Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG).d(GCGCTTAAGCGC): Monte Carlo computer simulation.
Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG).d(GCGCTTAAGCGC): Monte Carlo computer simulation.
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d(CGCGAATTCGCG).d(GCGCTTAAGCGC) 小沟中“水合脊柱”的理论考虑：蒙特卡罗计算机模拟。
DOI：
10.1073/pnas.85.6.1836
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发表时间：
1988
影响因子：
11.1
通讯作者：
Beveridge,DL
中科院分区：
文献类型：
--
作者：
Subramanian,PS;Ravishanker,G;Beveridge,DL
本文用液态蒙特卡罗计算机模拟方法，对正则B型寡核苷酸双链d(CGAATTCGCG)·d(GCGCTTAAGCGC)和1777个水分子组成的六方棱柱盒中的1777个水分子在周期边界条件下处理的体系，给出了B-型DNA小槽中水合作用的理论描述。从溶剂密度分布的角度对结果进行了分析。计算的小槽溶剂密度显示了相当大的局部化，表明了离散的溶剂化位置，并为定义良好的有序水结构提供了理论依据。在AATT序列中，这对应于H.R.Drew和R.E.Dickerson所描述的“水化脊椎”[(1981)J.Mol.比奥尔。151，-556]基于十二聚体水合物的X射线晶体结构。然而，我们发现，计算的有序水结构也延伸到CGCG侧翼序列，由鸟嘌呤残基的N_2氢键供体支持，表明水化的脊椎因此可以延伸到B-型DNA的小槽。这为L.A.Marky和K.J.Breslaer[(1984)Proc]观察到的正结合熵提供了可能的解释。娜塔莉。阿卡德。SCI。美国84,4359-4363]关于Netropsin与DNA的小沟的络合的A.T和C.G序列。讨论了这些结果对DNA在水中的热力学稳定性和小槽水化的序列特异性的影响。
A theoretical description of aqueous hydration in the minor groove of a B-form DNA is presented on the basis of a liquid-state Monte Carlo computer simulation on a system consisting of the oligonucleotide duplex d(CGCGAATTCGCG).d(GCGCTTAAGCGC) in a canonical B-form together with 1777 water molecules contained in a hexagonal prism cell and treated under periodic boundary conditions. The results are analyzed in terms of solvent density distributions. The calculated minor-groove solvent density shows considerable localization, indicative of discrete solvation sites and providing theoretical evidence for a well-defined ordered water structure. In the AATT sequence, this corresponds to the "spine of hydration" described by H. R. Drew and R. E. Dickerson [(1981) J. Mol. Biol. 151, 535-556] based on the x-ray crystal structure of the dodecamer hydrate. We find, however, that the calculated ordered water structure also extends into the CGCG flanking sequences, supported by the N2 hydrogen bond donors of the guanine residues and indicating that the spine of hydration could thus extend throughout the minor groove of a B-form DNA. This provides a possible explanation of the positive binding entropies observed by L. A. Marky and K. J. Breslauer [(1984) Proc. Natl. Acad. Sci. USA 84, 4359-4363] for both A.T and C.G sequences on the complexation of netropsin to the minor groove of DNAs. Implications of these results with regard to the thermodynamic stability of DNA in water and the sequence specificity of the minor groove hydration are discussed.