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Drobotenko MI, Lyasota OM, Hernandez-Caceres JL, Labrada RR, Svidlov AA, Dorohova АA, Baryshev MG, Nechipurenko YD, Pérez LV, Dzhimak SS. Abnormal open states patterns in the ATXN2 DNA sequence depends on the CAG repeats length. Int J Biol Macromol 2024; 276:133849. [PMID: 39004246 DOI: 10.1016/j.ijbiomac.2024.133849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/04/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
Hereditary ataxias are one of the «anticipation diseases» types. Spinocerebral ataxia type 2 occurs when the number of CAG repeats in the coding region of the ATXN2 gene exceeds 34 or more. In healthy people, the CAG repeat region in the ATXN2 gene usually consists of 22-23 CAG trinucleotides. Mutations that increase the length of CAG repeats can cause severe neurodegenerative and neuromuscular disorders known as trinucleotide repeat expansion diseases. The mechanisms causing such diseases are associated with non-canonical configurations that can be formed in the CAG repeat region during replication, transcription or repair. This makes it relevant to study the zones of open states that arise in the region of CAG repeats under torque. The purpose of this work is to study, using mathematical modeling, zones of open states in the region of CAG repeats of the ATXN2 gene, caused by torque. It has been established that the torque effect on the 1st exon of the ATXN2 gene, in addition to the formation of open states in the promoter region, can lead to the formation of additional various sizes open states zones in the CAG repeats region. Moreover, the frequency of additional large zones genesis increases with increasing number of CAG repeats. The inverse of this frequency correlates with the dependence of the disease onset average age on the CAG repeats length. The obtained results will allow us to get closer to understanding the genetic mechanisms that cause trinucleotide repeat diseases.
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Affiliation(s)
- Mikhail I Drobotenko
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russian Federation
| | - Oksana M Lyasota
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russian Federation
| | | | | | - Alexandr A Svidlov
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russian Federation
| | - Аnna A Dorohova
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russian Federation; Laboratory of Problems of Stable Isotope Spreading in Living Systems, Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russian Federation
| | - Mikhail G Baryshev
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russian Federation
| | - Yury D Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | | | - Stepan S Dzhimak
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russian Federation; Laboratory of Problems of Stable Isotope Spreading in Living Systems, Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russian Federation.
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Basov A, Dorohova A, Malyshko V, Moiseev A, Svidlov A, Bezhenar M, Nechipurenko Y, Dzhimak S. Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17. Int J Mol Sci 2023; 24:12137. [PMID: 37569512 PMCID: PMC10418495 DOI: 10.3390/ijms241512137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023] Open
Abstract
The influence of a single 2H/1H replacement on the frequency generation of different-size bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was studied by a developed algorithm and mathematical modeling without simplifications or averaging. This new approach showed the efficacy of researching DNA bubbles and open states both when all hydrogen bonds in nitrogenous base pairs are protium and after an 2H-substitution. After a single deuterium substitution under specific energies, it was demonstrated that the non-coding region of IFNA17 had a more significant regulatory role in bubble generation in the whole gene than the promoter had. It was revealed that a single deuterium substitution for protium has an influence on the frequency generation of DNA bubbles, which also depends on their size and is always higher for the smaller bubbles under the largest number of the studied energies. Wherein, compared to the natural condition under the same critical value of energy, the bigger raises of the bubble frequency occurrence (maximums) were found for 11-30 base pair (bp) bubbles (higher by 319%), 2-4 bp bubbles (higher by 300%), and 31 bp and over ones (higher by 220%); whereas the most significant reductions of the indicators (minimums) were observed for 11-30 bp bubbles (lower by 43%) and bubbles size over 30 bp (lower by 82%). In this study, we also analyzed the impact of several circumstances on the AT/GC ratio in the formation of DNA bubbles, both under natural conditions and after a single hydrogen isotope exchange. Moreover, based on the obtained data, substantial positive and inverse correlations were revealed between the AT/GC ratio and some factors (energy values, size of DNA bubbles). So, this modeling and variant of the modified algorithm, adapted for researching DNA bubbles, can be useful to study the regulation of replication and transcription in the genes under different isotopic substitutions in the nucleobases.
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Affiliation(s)
- Alexandr Basov
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, Krasnodar 350063, Russia; (A.B.); (V.M.)
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
| | - Anna Dorohova
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Vadim Malyshko
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, Krasnodar 350063, Russia; (A.B.); (V.M.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Arkadii Moiseev
- Scientific Department, Kuban State Agrarian University, Krasnodar 350004, Russia;
| | - Alexandr Svidlov
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Maria Bezhenar
- Department of Function Theory, Kuban State University, Krasnodar 350040, Russia;
| | - Yury Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Stepan Dzhimak
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
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Abstract
The current issue (volume 13 issue 6, 2021) is a Special Issue jointly dedicated to scientific content presented at the 20th triennial IUPAB Congress that was held in conjunction with both the 45th Annual Meeting of the Brazilian Biophysical Society (Sociedade Brasileira de Biofísica - SBBf) and the 50th Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology (Sociedade Brasileira de Bioquímica e Biologia Molecular - SBBq). In addition to describing the scientific and nonscientific content arising from the meeting this sub-editorial also provides a look back at some of the high points for Biophysical Reviews in the year 2021 before going on to describe a number of matters of interest to readers of the journal in relation to the coming year of 2022.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164 Japan
- Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
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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: 2.0] [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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Svidlov A, Drobotenko M, Basov A, Gerasimenko E, Malyshko V, Elkina A, Baryshev M, Dzhimak S. DNA Dynamics under Periodic Force Effects. Int J Mol Sci 2021; 22:7873. [PMID: 34360636 PMCID: PMC8345943 DOI: 10.3390/ijms22157873] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/22/2022] Open
Abstract
The sensitivity of DNA to electromagnetic radiation in different ranges differs depending on various factors. The aim of this study was to examine the molecular dynamics of DNA under the influence of external periodic influences with different frequencies. In the present paper, within the framework of a mechanical model without simplifications, we investigated the effect of various frequencies of external periodic action in the range from 1011 s-1 to 108 s-1 on the dynamics of a DNA molecule. It was shown that under the influence of an external periodic force, a DNA molecule can perform oscillatory movements with a specific frequency characteristic of this molecule, which differs from the frequency of the external influence ω. It was found that the frequency of such specific vibrations of a DNA molecule depends on the sequence of nucleotides. Using the developed mathematical model describing the rotational motion of the nitrogenous bases around the sugar-phosphate chain, it is possible to calculate the frequency and amplitude of the oscillations of an individual DNA area. Such calculations can find application in the field of molecular nanotechnology.
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Affiliation(s)
- Alexander Svidlov
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- 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;
| | - Mikhail Drobotenko
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
| | - Alexander Basov
- Department of Radiophysics and Nanothechnology, Physics Faculty, 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;
| | - Vadim Malyshko
- 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;
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Anna Elkina
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- 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;
| | - Mikhail Baryshev
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- 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;
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Stepan Dzhimak
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- 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;
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Hall D. Biophysical Reviews-A call to young biophysicists. Biophys Rev 2021; 13:289-294. [PMID: 34178166 PMCID: PMC8214647 DOI: 10.1007/s12551-021-00810-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
This Editorial for Volume 13, Issue 3 of Biophysical Reviews begins with a summary of the Issue contents. This is then followed by a discussion of some additional matters important to the journal. In particular, this Editorial offers some thoughts as to what constitutes a good scientific Commentary before announcing the call for nominations for the 'The 2022 Michèle Auger Award for Young Scientists' Independent Research'.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164 Japan
- Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
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