About: Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

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About: Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/toc/jctcce/9/1
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. (en)
Title	Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer (en)
skos:prefLabel	Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer (en)
skos:notation	RIV/00216224:14740/13:00067939!RIV14-MSM-14740___
http://linked.open...avai/riv/aktivita	I P
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(GAP208/11/1822)
http://linked.open...iv/cisloPeriodika	1
http://linked.open...vai/riv/dodaniDat	2014
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	108423
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/13:00067939
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/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 (en)
http://linked.open.../riv/klicoveSlovo	ATOMIC-RESOLUTION NUCLEIC-ACID STRUCTURES X-RAY B-DNA DODECAMER BASE-PAIR LEVEL COUPLING-CONSTANTS MONOVALENT CATIONS UNIQUE TETRANUCLEOTIDE SEQUENCES CRYSTAL-STRUCTURES MOLECULAR-DYNAMICS SIMULATIONS
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[42FC9C8D3299]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	Central european institute of technology Structure and dynamics of DNA. Advanced computational studies.
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	9
http://linked.open...iv/tvurceVysledku	Šponer, Jiří Lankaš, Filip Dršata, Tomáš Orozco, Modesto Morozov, Alexandre V Perez, Alberto
http://linked.open...ain/vavai/riv/wos	000313378700071
issn	1549-9618
number of pages	15 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ct300671y
http://localhost/t...ganizacniJednotka	14740

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