Svidlov Alexander, Drobotenko Mikhail, Basov Alexander, Gerasimenko Eugeny, Elkina Anna, Baryshev Mikhail, Nechipurenko Yury, Dzhimak Stepan
Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia.
Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia.
Entropy (Basel). 2021 Oct 31;23(11):1446. doi: 10.3390/e23111446.
Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation-dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases' vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.
细胞核内粘度的波动范围很广。当DNA分子从高粘度区域进入低粘度区域时，可能会出现开放状态、变性泡以及DNA链的解旋。分子的稳定性是通过与环境相互作用导致的能量耗散来实现的。处于扭曲状态的DNA分子的不同部分可能会经历超螺旋应力，这尤其归因于与溶剂相互作用所引起的复杂熵效应。在这项工作中，基于干扰素α17基因和果蝇基因片段的力学数学模型的数值解，分析了外部环境粘度对DNA分子动力学及其稳定性的影响。结果表明，粘度增加会导致含氮碱基角振动迅速稳定，而粘度降低则会改变DNA的动力学：含氮碱基角偏差的变化率增加，并且在每个时刻DNA链的角变形都会增加。这些过程会导致DNA不稳定，且这种不稳定性会随时间增加。因此，本文考虑了外部环境粘度对DNA含氮碱基振动运动能量耗散的影响。此外，基于所描述的核质流变行为不同指标下生理过程分子动力学模型的研究，将有助于更深入地理解活细胞中活性物质的非平衡物理过程。
