DNA中胞嘧啶核糖的灵活性：一项结合核磁共振13C自旋弛豫和分子动力学模拟的研究。
Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study.
作者信息
Duchardt Elke, Nilsson Lennart, Schleucher Jürgen
机构信息
Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden.
出版信息
Nucleic Acids Res. 2008 Jul;36(12):4211-9. doi: 10.1093/nar/gkn375. Epub 2008 Jun 25.
Abstract
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.
摘要
我们结合使用（13）C自旋弛豫核磁共振与分子动力学（MD）模拟，在皮秒到纳秒的时间尺度上对双链DNA内部的运动进行了表征。我们发现，Dickerson-Drew十二聚体（5'-CGCGAATTCGCG-3'）中所有胞嘧啶核糖部分的C-H向量都经历高振幅运动，而其他核苷酸基本上是刚性的。MD模拟表明，重新 puckering 是胞嘧啶核糖部分可能的运动模型。重新 puckering 发生的时间常数约为100皮秒。了解DNA动力学将有助于我们理解诸如胞嘧啶甲基转移酶等DNA结合蛋白的识别特异性。
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