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Matematicheskaya Biologiya i Bioinformatika, 2019, Volume 14, Issue 2, Pages 612–624
DOI: https://doi.org/10.17537/2019.14.612
(Mi mbb406)
 

This article is cited in 2 scientific papers (total in 2 papers)

Mathematical Modeling

Mathematical modeling of open states in double stranded DNA molecule depending on $^2H$/$^1H$ ratio

S. S. Dzhimakab, M. I. Drobotenkoab, A. A. Basovac, A. A. Svidlovb, M. G. Baryshevab

a Kuban State University, Krasnodar, Russian Federation
b Southern Research Center of the Russian Academy of Sciences, Rostov-on-Don, Russian Federation
c Kuban State Medical University, Krasnodar
Full-text PDF (455 kB) Citations (2)
References:
Abstract: The evaluation results of the possible deuterium atoms effect on the DNA base pair opening are presented in the article. The cause of these processes is the replacement of protium with deuterium atom due to the increase of energy required to break the hydrogen bond. These processes can be studied by method of mathematical modeling, with account of open states between base pairs being the key condition of the adequacy of the mathematical model of the DNA. The experiment data show that the presence of deuterium in a chain of nucleotides can cause - depending on the value of hydrogen bond disruption energy - both increase and decrease in probability of open states occurrence. For example: hydrogen bond disruption energy of 0.358$\cdot$10$^{-22}$ n$\cdot$м, non-zero probability of open states occurrence is observed in case of the absence of deuterium in the molecule, and with hydrogen bond disruption energy of 0.359$\cdot$10$^{-22}$ n$\cdot$м or more such probability equals zero. Also, when one deuterium atom is present in a molecule, non-zero probability is observed even with hydrogen bond disruption energy equal to 0.368$\cdot$10$^{-22}$ n$\cdot$м (i.e. more than 0.358$\cdot$10$^{-22}$ n$\cdot$м). Thus participation of deuterium atoms in the formation of hydrogen bonds of double helixes of a DNA molecule can cause the changes in the time required for transfer of genetic information, which can explain the effect of even minor deviations in deuterium concentration in a medium on metabolic processes in a living system.
Key words: DNA molecule, deuterium, rotational movements of nitrogenous bases, dynamics of a double-stranded DNA molecule, open states.
Funding agency Grant number
Ministry of Education and Science of the Russian Federation МК-3359.2017.4
АААА-А19-119040390083-6
Russian Foundation for Basic Research 19-44-230026
Received 24.09.2019, 10.12.2019, Published 11.12.2019
Document Type: Article
UDC: 577.323.36: 51-76
Language: Russian
Citation: S. S. Dzhimak, M. I. Drobotenko, A. A. Basov, A. A. Svidlov, M. G. Baryshev, “Mathematical modeling of open states in double stranded DNA molecule depending on $^2H$/$^1H$ ratio”, Mat. Biolog. Bioinform., 14:2 (2019), 612–624
Citation in format AMSBIB
\Bibitem{DzhDroBas19}
\by S.~S.~Dzhimak, M.~I.~Drobotenko, A.~A.~Basov, A.~A.~Svidlov, M.~G.~Baryshev
\paper Mathematical modeling of open states in double stranded DNA molecule depending on $^2H$/$^1H$ ratio
\jour Mat. Biolog. Bioinform.
\yr 2019
\vol 14
\issue 2
\pages 612--624
\mathnet{http://mi.mathnet.ru/mbb406}
\crossref{https://doi.org/10.17537/2019.14.612}
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