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Statements

Subject Item
n2:RIV%2F00216224%3A14740%2F13%3A00067939%21RIV14-MSM-14740___
rdf:type
skos:Concept n12:Vysledek
rdfs:seeAlso
http://pubs.acs.org/toc/jctcce/9/1
dcterms:description
The Dickerson-Drew dodecamer (DD) d[CGCGAATTCGCG](2) is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-mu s-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The Dickerson-Drew dodecamer (DD) d[CGCGAATTCGCG](2) is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-mu s-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states.
dcterms:title
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer
skos:prefLabel
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer
skos:notation
RIV/00216224:14740/13:00067939!RIV14-MSM-14740___
n12:predkladatel
n14:orjk%3A14740
n4:aktivita
n9:I n9:P
n4:aktivity
I, P(ED1.1.00/02.0068), P(GAP208/11/1822)
n4:cisloPeriodika
1
n4:dodaniDat
n10:2014
n4:domaciTvurceVysledku
n13:3223779
n4:druhVysledku
n7:J
n4:duvernostUdaju
n16:S
n4:entitaPredkladatele
n15:predkladatel
n4:idSjednocenehoVysledku
108423
n4:idVysledku
RIV/00216224:14740/13:00067939
n4:jazykVysledku
n20:eng
n4:klicovaSlova
MOLECULAR-DYNAMICS SIMULATIONS; UNIQUE TETRANUCLEOTIDE SEQUENCES; NUCLEIC-ACID STRUCTURES; B-DNA DODECAMER; BASE-PAIR LEVEL; X-RAY; COUPLING-CONSTANTS; MONOVALENT CATIONS; CRYSTAL-STRUCTURES; ATOMIC-RESOLUTION
n4:klicoveSlovo
n5:CRYSTAL-STRUCTURES n5:ATOMIC-RESOLUTION n5:MONOVALENT%20CATIONS n5:UNIQUE%20TETRANUCLEOTIDE%20SEQUENCES n5:B-DNA%20DODECAMER n5:NUCLEIC-ACID%20STRUCTURES n5:COUPLING-CONSTANTS n5:X-RAY n5:MOLECULAR-DYNAMICS%20SIMULATIONS n5:BASE-PAIR%20LEVEL
n4:kodStatuVydavatele
US - Spojené státy americké
n4:kontrolniKodProRIV
[42FC9C8D3299]
n4:nazevZdroje
Journal of Chemical Theory and Computation
n4:obor
n18:BO
n4:pocetDomacichTvurcuVysledku
1
n4:pocetTvurcuVysledku
6
n4:projekt
n19:ED1.1.00%2F02.0068 n19:GAP208%2F11%2F1822
n4:rokUplatneniVysledku
n10:2013
n4:svazekPeriodika
9
n4:tvurceVysledku
Lankaš, Filip Dršata, Tomáš Šponer, Jiří Orozco, Modesto Perez, Alberto Morozov, Alexandre V
n4:wos
000313378700071
s:issn
1549-9618
s:numberOfPages
15
n11:doi
10.1021/ct300671y
n21:organizacniJednotka
14740