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Dorohova A, Lyasota O, Dzhimak S, Svidlov A, Leontyeva O, Drobotenko M. Fluctuations in Medium Viscosity May Affect the Stability of the CAG Tract in the ATXN2 Gene. Biomedicines 2024; 12:2396. [PMID: 39457708 PMCID: PMC11504642 DOI: 10.3390/biomedicines12102396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 10/15/2024] [Accepted: 10/18/2024] [Indexed: 10/28/2024] Open
Abstract
Background: Trinucleotide repeats are the cause of many neurodegenerative diseases that are currently incurable. In this regard, the question of the causes of occurrence and methods of prevention or treatment of diseases caused by the expansion of repeats in the CAG tract of the ATXN2 gene remains relevant. Previously, it was shown that the frequency of occurrence of additional OS (open states) zones increases with increasing length of the CAG tract, and the value inverse to the frequency correlates with the age of disease onset. Methods: In this work, the influence of the viscosity of the medium and the external torque on the stability of the CAG tract in the ATXN2 gene was studied using mathematical modeling methods. Results: It has been established that the probability of the appearance of additional OS zones of significant size increases with an increase in the CAG of the tract (k > 40 CAG repeats) for all viscosity values, however, at k ≤ 40, the change in viscosity does not significantly affect the probability of additional OS zones in the tract. Conclusions: It was found that under normal conditions (absence of pathology), viscosity does not have a reliable effect on the stability of the DNA molecule, but when pathology appears, an increase in viscosity contributes to an increase in DNA stability, and, accordingly, a decrease has a negative effect on the stabilization of the DNA molecule. In the zone of close to incomplete penetrance of the disease, viscosity does not have a reliable effect on the stability of the CAG tract.
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Affiliation(s)
- Anna Dorohova
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia; (O.L.); (S.D.); (A.S.)
- Research Department, Kuban State University, 350040 Krasnodar, Russia; (O.L.); (M.D.)
| | - Oksana Lyasota
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia; (O.L.); (S.D.); (A.S.)
- Research Department, Kuban State University, 350040 Krasnodar, Russia; (O.L.); (M.D.)
| | - Stepan Dzhimak
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia; (O.L.); (S.D.); (A.S.)
- Research Department, Kuban State University, 350040 Krasnodar, Russia; (O.L.); (M.D.)
| | - Alexandr Svidlov
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia; (O.L.); (S.D.); (A.S.)
| | - Olga Leontyeva
- Research Department, Kuban State University, 350040 Krasnodar, Russia; (O.L.); (M.D.)
| | - Mikhail Drobotenko
- Research Department, Kuban State University, 350040 Krasnodar, Russia; (O.L.); (M.D.)
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Svidlov A, Drobotenko M, Basov A, Gerasimenko E, Elkina A, Baryshev M, Nechipurenko Y, Dzhimak S. Influence of Environmental Parameters on the Stability of the DNA Molecule. ENTROPY (BASEL, SWITZERLAND) 2021; 23:1446. [PMID: 34828144 PMCID: PMC8622188 DOI: 10.3390/e23111446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022]
Abstract
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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Affiliation(s)
- Alexander Svidlov
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
| | - Mikhail Drobotenko
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
| | - Alexander Basov
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Eugeny Gerasimenko
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Anna Elkina
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Mikhail Baryshev
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Yury Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Stepan Dzhimak
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
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