Abstract
The role of single protium–deuterium exchanges in formation of open-state bubbles is investigated using mathematical modeling methods. It is shown that the probability for formation of bubbles with a certain length (12 to 27 nucleotides) depends on localization of the deuterium atom in the DNA molecule and may be appreciably different from the general probability for occurrence of open states.
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REFERENCES
A. A. Grinevich and L. V. Yakushevich, “The influence of the DNA torque on the dynamics of transcription bubbles in plasmid PTTQ18,” J. Theor. Biol. 453, 68–77 (2018). https://doi.org/10.1016/j.jtbi.2018.04.036
T. Halenova, I. Zlatskiy, A. Syroeshkin, T. Maximova, and T. Pleteneva, “Deuterium-depleted water as adjuvant therapeutic agent for treatment of diet-induced obesity in rats,” Molecules. 25 (1), 23 (2020). https://doi.org/10.3390/molecules25010023
A. Basov, L. Fedulova, E. Vasilevskaya, and S. Dzhimak, “Possible mechanisms of biological effects observed in living systems during 2H/1H isotope fractionation and deuterium interactions with other biogenic isotopes,” Molecules. 24 (22), 4101 (2019). https://doi.org/10.3390/molecules24224101
V. N. Lobyshev and L. P. Kalinichenko, Isotope Effects of D 2 O in Biological Systems (Nauka, Moscow, 1978) [in Russian].
S. S. Dzhimak, A. A. Basov, G. F. Kopytov, D. V. Kashaev, M. E. Sokolov, O. M. Artsybasheva, K. S. Sharapov, and M. G. Baryshev, “Application of NMR spectroscopy to the determination of low concentrations of nonradioactive isotopes in liquid media,” Russ. Phys. J. 58 (7), 923–929 (2015). https://doi.org/10.1007/s11182-015-0591-9
N. V. Lobysheva, S. V. Nesterov, Yu. A. Skorobogatova, and V. I. Lobyshev, “The functional activity of mitochondria in deuterium depleted water,” Biophysics. 65 (2), 272–276 (2020). https://doi.org/10.1134/S0006350920020128
I. Zlatskiy, T. Pleteneva, A. Skripnikov, T. Grebennikova, T. Maksimova, N. Antipova, O. Levitskaya, M. Makarova, I. Selivanenko, and A. Syroeshkin, “Dependence of biocatalysis on D/H ratio: Possible fundamental differences for high-level biological taxons,” Molecules. 25 (18), 4173 (2020). https://doi.org/10.3390/molecules25184173
X. Zhang, M. Gaetani, A. Chernobrovkin, and R. A. Zubarev, “Anticancer effect of deuterium depleted water – redox disbalance leads to oxidative stress,” Mol. Cell. Proteomics. 18 (12), 2373–2387 (2019). https://doi.org/10.1074/mcp.RA119.001455
N. V. Yaglova, S. S. Obernikhin, V. V. Yaglov, and S. V. Nazimova, “Time-dependent effect of deuterium depletion on tumor growth and metastasis,” Russ. Open Med. J. 9 (2), e0210 (2020). https://doi.org/10.15275/rusomj.2020.0210
S. S. Dzhimak, A. A. Basov, A. A. Elkina, L. V. Fedulova, E. A. Kotenkova, E. R. Vasilevskaya, O. M. Lyasota, and M. G. Baryshev, “Influence of deuterium-depleted water on hepatorenal toxicity,” Jundishapur J. Nat. Pharm. Prod. 13 (2), e69557 (2018). https://doi.org/10.5812/jjnpp.69557
A. Basov, M. Drobotenko, A. Svidlov, E. Gerasimenko, V. Malyshko, A. Elkina, M. Baryshev, and S. Dzhimak, “Inequality in the frequency of the open states occurrence depends on single 2H/1H replacement in DNA,” Molecules. 25 (16), 3753 (2020). https://doi.org/10.3390/molecules25163753
S. S. Dzhimak, A. A. Svidlov, A. A. Basov, M. G. Baryshev, and M. I. Drobotenko, “The effect of single deuterium substitutions for protium in a DNA molecule on the occurrence of open states,” Biophysics. 63 (4), 497–500 (2018). https://doi.org/10.1134/S0006350918040061
S. S. Dzhimak, M. I. Drobotenko, A. A. Basov, A. A. Svidlov, L. V. Fedulova, O. M. Lyasota, and M. G. Baryshev, “Mathematical modeling of open state in DNA molecule depending on the deuterium concentration in the surrounding liquid media at different values of hydrogen bond disruption energy,” Dokl. Biochem. Biophys. 483 (1), 359–362 (2018). https://doi.org/10.1134/S1607672918060169
A. A. Grinevich and L. V. Yakushevich, “On the modeling of the motion of a transcription bubble under constant torque,” Biophysics. 61 (4), 539–546 (2016). https://doi.org/10.1134/S0006350916040126
M. I. Drobotenko, S. S. Dzhimak, A. A. Svidlov, A. A. Basov, O. M. Lyasota, and M. G. Baryshev, “A mathematical model for basepair opening in a DNA double helix,” Biophysics. 63 (2), 177–182 (2018). https://doi.org/10.1134/S0006350918020069
L. V. Yakushevich, “On the mechanical analogue of DNA,” J. Biol. Phys. 43 (1), 113–125 (2017). https://doi.org/10.1007/s10867-016-9437-0
L. V. Yakushevich and L. A. Krasnobaeva, “Forced oscillations of DNA bases,” Biophysics. 61 (2), 241–250 (2016). https://doi.org/10.1134/S000635091602024X
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The work was supported by the Russian Foundation for Basic Research, project no. 20-41-235002, and by the Krasnodar krai administration.
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Translated by M. Potapov
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Svidlov, A.A., Drobotenko, M.I., Basov, A.A. et al. Influence of the 2H/1H Isotope Composition of the Water Environment on the Probability of Denaturation Bubble Formation in a DNA Molecule. Phys. Wave Phen. 29, 180–185 (2021). https://doi.org/10.3103/S1541308X2102014X
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DOI: https://doi.org/10.3103/S1541308X2102014X