Cytosine ribose flexibility in DNA : a combined NMR 13C spin relaxation and molecular dynamics simulation study

Using (13)C spin relaxation NMR in combination with molecular dynamic (MD) simulations, we characterized internal motions within double-stranded DNA on the pico- to nano-second time scale. We found that the C-H vectors in all cytosine ribose moieties within the Dickerson-Drew dodecamer (5´-CGCGAATTCGCG-3´) are subject to high amplitude motions, while the other nucleotides are essentially rigid. MD simulations showed that repuckering is a likely motional model for the cytosine ribose moiety. Repuckering occurs with a time constant of around 100 ps. Knowledge of DNA dynamics will contribute to our understanding of the recognition specificity of DNA-binding proteins such as cytosine methyltransferase.

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Metadaten
Author:Elke Duchardt, Lennart Nilsson, Jürgen Schleucher
URN:urn:nbn:de:hebis:30-60285
Document Type:Article
Language:English
Date of Publication (online):12.11.2008
Year of first Publication:2008
Publishing Institution:Univ.-Bibliothek Frankfurt am Main
Source:Nucleic Acids Research 2008 July; 36(12): 4211–4219 ; Published online 2008 July. doi:10.1093/nar/gkn375
HeBIS PPN:208745114
Institutes:Biowissenschaften
Dewey Decimal Classification:570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Sondersammelgebiets-Volltexte Biologie
Note:
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Licence (German):License Logo Veröffentlichungsvertrag für Publikationen ohne Print on Demand

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