Russian version English version
Volume 14   Issue 2   Year 2019
Dzhimak S.S.1,2, Drobotenko M.I.1, Basov A.A.1,3, Svidlov A.A.2, Baryshev M.G.1,2

Mathematical Modeling of Open States in Double Stranded DNA Molecule Depending on 2H/1H Ratio

Mathematical Biology & Bioinformatics. 2019;14(2):612-624.

doi: 10.17537/2019.14.612.

References

 

  1. Petruş-Vancea A. 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. 2018;135(1):13-21. doi: 10.1007/s11240-018-1439-0
  2. Basov A.A., Fedulova L.V., Baryshev M.G., Dzhimak S.S. Deuterium-depleted water influence on the isotope 2H/1H regulation in body and individual adaptation. Nutrients. 2019;11(8):1903. doi: 10.3390/nu11081903
  3. Chira S., Raduly L., Braicu C., Jurj A., Cojocneanu-Petric R., Pop L., Pileczki V., Ionescu C., Berindan-Neagoe I. Premature senescence activation in DLD-1 colorectal cancer cells through adjuvant therapy to induce a miRNA profile modulating cellular death. Experimental and Therapeutic Medicine. 2018;16(2):1241-1249. doi: 10.3892/etm.2018.6324
  4. Lobyshev V.I. Biphasic response of biological objects on variation of low deuterium concentration in water. International Journal of High Dilution Research. 2018;17(2):12-13.
  5. Zlatska A., Gordiienko I., Vasyliev R., Zubov D., Gubar O., Rodnichenko A., Syroeshkin A., Zlatskiy I. In Vitro Study of Deuterium Effect on Biological Properties of Human Cultured Adipose-Derived Stem Cells. Scientific World Journal. 2018. Article ID 5454367. doi: 10.1155/2018/5454367
  6. Dzhimak S.S., Barishev M.G., Basov A.A., Timakov A.A. Influence of deuterium depleted water on freeze dried tissue isotopic composition and morphofunctional body performance in rats of different generations. Biophysics. 2014;59(4):614-619. doi: 10.1134/S0006350914040101
  7. Kozin S.V., Kravtsov A.A., Elkina A.A., Zlishcheva E.I., Barysheva E.V., Shurygina L.V., Moiseev A.V., Baryshev M.G. Isotope exchange of deuterium for protium in rat brain tissues changes brain tolerance to hypoxia. Biophysics. 2019;64(2):272-278. doi: 10.1134/S0006350919020106
  8. Kravtsov A.A., Kozin S.V., Vasilevskaya E.R., Elkina A.A., Fedulova L.V., Popov K.A., Malyshko V.V., Moiseev A.V., Shashkov D.I., Baryshev M.G. 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. 2018;8(2):42-51. doi: 10.6000/1927-5951.2018.08.02.3
  9. Strekalova T., Evans M., Chernopiatko A., Couch Y., Costa-Nunes J., Cespuglio R., Chesson L., Vignisse J., Steinbusch H. W., Anthony D. C., Pomytkin I., Lesch K. P. Deuterium content of water increases depression susceptibility: The potential role of a serotonin-related mechanism. Behavioral Brain Research. 2015;277:237-244. doi: 10.1016/j.bbr.2014.07.039
  10. Syroeshkin A.V., Antipova N.V., Zlatska A.V., Zlatskiy I.A., Skylska M.D., Grebennikova T.V., Goncharuk V.V. The effect of the deuterium depleted water on the biological activity of the eukaryotic cells. Journal of Trace Elements in Medicine and Biology. 2018;50:629-633. doi: 10.1016/j.jtemb.2018.05.004
  11. Basov A.A., Fedulova L.V., Vasilevskaya E.R., Dzhimak S.S. Possible mechanisms of biological effects observed in living systems during 2H/1H isotope fractionation and deuterium interactions with other biogenic isotopes. Molecules. 2019;24(22):4101. doi: 10.3390/molecules24224101
  12. Luo A.L., Zheng Y.L., Cong F.S. Research progress of biological effects of deuterium-depleted water. Journal of Shanghai Jiaotong University (Medical Science). 2018;38(4):467-471.
  13. Yavari K., Kooshesh L. Deuterium Depleted Water Inhibits the Proliferation of Human MCF7 Breast Cancer Cell Lines by Inducing Cell Cycle Arrest. Nutrition and Cancer. 2019;71(6):1019-1029. doi: 10.1080/01635581.2019.1595048
  14. Dzhimak S.S., Basov À.À., Elkina À.À., Fedulova L.V., Kotenkova Å.À., Vasilevskaya Å.R., Lyasota Î.Ì., Baryshev M.G. Influence of deuterium-depleted water on hepatorenal toxicity. Jundishapur Journal of Natural Pharmaceutical Products. 2018;13(2):e69557. doi: 10.5812/jjnpp.69557
  15. Basov A.A., Elkina A.A., Samkov A.A., Volchenko N.N., Moiseev A.V., Fedulova L.V., Baryshev M.G., Dzhimak S.S. 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. 2019;23(2):129-141. doi: 10.29252/ibj.23.2.129
  16. Rehakova R., Klimentova J., Cebova M., Barta A., Matuskova Z., Labas P., Pechanova O. Effect of Deuterium-Depleted Water on Selected Cardiometabolic Parameters in Fructose-Treated Rats. Physiol. Res. 2016;65(3):S401-S407.
  17. Yaglova N.V., Obernikhin S.S., Tsomartova D.A., Nazimova S.V., Yaglov V.V. 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. 2018;165(4):508-511. doi: 10.1007/s10517-018-4205-8
  18. Reaser P.B., Burch G.E. Determination of deuterium oxide in water by measurement of freezing point. Science. 1958;128(3321):415-416. doi: 10.1126/science.128.3321.415
  19. Parmon V.N. On the possibility of observing kinetic isotopic effects in the life cycles of living organisms at ultralow concentrations of deuterium. Her. Russ. Acad. Sci. 2015;85(2):170-172. doi: 10.1134/S1019331615020057
  20. Pedersen L.G., Bartolotti L., Li L. Deuterium and its role in the machinery of evolution. Journal of Theoretical Biology. 2006;238(4):914-918. doi: 10.1016/j.jtbi.2005.07.002
  21. Shigaev A.S., Ponomarev O.A., Lakhno V.D. Theoretical and experimental investigations of DNA open states. Mathematical Biology and Bioinformatics. 2013;8(2):553-664. doi: 10.17537/2013.8.553
  22. Manghi M., Destainville N. Physics of base-pairing dynamics in DNA. Physics Reports. 2016;631:1-41. doi: 10.1016/j.physrep.2016.04.001
  23. Vologodskii A., Frank-Kamenetskii M.D. DNA melting and energetics of the double helix. Physics of Life Reviews. 2018;25:1-21. doi: 10.1016/j.plrev.2017.11.012
  24. Peyrard M., Bishop A.R. Statistical Mechanics of a Nonlinear Model for DNA Denaturation. Physical Review Letters. 1989;62:2755-2758. doi: 10.1103/PhysRevLett.62.2755
  25. Alexandrov B.S., Gelev V., Monisova Y., Alexandrov L.B., Bishop A.R., Rasmussen K.O., Usheva A. A nonlinear dynamic model of DNA with a sequence-dependent stacking term. Nucleic Acids Res. 2009;37(7):2405-2410. doi: 10.1093/nar/gkp016
  26. Yakushevich L.V., Krasnobaeva L.A. Forced Oscillations of DNA Bases. Biophysics. 2016;61(2):241-250. doi: 10.1134/S000635091602024X
  27. Grinevich A.A., Yakushevich L.V. The influence of the DNA torque on the dynamics of transcription bubbles in plasmid PTTQ18. Journal of Theoretical Biology. 2018;453:68-77. doi: 10.1016/j.jtbi.2018.04.036
  28. Drobotenko M.I., Dzhimak S.S., Svidlov A.A., Basov A.A., Lyasota O.M., Baryshev M.G. A Mathematical Model for Basepair Opening in a DNA Double Helix Biophysics. 2018;63(2):177-182.
  29. Grinevich A.A., Yakushevich L.V. On the modeling of the motion of a transcription bubble under constant torque. Biophysics. 2016;61(4):539-546. doi: 10.1134/S0006350916040126
  30. Bockelmann U., Thomen Ph., Essevaz-Roulet B., Viasnoff V., Heslot F. Unzipping DNA with optical tweezers: High sequence sensitivity and force flips. Biophysical Journal. 2002;82:1537-1553. doi: 10.1016/S0006-3495(02)75506-9
  31. Xie X., Zubarev R.A. Isotopic Resonance Hypothesis: Experimental Verification by Escherichia coli Growth Measurements. Scientific reports. 2015;5(9215). doi: 10.1038/srep09215
Table of Contents Original Article
Math. Biol. Bioinf.
2019;14(2):612-624
doi: 10.17537/2019.14.612
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

  Copyright IMPB RAS © 2005-2024