Gorb Leonid, Shishkin Oleg V, Zubatiuk Tetiana
Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnogo str., 03680 Kyiv, Ukraine.
QSAR Lab Ltd., Trzy Lipy 3, B, 80-172 Gdańsk, Poland.
BBA Adv. 2023 Feb 11;3:100082. doi: 10.1016/j.bbadva.2023.100082. eCollection 2023.
In this review, we analyze and systematize our computational studies of the nucleic acid duplex formations and thermodynamic stability under the different factors of investigation. The proposed structural models of mini-helix contains N nucleobase pairs (N = 3-5); QM structural data suggest that the helical conformations of mini-helix adopt geometrical parameters comparable to those of natural A- and B-DNA forms under specific conditions as micro hydration and charge compensation. The gas-phase models adopt non regular conformations between the helical form and a ladder form.. The natural helical shape of DNA mini-helix is stabilized by the presence of counterions or by explicit micro-hydration of the major and minor groves. The presence of aqueous solution is shown as a minor factor for the helical shape formation. The studies are performed at the level of density functional theory.
在本综述中，我们分析并系统化了我们对在不同研究因素下核酸双链体形成和热力学稳定性的计算研究。所提出的小螺旋结构模型包含N个核碱基对（N = 3 - 5）；量子力学结构数据表明，在特定条件下，如微水合作用和电荷补偿，小螺旋的螺旋构象采用与天然A - 和B - DNA形式相当的几何参数。气相模型采用螺旋形式和梯状形式之间的不规则构象。DNA小螺旋的天然螺旋形状通过抗衡离子的存在或通过大沟和小沟的明确微水合作用而稳定。水溶液的存在被证明是螺旋形状形成的次要因素。这些研究是在密度泛函理论水平上进行的。
