Structure and Binding Energy of Double-Stranded A-DNA Mini-helices: Quantum-Chemical Study

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• 作者：Tetiana Zubatiuk ; Maxim A. Kukuev ; Alexandra S. Korolyova ; Leonid Gorb ; Alexey Nyporko ; Dmytro Hovorun ; Jerzy Leszczynski
• 刊名：Journal of Physical Chemistry B
• 出版年：2015
• 出版时间：October 8, 2015
• 年：2015
• 卷：119
• 期：40
• 页码：12741-12749
• 全文大小：461K
• ISSN：1520-5207

文摘

A-DNA is thought to play a significant biological role in gene expression due to its specific conformation and binding features. In this study, double-stranded mini-helices (dA:dT)₃ and (dG:dC)₃ in A-like DNA conformation were investigated. M06-2X/6-31G(d,p) method has been utilized to identify the optimal geometries and predict physicochemical parameters of these systems. The results show the ability of the corresponding mini-helices to preserve their A-like conformation under the influences of solvent, charge, and Na⁺ counterions. Presented structural and energetic data offer evidence that two steps of GG/CC or AA/TT are already enough to turn the DNA helix to generate different forms by favoring specific values of roll and slide at a local level. Our calculations support the experimentally known fact that AA/TT steps prefer the B-form over the A-ones, whereas GG/CC steps may be found in either the B- or A-form. The stability of mini-helices at the level of total energy analysis, 螖E_total^(A鈥揃), is discussed.