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Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque
The formation and dynamics of the open states in a double-stranded DNA molecule are largely determined by its mechanical parameters. The main one is the torque. However, the experimental study of DNA dynamics and the occurrence of open states is limited by the spatial resolution of available biophys...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9025193/ https://www.ncbi.nlm.nih.gov/pubmed/35457247 http://dx.doi.org/10.3390/ijms23084428 |
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author | Dzhimak, Stepan Svidlov, Alexandr Elkina, Anna Gerasimenko, Eugeny Baryshev, Mikhail Drobotenko, Mikhail |
author_facet | Dzhimak, Stepan Svidlov, Alexandr Elkina, Anna Gerasimenko, Eugeny Baryshev, Mikhail Drobotenko, Mikhail |
author_sort | Dzhimak, Stepan |
collection | PubMed |
description | The formation and dynamics of the open states in a double-stranded DNA molecule are largely determined by its mechanical parameters. The main one is the torque. However, the experimental study of DNA dynamics and the occurrence of open states is limited by the spatial resolution of available biophysical instruments. Therefore, in this work, on the basis of a mechanical mathematical model of DNA, calculations of the torque effect on the process of occurrence and dynamics of open states were carried out for the interferon alpha 17 gene. It was shown that torsion action leads to the occurrence of rotational movements of nitrogenous bases. This influence is nonlinear, and an increase in the amplitude of the torsion action does not lead to an automatic increase in the amplitude of rotational movements and an increase in the zones’ open states. Calculations with a constant torsion moment demonstrate that open states zones are more often formed at the boundaries of the gen and in regions with a predominance of A–T pairs. It is shown, that for the occurrence of open states in the part of the gene that contains a small number of A–T pairs, a large amount of torque is required. When the torque is applied to a certain region of the gene, the probability of the formation of the open state depends on the content of A–T pairs in this region, the size of this region, and on the exposure time. For this mathematical model, open states zones can be closed when the torsion action stops. The simulation results showed that the values of the torsion moment required for the appearance of open states zones, in some cases, are close to experimentally measured (13–15 pN·nm). |
format | Online Article Text |
id | pubmed-9025193 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-90251932022-04-23 Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque Dzhimak, Stepan Svidlov, Alexandr Elkina, Anna Gerasimenko, Eugeny Baryshev, Mikhail Drobotenko, Mikhail Int J Mol Sci Article The formation and dynamics of the open states in a double-stranded DNA molecule are largely determined by its mechanical parameters. The main one is the torque. However, the experimental study of DNA dynamics and the occurrence of open states is limited by the spatial resolution of available biophysical instruments. Therefore, in this work, on the basis of a mechanical mathematical model of DNA, calculations of the torque effect on the process of occurrence and dynamics of open states were carried out for the interferon alpha 17 gene. It was shown that torsion action leads to the occurrence of rotational movements of nitrogenous bases. This influence is nonlinear, and an increase in the amplitude of the torsion action does not lead to an automatic increase in the amplitude of rotational movements and an increase in the zones’ open states. Calculations with a constant torsion moment demonstrate that open states zones are more often formed at the boundaries of the gen and in regions with a predominance of A–T pairs. It is shown, that for the occurrence of open states in the part of the gene that contains a small number of A–T pairs, a large amount of torque is required. When the torque is applied to a certain region of the gene, the probability of the formation of the open state depends on the content of A–T pairs in this region, the size of this region, and on the exposure time. For this mathematical model, open states zones can be closed when the torsion action stops. The simulation results showed that the values of the torsion moment required for the appearance of open states zones, in some cases, are close to experimentally measured (13–15 pN·nm). MDPI 2022-04-17 /pmc/articles/PMC9025193/ /pubmed/35457247 http://dx.doi.org/10.3390/ijms23084428 Text en © 2022 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 Dzhimak, Stepan Svidlov, Alexandr Elkina, Anna Gerasimenko, Eugeny Baryshev, Mikhail Drobotenko, Mikhail Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque |
title | Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque |
title_full | Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque |
title_fullStr | Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque |
title_full_unstemmed | Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque |
title_short | Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque |
title_sort | genesis of open states zones in a dna molecule depends on the localization and value of the torque |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9025193/ https://www.ncbi.nlm.nih.gov/pubmed/35457247 http://dx.doi.org/10.3390/ijms23084428 |
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