Mathematical modeling of open states in double stranded DNA molecule depending on $^2H$/$^1H$ ratio
Matematičeskaâ biologiâ i bioinformatika, Tome 14 (2019) no. 2, pp. 612-624.

Voir la notice de l'article provenant de la source Math-Net.Ru

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.
@article{MBB_2019_14_2_a18,
     author = {S. S. Dzhimak and M. I. Drobotenko and A. A. Basov and A. A. Svidlov and M. G. Baryshev},
     title = {Mathematical modeling of open states in double stranded {DNA} molecule depending on $^2H$/$^1H$ ratio},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
     pages = {612--624},
     publisher = {mathdoc},
     volume = {14},
     number = {2},
     year = {2019},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/MBB_2019_14_2_a18/}
}
TY  - JOUR
AU  - S. S. Dzhimak
AU  - M. I. Drobotenko
AU  - A. A. Basov
AU  - A. A. Svidlov
AU  - M. G. Baryshev
TI  - Mathematical modeling of open states in double stranded DNA molecule depending on $^2H$/$^1H$ ratio
JO  - Matematičeskaâ biologiâ i bioinformatika
PY  - 2019
SP  - 612
EP  - 624
VL  - 14
IS  - 2
PB  - mathdoc
UR  - http://geodesic.mathdoc.fr/item/MBB_2019_14_2_a18/
LA  - ru
ID  - MBB_2019_14_2_a18
ER  - 
%0 Journal Article
%A S. S. Dzhimak
%A M. I. Drobotenko
%A A. A. Basov
%A A. A. Svidlov
%A M. G. Baryshev
%T Mathematical modeling of open states in double stranded DNA molecule depending on $^2H$/$^1H$ ratio
%J Matematičeskaâ biologiâ i bioinformatika
%D 2019
%P 612-624
%V 14
%N 2
%I mathdoc
%U http://geodesic.mathdoc.fr/item/MBB_2019_14_2_a18/
%G ru
%F MBB_2019_14_2_a18
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. Matematičeskaâ biologiâ i bioinformatika, Tome 14 (2019) no. 2, pp. 612-624. http://geodesic.mathdoc.fr/item/MBB_2019_14_2_a18/

[1] A. Petruş-Vancea, “Cell ultrastructure and chlorophyll pigments in hyperhydric and non-hyperhydric Beta vulgaris var. Conditiva plantlets, treated with deuterium depleted water”, Plant Cell, Tissue and Organ Culture, 135:1 (2018), 13–21 | DOI

[2] A. A. Basov, L. V. Fedulova, M. G. Baryshev, S. S. Dzhimak, “Deuterium-depleted water influence on the isotope $^2$H/$^1$H regulation in body and individual adaptation”, Nutrients, 11:8 (2019), 1903 | DOI

[3] S. Chira, L. Raduly, C. Braicu, A. Jurj, R. Cojocneanu-Petric, L. Pop, V. Pileczki, C. Ionescu, I. Berindan-Neagoe, “Premature senescence activation in DLD-1 colorectal cancer cells through adjuvant therapy to induce a miRNA profile modulating cellular death”, Experimental and Therapeutic Medicine, 16:2 (2018), 1241–1249

[4] V. I. Lobyshev, “Biphasic response of biological objects on variation of low deuterium concentration in water”, International Journal of High Dilution Research, 17:2 (2018), 12–13

[5] A. Zlatska, I. Gordiienko, R. Vasyliev, D. Zubov, O. Gubar, A. Rodnichenko, A. Syroeshkin, I. Zlatskiy, “In Vitro Study of Deuterium Effect on Biological Properties of Human Cultured Adipose-Derived Stem Cells”, Scientific World Journal, 2018, 5454367 | DOI

[6] S. S. Dzhimak, M. G. Barishev, A. A. Basov, A. A. Timakov, “Influence of deuterium depleted water on freeze dried tissue isotopic composition and morphofunctional body performance in rats of different generations”, Biophysics, 59:4 (2014), 614–619 | DOI

[7] S. V. Kozin, A. A. Kravtsov, A. A. Elkina, E. I. Zlishcheva, E. V. Barysheva, L. V. Shurygina, A. V. Moiseev, M. G. Baryshev, “Isotope exchange of deuterium for protium in rat brain tissues changes brain tolerance to hypoxia”, Biophysics, 64:2 (2019), 272–278 | DOI

[8] A. A. Kravtsov, S. V. Kozin, E. R. Vasilevskaya, A. A. Elkina, L. V. Fedulova, K. A. Popov, V. V. Malyshko, A. V. Moiseev, D. I. Shashkov, M. G. Baryshev, “Effect of Drinking Ration with Reduced Deuterium Content on Brain Tissue Prooxidant-Antioxidant Balance in Rats with Acute Hypoxia Model”, Journal of Pharmacy and Nutrition Sciences, 8:2 (2018), 42–51 | DOI

[9] T. Strekalova, M. Evans, A. Chernopiatko, Y. Couch, J. Costa-Nunes, R. Cespuglio, L. Chesson, J. Vignisse, H. W. Steinbusch, D. C. Anthony, I. Pomytkin, K. P. Lesch, “Deuterium content of water increases depression susceptibility: The potential role of a serotonin-related mechanism”, Behavioral Brain Research, 277 (2015), 237–244 | DOI

[10] A. V. Syroeshkin, N. V. Antipova, A. V. Zlatska, I. A. Zlatskiy, M. D. Skylska, T. V. Grebennikova, V. V. Goncharuk, “The effect of the deuterium depleted water on the biological activity of the eukaryotic cells”, Journal of Trace Elements in Medicine and Biology, 50 (2018), 629–633 | DOI

[11] A. A. Basov, L. V. Fedulova, E. R. Vasilevskaya, S. S. Dzhimak, “Possible mechanisms of biological effects observed in living systems during $^2$H/$^1$H isotope fractionation and deuterium interactions with other biogenic isotopes”, Molecules, 24:22 (2019), 4101 | DOI

[12] A. L. Luo, Y. L. Zheng, F. S. Cong, “Research progress of biological effects of deuterium-depleted water”, Journal of Shanghai Jiaotong University (Medical Science), 38:4 (2018), 467–471

[13] K. Yavari, L. Kooshesh, “Deuterium Depleted Water Inhibits the Proliferation of Human MCF7 Breast Cancer Cell Lines by Inducing Cell Cycle Arrest”, Nutrition and Cancer, 71:6 (2019), 1019–1029 | DOI

[14] S. S. Dzhimak, A. A. Basov, A. A. Elkina, L. V. Fedulova, E. A. Kotenkova, E. R. Vasilevskaya, O. M. Lyasota, M. G. Baryshev, “Influence of deuterium-depleted water on hepatorenal toxicity”, Jundishapur Journal of Natural Pharmaceutical Products, 13:2 (2018), e69557 | DOI

[15] A. A. Basov, A. A. Elkina, A. A. Samkov, N. N. Volchenko, A. V. Moiseev, L. V. Fedulova, M. G. Baryshev, S. S. Dzhimak, “Influence of deuterium depleted water on the isotope D/H composition of liver tissue and morphological development of rats at different periods of ontogenesis”, Iranian Biomedical Journal, 23:2 (2019), 129–141 | DOI

[16] R. Rehakova, J. Klimentova, M. Cebova, A. Barta, Z. Matuskova, P. Labas, O. Pechanova, “Effect of Deuterium-Depleted Water on Selected Cardiometabolic Parameters in Fructose-Treated Rats”, Physiol. Res., 65, Suppl. 3 (2016), S401–S407 | DOI

[17] N. V. Yaglova, S. S. Obernikhin, D. A. Tsomartova, S. V. Nazimova, V. V. Yaglov, “Expression of Transcription Factor PRH/Hhex in Adrenal Chromaffin Cells in the Postnatal Development and Its Role in the Regulation of Proliferative Processes”, Bulletin of Experimental Biology and Medicine, 165:4 (2018), 508–511 | DOI

[18] P. B. Reaser, G. E. Burch, “Determination of deuterium oxide in water by measurement of freezing point”, Science, 128:3321 (1958), 415–416 | DOI

[19] V. N. Parmon, “On the possibility of observing kinetic isotopic effects in the life cycles of living organisms at ultralow concentrations of deuterium”, Her. Russ. Acad. Sci., 85:2 (2015), 170–172 | DOI

[20] L. G. Pedersen, L. Bartolotti, L. Li, “Deuterium and its role in the machinery of evolution”, Journal of Theoretical Biology, 238:4 (2006), 914–918 | DOI | Zbl

[21] A. S. Shigaev, O. A. Ponomarev, V. D. Lakhno, “Theoretical and experimental investigations of DNA open states”, Mathematical Biology and Bioinformatics, 8:2 (2013), 553–664 | DOI

[22] M. Manghi, N. Destainville, “Physics of base-pairing dynamics in DNA”, Physics Reports, 631 (2016), 1–41 | DOI | MR

[23] A. Vologodskii, M. D. Frank-Kamenetskii, “DNA melting and energetics of the double helix”, Physics of Life Reviews, 25 (2018), 1–21 | DOI

[24] M. Peyrard, A. R. Bishop, “Statistical Mechanics of a Nonlinear Model for DNA Denaturation”, Physical Review Letters, 62 (1989), 2755–2758 | DOI

[25] B. S. Alexandrov, V. Gelev, Y. Monisova, L. B. Alexandrov, A. R. Bishop, K. O. Rasmussen, A. Usheva, “A nonlinear dynamic model of DNA with a sequence-dependent stacking term”, Nucleic Acids Res, 37:7 (2009), 2405–2410 | DOI

[26] L. V. Yakushevich, L. A. Krasnobaeva, “Forced Oscillations of DNA Bases”, Biophysics, 61:2 (2016), 241–250 | DOI

[27] A. A. Grinevich, L. V. Yakushevich, “The influence of the DNA torque on the dynamics of transcription bubbles in plasmid PTTQ18”, Journal of Theoretical Biology, 453 (2018), 68–77 | DOI | MR | Zbl

[28] M. I. Drobotenko, S. S. Dzhimak, A. A. Svidlov, A. A. Basov, O. M. Lyasota, M. G. Baryshev, “A Mathematical Model for Basepair Opening in a DNA Double Helix”, Biophysics, 63:2 (2018), 177–182 | DOI

[29] A. A. Grinevich, L. V. Yakushevich, “On the modeling of the motion of a transcription bubble under constant torque”, Biophysics, 61:4 (2016), 539–546 | DOI

[30] U. Bockelmann, Ph. Thomen, B. Essevaz-Roulet, V. Viasnoff, F. Heslot, “Unzipping DNA with optical tweezers: High sequence sensitivity and force flips”, Biophysical Journal, 82 (2002), 1537–1553 | DOI

[31] X. Xie, R. A. Zubarev, “Isotopic Resonance Hypothesis: Experimental Verification by Escherichia coli Growth Measurements”, Scientific reports, 5 (2015), 9215 | DOI