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.
Author: | Elke Duchardt-FernerORCiDGND, Lennart Nilsson, Jürgen Schleucher |
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URN: | urn:nbn:de:hebis:30-60285 |
DOI: | https://doi.org/10.1093/nar/gkn375 |
ISSN: | 1362-4962 |
ISSN: | 0305-1048 |
Pubmed Id: | https://pubmed.ncbi.nlm.nih.gov/18579564 |
Parent Title (English): | Nucleic acids research |
Publisher: | Oxford Univ. Press |
Place of publication: | Oxford |
Document Type: | Article |
Language: | English |
Date of Publication (online): | 2008/11/12 |
Date of first Publication: | 2008/06/25 |
Publishing Institution: | Universitätsbibliothek Johann Christian Senckenberg |
Release Date: | 2008/11/12 |
Volume: | 36 |
Issue: | 12 |
Page Number: | 9 |
First Page: | 4211 |
Last Page: | 4219 |
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. |
Source: | Nucleic Acids Research 2008 July; 36(12): 4211–4219 ; Published online 2008 July. doi:10.1093/nar/gkn375 |
HeBIS-PPN: | 208745114 |
Institutes: | Biowissenschaften / Biowissenschaften |
Dewey Decimal Classification: | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
Sammlungen: | Sammlung Biologie / Sondersammelgebiets-Volltexte |
Licence (German): | ![]() |