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:	Alexander Svidlov, Mikhail Drobotenko, Alexander Basov, Eugeny Gerasimenko, Anna Elkina, Mikhail Baryshev, Yury Nechipurenko, Stepan Dzhimak
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	DNA mathematical model entropy solvent viscosity rotational movements of nitrogenous bases dynamics of a double-stranded DNA molecule Science Q Astrophysics QB460-466 Physics QC1-999
Acceso en línea:	https://doaj.org/article/5bf227e18e544c15ac7a0be6e05dd2c3
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id	oai:doaj.org-article:5bf227e18e544c15ac7a0be6e05dd2c3
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spelling	oai:doaj.org-article:5bf227e18e544c15ac7a0be6e05dd2c32021-11-25T17:29:43ZInfluence of Environmental Parameters on the Stability of the DNA Molecule10.3390/e231114461099-4300https://doaj.org/article/5bf227e18e544c15ac7a0be6e05dd2c32021-10-01T00:00:00Zhttps://www.mdpi.com/1099-4300/23/11/1446https://doaj.org/toc/1099-4300Fluctuations 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.Alexander SvidlovMikhail DrobotenkoAlexander BasovEugeny GerasimenkoAnna ElkinaMikhail BaryshevYury NechipurenkoStepan DzhimakMDPI AGarticleDNAmathematical modelentropysolvent viscosityrotational movements of nitrogenous basesdynamics of a double-stranded DNA moleculeScienceQAstrophysicsQB460-466PhysicsQC1-999ENEntropy, Vol 23, Iss 1446, p 1446 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	DNA mathematical model entropy solvent viscosity rotational movements of nitrogenous bases dynamics of a double-stranded DNA molecule Science Q Astrophysics QB460-466 Physics QC1-999
spellingShingle	DNA mathematical model entropy solvent viscosity rotational movements of nitrogenous bases dynamics of a double-stranded DNA molecule Science Q Astrophysics QB460-466 Physics QC1-999 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
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.
format	article
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
title	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_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_sort	influence of environmental parameters on the stability of the dna molecule
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/5bf227e18e544c15ac7a0be6e05dd2c3
work_keys_str_mv	AT alexandersvidlov influenceofenvironmentalparametersonthestabilityofthednamolecule AT mikhaildrobotenko influenceofenvironmentalparametersonthestabilityofthednamolecule AT alexanderbasov influenceofenvironmentalparametersonthestabilityofthednamolecule AT eugenygerasimenko influenceofenvironmentalparametersonthestabilityofthednamolecule AT annaelkina influenceofenvironmentalparametersonthestabilityofthednamolecule AT mikhailbaryshev influenceofenvironmentalparametersonthestabilityofthednamolecule AT yurynechipurenko influenceofenvironmentalparametersonthestabilityofthednamolecule AT stepandzhimak influenceofenvironmentalparametersonthestabilityofthednamolecule
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Influence of Environmental Parameters on the Stability of the DNA Molecule

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