Density Functional Theory Investigation on Muon Hyperfine Interaction in Methylated Guanine-Cytosine Double-Strand DNA

Ammaina Jamaludin; Shukri Sulaiman; Wan Nuradhilah Zaharim; Ang Lee Sin

doi:10.5614/j.math.fund.sci.2024.56.3.2

Authors

Ammaina Jamaludin Computational Physics Laboratory, School of Distance Education, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
Shukri Sulaiman Computational Physics Laboratory, School of Distance Education, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
Wan Nuradhilah Zaharim Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
Ang Lee Sin Faculty of Applied Sciences, Universiti Teknologi MARA, Perlis Branch, Arau Campus, 02600 Arau, Perlis, Malaysia

DOI:

https://doi.org/10.5614/j.math.fund.sci.2024.56.3.2

Keywords:

DFT, DNA, hyperfine interaction, methylation, muon

Abstract

The aims of this study were to determine the most likely Mu trapping sites based on total energy consideration as well as identifying the associated muon hyperfine coupling constant of 1, 2, and 3 methylated guanine-cytosine base pair double-strand DNA. The Density Functional Theory method was used at B3LYP/6-31G level of theory to accomplish the objectives of the investigation. The relative energy in the 3 methylated guanine-cytosine base pair double-strand DNA molecule showed that N7 sites in the guanine base have the lowest energy, followed by N3, and C8 sites. It was found that the addition of a methyl group at the C5 atom in the cytosine base does change the stability of the C8 sites in the 3 methylated guanine-cytosine base pair double-strand DNA molecule, but the associated muon hyperfine coupling constant (HFCC) is not affected. The results of this study indicate that there will be no overlaps in the resonance dips due to N7, N3, and all C8 sites of the guanine bases and N3, C5, and C6 sites of the cytosine bases in the Avoided Level Crossing Muon Spin Resonance spectrum.

References

Watson, J.D. & Crick, F.H., Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid, Nature, 171(4356), pp. 737-738, 1953.

Holmlin, R.E., Dandliker, P.J. & Barton, J.K., Charge Transfer Through the DNA Base Stack, Angewandte Chemie International Edition in English, 36(24), pp. 2714-2730, 1997.

Singal, R. & Ginder, G.D., DNA Methylation, Blood, The Journal of the American Society of Hematology, 93(12), pp. 4059-4070, 1999.

Almatarneh, M.H., Kayed, G.G., Al Abbad, S.S., Alsunaidi, Z.H., Al-Sheraideh, M.S. & Zhao, Y., Mechanistic Study on DNA Mutation of the Cytosine Methylation Reaction At C5 Position, Arabian Journal of Chemistry, 15(8), 103956, 2022.

Hihath, J., Guo, S., Zhang, P. & Tao, N., Effects of Cytosine Methylation on DNA Charge Transport, Journal of Physics: Condensed Matter, 24(16), 164204, 2012.

Kumar, S., Chinnusamy, V. & Mohapatra, T., Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond, Frontiers in Genetics, 9, 640, 2018.

Labet, V., Morell, C., Cadet, J., Eriksson, L.A. & Grand, A., Hydrolytic Deamination of 5-Methylcytosine in Protic Medium: A Theoretical Study, The Journal of Physical Chemistry A, 113(11), pp. 2524-2533, 2009.

Wiebauer, K., Neddermann, P., Hughes, M. & Jiricny, J., The Repair of 5-Methylcytosine Deamination Damage, DNA Methylation: Molecular Biology and Biological Significance, pp. 510-522, 1993.

Walker, D.C., Muonium. A Light Isotope of Hydrogen, The Journal of Physical Chemistry, 85(26), pp. 3960-3971, 1981.

Ghandi, K. & MacLean, Muons as Hyperfine Interaction Probes in Chemistry, Hyperfine Interactions, 230, pp. 17-34, 2015.

Mohr, P.J., Taylor, B.N. & Newell, D.B., CODATA Recommended Values of the Fundamental Physical Constants, 2006, Journal of Physical and Chemical Reference Data, 37(3), pp. 1187-1284, 2008.

Torikai, E., Nagamine, K., Pratt, F.L., Watanabe, I., Ikedo, Y., Urabe, H. & Grimm, H., Probing Electron Transfer in DNA-new Life Science with Muons, Hyperfine interactions, 138, pp. 509-513, 2001.

Hubbard, P.L., Oganesyan, V.S., Sulaimanov, N., Butt, J.N. & Jayasooriya, U.A., Avoided Level Crossing Muon Spectroscopy of Free Radicals Formed by Muonium Addition to the Constituents of DNA, The Journal of Physical Chemistry A, 108(42), pp. 9302-9309, 2004.

Scheicher, R.H., Torikai, E., Pratt, F.L., Nagamine, K. & Das, T.P., Comparative Theoretical Study of Hyperfine Interactions of Muonium in A-and B-form DNA, in HFI/NQI 2004: Proceedings of the 13th International Conference on Hyperfine Interactions and 17th International Symposium on Nuclear Quadrupole Interactions (HFI/NQI 2004) Bonn, Germany, Springer Berlin Heidelberg, pp. 53-57, 2004.

Torikai, E., Hori, H., Hirose, E. & Nagamine, K., Electron Transfer in DNA Probed by the Muon Labelling Method: A New Interpretation, Physica B: Condensed Matter, 374, pp. 441-443, 2006.

Hubbard, P.L., Tani, A., Oganesyan, V.S., Butt, J.N., Cottrell, S.P. & Jayasooriya, U.A., Different Responses to Muon Implantation in Single-and Double-stranded DNA, Physica B: Condensed Matter, 374, pp. 437-440, 2006.

Nagamine, K., Torikai, E., Shimomura, K., Ikedo, Y. & Schultz, J.S., Molecular Radiation Biological Effect in Wet Protein and DNA Observed in the Measurements of Labeled Electron with Muons, Physica B: Condensed Matter, 404(5-7), pp. 953-956, 2009.

Pant, A.D., Sugawara, Y., Yanagihara, I., Khanal, G.P., Shiraki, I., Higemoto, W., Shimomura, K., Ishida, K., Pratt, F.L., Torikai, E. & Nagamine, K., Hydration Effect on Electron Transfer in Cytochrome C Monitored by SR, in Proceedings of the 2nd International Symposium on Science at J-PARC-Unlocking the Mysteries of Life, Matter and the Universe, pp. 033007, 2015.

McKenzie, I., Hydrogen-atom Addition to Nucleobases in the Solid State: Characterization of the Corresponding Muoniated Radicals Using SR, The Journal of Physical Chemistry B, 123(21), pp. 4540-4549, 2019.

Oganesyan, V.S., Hubbard, P.L., Butt, J.N. & Jayasooriya, U.A., Laying the Foundation for Understanding Muon Implantation in DNA: Ab Initio DFT Calculations of the Nucleic Acid Base Muonium Adducts, Physica B: Condensed Matter, 326(1-4), pp. 25-29, 2003.

Scheicher, R.H., Das, T.P., Torikai, E., Pratt, F.L. & Nagamine, K., First-principles Study of Muonium in A-and B-form DNA, Physica B: Condensed Matter, 374, pp. 448-450, 2006.

Goli, M. & Jalili, S., How Intrinsic Nuclear Nonadiabaticity Affects Molecular Structure, Electronic Density, and Conformational Stability: Insights from the Multicomponent DFT Calculations of Mu/H Isotopologues, International Journal of Quantum Chemistry, 118(22), e25758, 2018.

Zaharim, W.N., Rozak, H., Sulaiman, S., Ahmad, S.N.A., Baseri, D.F.H., Mohd-Tajudin, S.S., Sin, A.L. & Watanabe, I., Density Functional Theory Investigation of Hyperfine Interaction in DNA Nucleobase and Nucleotide Muoniated Radicals, Journal of the Physical Society of Japan, 90(4), pp. 044301, 2021.

Zaharim, W.N., Ahmad, S.N., Sulaiman, S., Rozak, H., Hasan Baseri, D.F., Mohamad Rosli, N.A., Mohd-Tajudin, S.S., Ang, L.S. & Watanabe, I., Density Functional Theory Study of 12mer Single-strand Guanine Oligomer and Associated Muon Hyperfine Interaction, ACS Omega, 6(44), pp. 29641-29650, 2021.

Jamaludin, A., Zaharim, W.N., Sulaiman, S., Rozak, H., Sin, A.L. & Watanabe, I., Density Functional Theory Investigation of Muon Hyperfine Interaction in Guanine-cytosine Double-strand DNA, Journal of the Physical Society of Japan, 91(2), 024301, 2022.

Zaharim, W.N., Sulaiman, S., Abu Bakar, S.N., Ismail, N.E., Jamaludin, A., Rozlan, A.F., Sin, A.L. & Watanabe, I., Density Functional Theory Study of Muon Hyperfine Interactions in 12mer Single-strand Adenine, Cytosine, and Thymine Oligomers, Journal of the Physical Society of Japan, 91(9), 094301, 2022.

Hanwell, M.D., Curtis, D.E., Lonie, D.C., Vandermeersch, T., Zurek, E. & Hutchison, G.R., Avogadro: An Advanced Semantic Chemical Editor, Visualization, and Analysis Platform, Journal of cheminformatics, 4, pp. 1-17, 2012.

Frisch, A., Gaussian 09W Reference, Wallingford, USA, 25p, 2009.

Ahmad, S.N., Zaharim, W.N., Sulaiman, S., Hasan Baseri, D.F., Mohd Rosli, N.A., Ang, L.S., Yahaya, N.Z. & Watanabe, I., Density Functional Theory Studies of the Electronic Structure and Muon Hyperfine Interaction in [Au25 (SR)18] 0 and [Au25 (SeR) 18] 0 Nanoclusters, ACS omega, 5(51), pp. 33253-33261, 2020.

Moller. J.S., Ceresoli, D., Lancaster, T., Marzari, N. & Blundell, S.J., Quantum States of Muons in Fluorides, Physical Review, 87(12), 121108, 2013.

Yu, D., Percival, P.W., Brodovitch, J.C., Leung, S.K., Kiefl, R.F., Venkateswaran, K. & Cox, S.F., Structure and Intramolecular Motion of Muonium-substituted Cyclohexadienyl Radicals, Chemical physics, 142(2), pp. 229-236, 1990.

Percival, P.W., Addison-Jones, B., Brodovitch, J.C., Ghandi, K. & Schuth, J., Free Radicals Formed by H (Mu) Addition to Pyrene, Canadian journal of chemistry, 77(3), pp. 326-331, 1999.

Brodovitch, J.C., Addison-Jones, B., Ghandi, K., McKenzie, I., Percival, P.W. & Schuth, J., Free Radicals Formed by H (Mu) Addition to Fluoranthene, Canadian journal of chemistry, 81(1), pp. 1-6, 2003.

Roduner, E., The Positive Muon as a Probe in Free Radical Chemistry: Potential and Limitations of The SR Techniques, Springer Science & Business Media, 2012.

Zaharim, W.N., Shukri, S., Mohd Tajudin, S.S., Abu Bakar, S.N., Ismail, N.E., Rozak, H. & Watanabe, I., Basis Set Effects in Density Functional Theory Calculation of Muoniated Cytosine Nucleobase, Key Engineering Materials, 860, pp. 282-287, 2020.

Dennington, R.D.I.I., Keith, T.A. & Millam, J.M., GaussView, version 6.0. 16, Semichem Inc Shawnee Mission KS, 2016.

Bertran, J., Oliva, A., Rodr?guez-Santiago, L. & Sodupe, M., Single Versus Double Proton-transfer Reactions in Watson-crick Base Pair Radical Cations. a Theoretical Study, Journal of the American Chemical Society, 120(32), pp. 8159-8167, 1998.

Bera, P.P. & Schaefer III, H.F., SG?H)??C and G?(C?H)? Radicals Derived from the Guanine Cytosine Base Pair Cause DNA Subunit Lesions, Proceedings of the National Academy of Sciences, 102(19), pp. 6698-6703, 2005.

Rosenberg, J.M., Seeman, N.C., Day, R.O. & Rich, A., RNA Double Helices Generated from Structures of Double Helical Dinucleoside Phosphates, Biochemical and Biophysical Research Communications, 69(4), pp. 979-987, 1976.

Cartmell, E. & Fowles, G.W.A., Valency and Molecular Structure55666, international reviews in physical chemistry, 2013.