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Nucleic Acids Research Advance Access originally published online on June 25, 2008
Nucleic Acids Research 2008 36(12):4211-4219; doi:10.1093/nar/gkn375
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Nucleic Acids Research, 2008, Vol. 36, No. 12 4211-4219
© 2008 The Author(s)
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.

RNA

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

Elke Duchardt1,*, Lennart Nilsson2 and Jürgen Schleucher1

1Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå and 2Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57 Huddinge, Sweden

*To whom correspondence should be addressed. Tel: +49 69 7982 9271; Email: duchardt{at}bio.uni-frankfurt.de

Correspondence may also be addressed to Jürgen Schleucher. Tel: +46 90 786 5388; Fax: +46 90 786 9795; Email: jurgen.schleucher{at}chem.umu.se

Received March 22, 2008. Revised May 25, 2008. Accepted May 28, 2008.

Using 13C 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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