The Possibility of Blocking the Process of DNA Base Pairs Opening by Hydrogen Peroxide
DOI:
https://doi.org/10.15407/ujpe64.6.500Keywords:
DNA base pairs, hydrogen peroxide, ion therapyAbstract
One of the most progressive methods of cancer treatment is the ion beam therapy. Simulations of the water radiolysis show that the most long-living species in the cell medium are hydrogen peroxide (H2O2) molecules. But up to the present time, the role of H2O2 molecules in the deactivation of cancer cells has not been determined yet. To understand the possible role of H2O2 in the ion beam therapy, the competitive interaction of H2O and H2O2 molecules with nucleic bases in a pair on the different stages of genetic information transfer is studied in the present work. The method of atom-atomic potential functions is used in the calculations. It is shown that some configurations of A·T, and G·C complementary pairs are stabilized much
better by an H2O2 molecule as compared to a water molecule. The formation of such interaction complexes can terminate the processes of DNA unzipping by enzymes and consequently block the genetic information transfer processes in cancer cells during the ion beam treatment. An experimental method of verification of the interaction of hydrogen peroxide with nucleic base pairs is proposed.
References
W.H. Bragg, R. Kleeman. LXXIV. On the ionization curves of radium. The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science 48, 726 (1904). https://doi.org/10.1080/14786440409463246
E. Surdutovich, A.V. Yakubovich, A.V. Solov'yov. Multiscale approach to radiation damage induced by ion beams: complex DNA damage and effects of thermal spikes. Europ. Phys. J. D 60, 101 (2010). https://doi.org/10.1140/epjd/e2010-00232-3
M. Kr?amer, M. Durante. Ion beam transport calculations and treatment plans in particle therapy. Eur. Phys. J. D 60, 195 (2010). https://doi.org/10.1140/epjd/e2010-00077-8
P.L. Olive. The role of DNA single- and double-strand breaks in cell killing by ionizing radiation. Radiation Research 150, 11 (1998). https://doi.org/10.2307/3579807
C.M. Gustafsson. Mechanistic Studies of DNA Repair (Royal Swedish Academy of Sciences, 2015).
M.S. Kreipl, W. Friedland, H.G. Paretzke. Time- and space-resolved Monte Carlo study of water radiolysis for photon, electron and ion irradiation. Radiation and Environmental Biophysics 48, 11 (2008). https://doi.org/10.1007/s00411-008-0194-8
S. Uehara, H. Nikjoo. Monte Carlo simulation of water radiolysis for low-energy charged particles. Journal of Radiation Research 47, 69 (2006). https://doi.org/10.1269/jrr.47.69
D. Boscolo, M. Kr?amer, M. Durante, M.C. Fuss, E. Scifoni. Trax-chem: A pre-chemical and chemical stage extension of the particle track structure code trax in water targets. Chemical Physics Letters 698, 11 (2018). https://doi.org/10.1016/j.cplett.2018.02.051
D.V. Piatnytskyi, O.O. Zdorevskyi, S.M. Perepelytsya, S.N. Volkov. Understanding the mechanism of DNA deactivation in ion therapy of cancer cells: hydrogen peroxide action. Europ. Phys. J. D 69, 255 (2015). https://doi.org/10.1140/epjd/e2015-60210-9
D.V. Piatnytskyi, S.N. Volkov. Complexes of hydrogen peroxide and DNA phosphate group in quantum-chemical calculations. Biophys. Bulletin 39, 5 (2018). https://doi.org/10.26565/2075-3810-2018-39-01
O. Zdorevskyi, D. Piatnytskyi, S.N. Volkov. Blocking of DNA specific recognition sites by hydrogen peroxide molecules in the process of ion beam therapy of cancer cells. arXiv preprint , arXiv:1811.11026 (2018). https://doi.org/10.15407/dopovidi2019.06.082
C. Bustamante, Z. Bryant, S.B. Smith. Ten years of tension: single-molecule DNA mechanics. Nature 6921, 423 (2003). https://doi.org/10.1038/nature01405
U. Bockelmann, Ph. Thomen, B. Essevaz-Roulet, V. Viasnoff, F. Heslot. Unzipping DNA with optical tweezers: high sequence sensitivity and force flips. Biophys. J. 82, 1537 (2002). https://doi.org/10.1016/S0006-3495(02)75506-9
J.M. Huguet, C.V. Bizarro, N. Forns, S.B. Smith, C. Bustamante, F. Ritort. Single-molecule derivation of salt dependent base-pair free energies in DNA. Proc. of the Nat. Acad. of Sci. 107, 15431 (2010). https://doi.org/10.1073/pnas.1001454107
K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, A.D. Mackerell. Charmm general force field: A force field for drug-like molecules compatible with the charmm all-atom additive biological force fields. J. Computat. Chem. 31, 671 (2010). https://doi.org/10.1002/jcc.21367
T.E. Cheatham, D.A. Case. Twenty-five years of nucleic acid simulations. Biopolymers 99, 969 (2013). https://doi.org/10.1002/bip.22331
R Lavery. Modeling nucleic acids: fine structure, flexibility and conformational transitions. Adv. Comput. Biol. 1, 69 (1994).
J.W. Eaton, D. Bateman, S. Hauberg, R. Wehbring. GNU Octave Version 4.2.1 Manual: a High-Level Interactive Language for Numerical Computations (2017).
V.I. Poltev, N.V. Shulyupina. Simulation of interactions between nucleic acid bases by refined atom-atom potential functions. J. of Biomol. Struct. and Dynamics 4, 739 (1986). https://doi.org/10.1080/07391102.1986.10508459
V.B. Zhurkin, V.I. Poltev, V.L. Florent'ev. Atom-atomic potential functions for conformational calculations of nucleic acids. Molekul. Biolog. 14, 1116 (1980).
S.A. Clough, Y. Beers, G.P. Klein, L.S. Rothman. Dipole moment of water from Stark measurements of H2O, HDO, and D2O. J. Chem. Phys. 59, 2254 (1973). https://doi.org/10.1063/1.1680328
J.T. Massey, D.R. Bianco. The microwave spectrum of hydrogen peroxide. J. Chem. Phys. 22, 442 (1954). https://doi.org/10.1063/1.1740088
S.T. Moin, T.S. Hofer, B.R. Randolf, B.M. Rode. An ab initio quantum mechanical charge field molecular dynamics simulation of hydrogen peroxide in water. Computat. Theor. Chem. 980, 15 (2012). https://doi.org/10.1016/j.comptc.2011.11.006
E.A. Orabi, A.M. English. A simple additive potential model for simulating hydrogen peroxide in chemical and biological systems. J. Chem. Theory Computat. 14, 2808 (2018). https://doi.org/10.1021/acs.jctc.8b00246
B.E. Hingerty, R.H. Ritchie, T.L. Ferrell, J.E. Turner. Dielectric effects in biopolymers: The theory of ionic saturation revisited. Biopolymers 24, 427 (1985). https://doi.org/10.1002/bip.360240302
S. Diekmann. Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biology 205, 787 (1989). https://doi.org/10.1016/0022-2836(89)90324-0
X.-J. Lu, W.K. Olson. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucl. Acids Research 31, 5108 (2003). https://doi.org/10.1093/nar/gkg680
W. Humphrey, A. Dalke, K. Schulten. VND: visual molecular dynamics.J. Mol. Graphics 14, 33 (1996). https://doi.org/10.1016/0263-7855(96)00018-5
O. Zdorevskyi, S.N. Volkov. Possible scenarios of DNA double-helix unzipping process in single-molecule manipulation experiments. Europ. Biophys. J. 47, 917 (2018). https://doi.org/10.1007/s00249-018-1313-3
E.S. Kryachko, S.N. Volkov. Preopening of the DNA base pairs. Intern. J. Quant. Chem. 82, 193 (2001). https://doi.org/10.1002/qua.1040
E. Giudice, P. V?arnai, R. Lavery. Base pair opening within b-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Phys. Phys. D 31, 1434 (2003). https://doi.org/10.1093/nar/gkg239
V.I. Poltev, E.H. Gonzalez, A.V. Teplukhin. Possible role of rare tautomers of nucleic bases in mutagenesis: Effect of hydration on tautomer equilibrium. Molecular Biology 29, 213 (1995).
L. Gorb, Y. Podolyan, P. Dziekonski, W.A. Sokalski, J. Leszczynski. Double-proton transfer in adenine-thymine and guanine-cytosine base pairs. A post-Hartree-Fock ab initio study. J. Amer. Chem. Soc. 126, 10119 (2004). https://doi.org/10.1021/ja049155n
J.A. Dobado, J. Molina. Adenine-hydrogen peroxide system: DFT and MP2 investigation. J. Phys. Chem. A 103, 4755 (1999). https://doi.org/10.1021/jp990671n
S.N. Volkov, E.V. Paramonova, A.V. Yakubovich, A.V. Solov'yov. Micromechanics of base pair unzipping in the DNA duplex. J. Phys.: Condensed Matter 24, 035104 (2011). https://doi.org/10.1088/0953-8984/24/3/035104
B. Prescott, W. Steinmetz, G.J. Thomas, jr. Characterization of DNA structures by laser Raman spectroscopy. Biopolymers: Original Research on Biomolecules 23, 235 (1984). https://doi.org/10.1002/bip.360230206
V.Y. Maleev, M.A. Semenov, A.I. Gasan, V.A. Kashpur. Physical properties of the DNA-water system. Biofizika 38, 768 (1993).
R. Galletto, M.J. Jezewska, W. Bujalowski. Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: quantitative analysis of the rate of the dsDNA unwinding, processivity and kinetic step-size of the Escherichia coli DNAb helicase using rapid quench-flow method. J. Mol. Biol. 343, 83 (2004). https://doi.org/10.1016/j.jmb.2004.07.055
Downloads
Published
How to Cite
Issue
Section
License
Copyright Agreement
License to Publish the Paper
Kyiv, Ukraine
The corresponding author and the co-authors (hereon referred to as the Author(s)) of the paper being submitted to the Ukrainian Journal of Physics (hereon referred to as the Paper) from one side and the Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine, represented by its Director (hereon referred to as the Publisher) from the other side have come to the following Agreement:
1. Subject of the Agreement.
The Author(s) grant(s) the Publisher the free non-exclusive right to use the Paper (of scientific, technical, or any other content) according to the terms and conditions defined by this Agreement.
2. The ways of using the Paper.
2.1. The Author(s) grant(s) the Publisher the right to use the Paper as follows.
2.1.1. To publish the Paper in the Ukrainian Journal of Physics (hereon referred to as the Journal) in original language and translated into English (the copy of the Paper approved by the Author(s) and the Publisher and accepted for publication is a constitutive part of this License Agreement).
2.1.2. To edit, adapt, and correct the Paper by approval of the Author(s).
2.1.3. To translate the Paper in the case when the Paper is written in a language different from that adopted in the Journal.
2.2. If the Author(s) has(ve) an intent to use the Paper in any other way, e.g., to publish the translated version of the Paper (except for the case defined by Section 2.1.3 of this Agreement), to post the full Paper or any its part on the web, to publish the Paper in any other editions, to include the Paper or any its part in other collections, anthologies, encyclopaedias, etc., the Author(s) should get a written permission from the Publisher.
3. License territory.
The Author(s) grant(s) the Publisher the right to use the Paper as regulated by sections 2.1.1–2.1.3 of this Agreement on the territory of Ukraine and to distribute the Paper as indispensable part of the Journal on the territory of Ukraine and other countries by means of subscription, sales, and free transfer to a third party.
4. Duration.
4.1. This Agreement is valid starting from the date of signature and acts for the entire period of the existence of the Journal.
5. Loyalty.
5.1. The Author(s) warrant(s) the Publisher that:
– he/she is the true author (co-author) of the Paper;
– copyright on the Paper was not transferred to any other party;
– the Paper has never been published before and will not be published in any other media before it is published by the Publisher (see also section 2.2);
– the Author(s) do(es) not violate any intellectual property right of other parties. If the Paper includes some materials of other parties, except for citations whose length is regulated by the scientific, informational, or critical character of the Paper, the use of such materials is in compliance with the regulations of the international law and the law of Ukraine.
6. Requisites and signatures of the Parties.
Publisher: Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine.
Address: Ukraine, Kyiv, Metrolohichna Str. 14-b.
Author: Electronic signature on behalf and with endorsement of all co-authors.
.png){kind=small}
