Influence of Environmental Parameters on the Stability of the DNA Molecule
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 dissipat...
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MDPI AG
2021-10-01
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| author | Alexander Svidlov Mikhail Drobotenko Alexander Basov Eugeny Gerasimenko Anna Elkina Mikhail Baryshev Yury Nechipurenko Stepan Dzhimak |
| author_facet | Alexander Svidlov Mikhail Drobotenko Alexander Basov Eugeny Gerasimenko Anna Elkina Mikhail Baryshev Yury Nechipurenko Stepan Dzhimak |
| author_sort | Alexander Svidlov |
| collection | DOAJ |
| description | 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. |
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| id | doaj.art-5bf227e18e544c15ac7a0be6e05dd2c3 |
| institution | Directory Open Access Journal |
| issn | 1099-4300 |
| language | English |
| last_indexed | 2024-03-10T05:31:25Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Entropy |
| spelling | doaj.art-5bf227e18e544c15ac7a0be6e05dd2c32023-11-22T23:15:05ZengMDPI AGEntropy1099-43002021-10-012311144610.3390/e23111446Influence of Environmental Parameters on the Stability of the DNA MoleculeAlexander Svidlov0Mikhail Drobotenko1Alexander Basov2Eugeny Gerasimenko3Anna Elkina4Mikhail Baryshev5Yury Nechipurenko6Stepan Dzhimak7Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, RussiaDepartment of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, RussiaDepartment of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, RussiaDepartment of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, RussiaDepartment of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, RussiaDepartment of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, RussiaDepartment of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, RussiaFluctuations 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.https://www.mdpi.com/1099-4300/23/11/1446DNAmathematical modelentropysolvent viscosityrotational movements of nitrogenous basesdynamics of a double-stranded DNA molecule |
| spellingShingle | Alexander Svidlov Mikhail Drobotenko Alexander Basov Eugeny Gerasimenko Anna Elkina Mikhail Baryshev Yury Nechipurenko Stepan Dzhimak Influence of Environmental Parameters on the Stability of the DNA Molecule Entropy DNA mathematical model entropy solvent viscosity rotational movements of nitrogenous bases dynamics of a double-stranded DNA molecule |
| title | Influence of Environmental Parameters on the Stability of the DNA Molecule |
| title_full | Influence of Environmental Parameters on the Stability of the DNA Molecule |
| title_fullStr | Influence of Environmental Parameters on the Stability of the DNA Molecule |
| title_full_unstemmed | Influence of Environmental Parameters on the Stability of the DNA Molecule |
| title_short | Influence of Environmental Parameters on the Stability of the DNA Molecule |
| title_sort | influence of environmental parameters on the stability of the dna molecule |
| topic | DNA mathematical model entropy solvent viscosity rotational movements of nitrogenous bases dynamics of a double-stranded DNA molecule |
| url | https://www.mdpi.com/1099-4300/23/11/1446 |
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