Shih C C, Georghiou S
Department of Physics, The University of Tennessee, Knoxville 37996-1200, USA.
J Biomol Struct Dyn. 2000 Apr;17(5):921-32. doi: 10.1080/07391102.2000.10506580.
The harmonic dynamics of normal modes of double-stranded DNA in a viscous fluid are investigated. The model DNA consists of two backbone-supported DNA strands coiling around a common helix axis with base stacking, sugar puckering, interstrand hydrogen bonding, and intrastrand sugar-base interactions assigned values based on published data. Assuming that the DNA bases are shielded from direct bombardment by the solvent, analytical solutions are obtained. The dissipation and fluctuation of the normal modes of the bases moving along the spirals display the effect of the medium indirectly through interactions with the backbone. The dynamics of the backbone are found to be overdamped with the characteristic damping times extending to the picosecond region for disturbance in position and to the sub-picosecond region for disturbance in velocity. In addition to the dynamic mode of a rigid rod, the motions of the bases are coupled to the motions of the backbone with comparable amplitudes for disturbance in position. For disturbance in velocity, however, the bases are effectively at rest, not being able to follow the motions of the backbone. The angular frequencies of the underdamped vibrational modes, identified as the ringing modes of the bases with the backbone effectively at rest, are insensitive to the viscosity and lie in the low frequency region of the Raman spectrum. These findings indicate that the backbone of DNA plays a significant role in modulating the dynamics of double-stranded DNA in an overdamping environment. This modulation of the dynamics of the motions of the bases in DNA by environmental impediments to molecular motion is briefly discussed in connection with protein- and drug- DNA interactions as well as gene regulation.
研究了粘性流体中双链DNA正常模式的谐波动力学。模型DNA由两条由骨架支撑的DNA链组成，它们围绕共同的螺旋轴盘绕，碱基堆积、糖环构象、链间氢键以及链内糖-碱基相互作用根据已发表的数据赋值。假设DNA碱基免受溶剂的直接轰击，从而获得了解析解。沿着螺旋运动的碱基正常模式的耗散和涨落通过与骨架的相互作用间接显示了介质的影响。发现骨架的动力学是过阻尼的，对于位置扰动，特征阻尼时间延伸到皮秒区域，对于速度扰动，特征阻尼时间延伸到亚皮秒区域。除了刚性杆的动态模式外，对于位置扰动，碱基的运动与骨架的运动以相当的幅度耦合。然而，对于速度扰动，碱基实际上处于静止状态，无法跟随骨架的运动。欠阻尼振动模式的角频率，被确定为骨架有效静止时碱基的振铃模式，对粘度不敏感，且位于拉曼光谱的低频区域。这些发现表明，在过阻尼环境中，DNA骨架在调节双链DNA动力学方面起着重要作用。结合蛋白质与DNA、药物与DNA的相互作用以及基因调控，简要讨论了环境对分子运动的阻碍对DNA中碱基运动动力学的这种调节作用。
