Pastor Nina
Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México.
Biophys J. 2005 May;88(5):3262-75. doi: 10.1529/biophysj.104.058339. Epub 2005 Mar 4.
DNA geometry depends on relative humidity. Using the CHARMM22 force field to push B-DNA to A-DNA, a molecular dynamics simulation of a mixed-sequence 24-basepair DNA double-stranded oligomer, starting from B-DNA, was carried out to explore both the mechanism of the transition and the evolution of hydration patterns on the surface of DNA. Over the 11-ns trajectory, the transition recapitulates the slide-first, roll-later mechanism, is opposed by DNA electrostatics, and is favored by an increasing amount of condensed sodium ions. Hydration was characterized by counting the hydrogen bonds between water and DNA, and by the number of water bridges linking two DNA atoms. The number of hydrogen bonds between water and DNA remains constant during the transition, but there is a 40% increase in the number of water bridges, in agreement with the principle of economy of hydration. Water bridges emerge as delicate sensors of both structure and dynamics of DNA. Both local flexibility and the frustration of the water network on the surface of DNA probably account for the low populations and short residence times of the bridges, and for the lubricant role of water in ligand-DNA interactions.
DNA的几何结构取决于相对湿度。利用CHARMM22力场将B型DNA转变为A型DNA，对一个混合序列的24碱基对DNA双链寡聚物从B型DNA开始进行了分子动力学模拟，以探究转变机制以及DNA表面水化模式的演变。在11纳秒的轨迹中，这种转变重现了先滑动、后滚动的机制，受到DNA静电作用的阻碍，而浓缩钠离子数量的增加则有利于这种转变。通过计算水与DNA之间的氢键以及连接两个DNA原子的水桥数量来表征水化情况。在转变过程中，水与DNA之间的氢键数量保持不变，但水桥数量增加了40%，这与水化经济性原则相符。水桥成为DNA结构和动力学的灵敏传感器。DNA表面局部的灵活性以及水网络的受挫可能是导致水桥数量少、停留时间短的原因，也是水在配体与DNA相互作用中起到润滑作用的原因。
