n4:STEPS n4:FLEXIBILITY n4:DODECAMER n4:SIMULATIONS n4:CONFORMATIONS n4:RECOGNITION n4:FLUCTUATIONS
n3:kodStatuVydavatele
GB - Spojené království Velké Británie a Severního Irska
n3:kontrolniKodProRIV
[61FEF51C6424]
n3:nazevZdroje
Nucleic Acids Research
n3:obor
n13:CF
n3:pocetDomacichTvurcuVysledku
1
n3:pocetTvurcuVysledku
19
n3:projekt
n7:GAP208%2F11%2F1822 n7:GA14-21893S n7:ED1.1.00%2F02.0068
n3:rokUplatneniVysledku
n15:2014
n3:svazekPeriodika
42
n3:tvurceVysledku
Mitchell, Jonathan Pasi, Marco Maddocks, John H. Case, David A. Beveridge, David Dans, Pablo D. Petkevičiüté, Daiva Cheatham III., Thomas Špačková, Naďa Laughton, Charles Lavery, Richard Orozco, Modesto Osman, Roman Lankaš, Filip Pérez, Alberto Bishop, Thomas C. Šponer, Jiří Jayaram, B. Zakrzewska, Krystyna
n3:wos
000347689500044
s:issn
0305-1048
s:numberOfPages
12
n10:doi
10.1093/nar/gku855
n17:organizacniJednotka
14740