Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
J Phys Chem B. 2010 Mar 18;114(10):3633-8. doi: 10.1021/jp907513w.
Confinement and surface specific interactions can induce structures otherwise unstable at that temperature and pressure. Here we study the groove specific water dynamics in the nucleic acid sequences, poly-AT and poly-GC, in long B-DNA duplex chains by large scale atomistic molecular dynamics simulations, accompanied by thermodynamic analysis. While water dynamics in the major groove remains insensitive to the sequence differences, exactly the opposite is true for the minor groove water. Much slower water dynamics observed in the minor grooves (especially in the AT minor) can be attributed to an enhanced tetrahedral ordering (<t(h)>) of water. The largest value of <t(h)> in the AT minor groove is related to the spine of hydration found in X-ray structure. The calculated configurational entropy (S(C)) of the water molecules is found to be correlated with the self-diffusion coefficient of water in different region via Adam-Gibbs relation D = A exp(-B/TS(C)), and also with <t(h)>.
限制和表面特定相互作用可以诱导在该温度和压力下不稳定的结构。在这里，我们通过大规模原子分子动力学模拟，伴随着热力学分析，研究了长 B-DNA 双链中核酸序列聚-AT 和聚-GC 中的沟特异水动力学。虽然主沟中的水动力学对序列差异不敏感，但小沟中的水动力学则完全相反。在小沟中观察到的水动力学慢得多（尤其是在 AT 小沟中），可以归因于水的四面体有序度（<t(h)>）增强。在 AT 小沟中，<t(h)>的最大值与 X 射线结构中发现的水合脊柱有关。通过 Adam-Gibbs 关系 D = A exp(-B/TS(C))，发现水分子的构型熵（S(C)）与不同区域中水的自扩散系数相关，也与<t(h)>相关。
