Briki F, Genest D
Centre de Biophysique Moléculaire, CNRS, Orleans, France.
J Biomol Struct Dyn. 1993 Aug;11(1):43-56. doi: 10.1080/07391102.1993.10508708.
We report an analysis of a 200 ps Molecular Dynamics simulation of the double stranded oligonucleotide d(CTGATCAG) in the presence of 1534 water molecules and 14 Na+ ions. We focus on the opening process of Thymine 5, by analyzing in detail the glycosidic bond rotational motion about the helix axis. The present analysis is mainly based on autocorrelation functions and on mean square displacements. We show that the opening of the base has a Brownian character and we find a rotational diffusion coefficient of 4.7 rad2s-1. Furthermore we estimate the DNA torsional constant to be about 0.5 10(-18) J.rad-2 and the RMS of the angular displacement to be 8.3 degrees. All these values are in fair agreement with those determined experimentally by fluorescence polarization of DNA-Ethidium bromide complexes. This shows that the rotational motions of the bases detected in the range 10(-9)-10(-7) s. by fluorescence techniques are the same as those analyzed in the present study (10(-12)-2 10(-10) s).
我们报告了在存在1534个水分子和14个钠离子的情况下，对双链寡核苷酸d(CTGATCAG)进行的200皮秒分子动力学模拟分析。我们通过详细分析围绕螺旋轴的糖苷键旋转运动，重点研究胸腺嘧啶5的打开过程。目前的分析主要基于自相关函数和均方位移。我们表明碱基的打开具有布朗运动特征，并且发现旋转扩散系数为4.7弧度²秒⁻¹。此外，我们估计DNA扭转常数约为0.5×10⁻¹⁸焦耳·弧度⁻²，角位移的均方根为8.3度。所有这些值与通过DNA-溴化乙锭复合物的荧光偏振实验测定的值相当一致。这表明通过荧光技术在10⁻⁹ - 10⁻⁷秒范围内检测到的碱基旋转运动与本研究中分析的运动相同(10⁻¹² - 2×10⁻¹⁰秒)。
