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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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Autores principales: Svidlov, Alexander, Drobotenko, Mikhail, Basov, Alexander, Gerasimenko, Eugeny, Elkina, Anna, Baryshev, Mikhail, Nechipurenko, Yury, Dzhimak, Stepan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8622188/
https://www.ncbi.nlm.nih.gov/pubmed/34828144
http://dx.doi.org/10.3390/e23111446
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author Svidlov, Alexander
Drobotenko, Mikhail
Basov, Alexander
Gerasimenko, Eugeny
Elkina, Anna
Baryshev, Mikhail
Nechipurenko, Yury
Dzhimak, Stepan
author_facet Svidlov, Alexander
Drobotenko, Mikhail
Basov, Alexander
Gerasimenko, Eugeny
Elkina, Anna
Baryshev, Mikhail
Nechipurenko, Yury
Dzhimak, Stepan
author_sort Svidlov, Alexander
collection PubMed
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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spelling pubmed-86221882021-11-27 Influence of Environmental Parameters on the Stability of the DNA Molecule Svidlov, Alexander Drobotenko, Mikhail Basov, Alexander Gerasimenko, Eugeny Elkina, Anna Baryshev, Mikhail Nechipurenko, Yury Dzhimak, Stepan Entropy (Basel) Article 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. MDPI 2021-10-31 /pmc/articles/PMC8622188/ /pubmed/34828144 http://dx.doi.org/10.3390/e23111446 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Svidlov, Alexander
Drobotenko, Mikhail
Basov, Alexander
Gerasimenko, Eugeny
Elkina, Anna
Baryshev, Mikhail
Nechipurenko, Yury
Dzhimak, Stepan
Influence of Environmental Parameters on the Stability of the 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 Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8622188/
https://www.ncbi.nlm.nih.gov/pubmed/34828144
http://dx.doi.org/10.3390/e23111446
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