Ojha Rajendra P, Tiwari Rakesh K
Biophysics Unit, Department of Physics, DDU Gorakhpur University, Gorakhpur 273 009, India.
Nucleic Acids Res. 2003 Nov 1;31(21):6373-80. doi: 10.1093/nar/gkg796.
A theoretical model for the hydration pattern and motion of ions around the triple helical DNA with mixed sequences d(GACTGGTGAC)d(GTCACCAGTC)*d(GACTGGTGAC) in solution, during MD simulation, using the particle mesh Ewald sum method, is elaborated here. The AMBER 5.0 force field has been used during the simulation in solvent. The simulation studies support a dynamically stable atmosphere around the DNA triplex in solution over the entire length of the trajectory. The results have been compared with Hoogsteen triplexes and examined in the context of the observed behaviour of hydration in crystallographic data of duplexes. The dynamical organization of counterions and water molecules around the triplex formed by mixed sequences is described here. It has been observed that cations prefer to bind between two adjoining purines of the second and the third strands. The idea of localized complexes (mobile counterions in unspecific electronegative pockets around the DNA triplex with water molecules) may have important implications for understanding the specificity of the interactions of nucleic acids with proteins and other ligands.
本文阐述了一个理论模型，用于研究在分子动力学（MD）模拟过程中，溶液中具有混合序列d(GACTGGTGAC)d(GTCACCAGTC)*d(GACTGGTGAC)的三链螺旋DNA周围离子的水合模式和运动，采用了粒子网格埃瓦尔德求和方法。模拟过程中使用了AMBER 5.0力场。模拟研究表明，在整个轨迹长度上，溶液中的DNA三链体周围存在动态稳定的氛围。将结果与Hoogsteen三链体进行了比较，并结合双链体晶体学数据中观察到的水合行为进行了研究。本文描述了由混合序列形成的三链体周围反离子和水分子的动态组织。据观察，阳离子倾向于结合在第二条和第三条链相邻的两个嘌呤之间。局部复合物（DNA三链体周围非特异性负电口袋中带有水分子的移动反离子）的概念可能对理解核酸与蛋白质及其他配体相互作用的特异性具有重要意义。
