Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F13%3A00067939" target="_blank" >RIV/00216224:14740/13:00067939 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/13:00391758 RIV/61388963:_____/13:00391758
Result on the web
<a href="http://pubs.acs.org/toc/jctcce/9/1" target="_blank" >http://pubs.acs.org/toc/jctcce/9/1</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/ct300671y" target="_blank" >10.1021/ct300671y</a>

Result language
angličtina
Original language name
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer
Original language 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 basedon 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.
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
BO - Biophysics
OECD FORD branch
—

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2013
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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