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Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study.
Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
2008 (English)In: Nucleic acids research, ISSN 1362-4962, Vol. 36, no 12, 4211-9 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2008. Vol. 36, no 12, 4211-9 p.
URN: urn:nbn:se:umu:diva-22413DOI: 10.1093/nar/gkn375PubMedID: 18579564OAI: diva2:216301
Available from: 2009-05-07 Created: 2009-05-07 Last updated: 2011-03-30

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Schleucher, Jürgen
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Department of Medical Biochemistry and Biophysics

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