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.
Duchardt
Elke
E
Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden. duchardt@bio.uni-frankfurt.de
Nilsson
Lennart
L
Schleucher
Jürgen
J
D003198:Computer Simulation; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D009038:Motion; D019906:Nuclear Magnetic Resonance, Biomolecular; D012266:Ribose / Q000737:chemistry*
D012266:Ribose; D003596:Cytosine; D004247:DNA