Ukrainian Journal of Physical Optics
2024 Volume 25, Issue 4
MECHANISMS AND PARAMETERS OF THE BINDING OF THE FLAVONOID QUERCETIN TO DNA IN AN AQUEOUS SOLUTION
S. Kutovyy, D. Fedorovich, R. Savchuk, A. Naumenko and L. Palchykivska
S. Kutovyy Taras Shevchenko National University of Kyiv, Faculty of Physics; D. Fedorovich, Taras Shevchenko National University of Kyiv, Faculty of Physics; R. Savchuk, Taras Shevchenko National University of Kyiv, Faculty of Physics; A. Naumenko Taras Shevchenko National University of Kyiv, Faculty of Physics; L. Palchykivska Institute of Molecular Biology and Genetics (NAS of Ukraine), Department of Molecular and Quantum Biophysics
Ukr. J. Phys. Opt.
Vol. 25
,
Issue 4 , pp. 04008 - 04021 (2024).
doi:10.3116/16091833/Ukr.J.Phys.Opt.2024.04008
ABSTRACT
Keywords:
DNA, quercetin, McGhee-von Hippel binding equation, absorption spectra, fluorescence spectra.
UDC:
535.34; 535.37
- Srivastava, S., Somasagara, R. R., Hegde, M., Nishana, M., Kumar, Tadi S., Srivastava, M., Choudhary, B., and Raghavan, S. C. (2016). Quercetin, a Natural Flavonoid Interacts with DNA, Arrests Cell Cycle and Causes Tumor Regression by Activating Mitochondrial Pathway of Apoptosis. Scientific Reports, 6, 24049. doi:10.1038/srep24049
- Aghababaei, F. and Hadidi, M. (2023). Recent Advances in Potential Health Benefits of Quercetin. Pharmaceuticals, 16(7), 1020. doi:10.3390/ph16071020
- Bentz, A. B. (2009). A review of quercetin: chemistry, antioxidant properties, and bioavailability. Journal of Young Investigators, 19.
- David, A. V. A., Arulmoli, R. and Parasuraman, S. (2016). Overviews of biological importance of quercetin: a bioactive flavonoid. Pharmacognosy Reviews, 10(20), 84-89. doi:10.4103/0973-7847.194044
- Rauf, A., Imran, M., Khan, I. A., ur-Rehman, M., Gilani, S. A., Mehmood, Z., and Mubarak, M. S. (2018). Anticancer potential of quercetin: a comprehensive review. Phytotherapy Research, 32(11), 2109−2130. doi:10.1002/ptr.6155
- Sha,Y., Chen, X., Niu, B., and Chen, Q. (2017). The Interaction Mode of Groove Binding Between Quercetin and Calf Thymus DNA Based on Spectrometry and Simulation. Chemistry & Biodiversity, 14(10), e1700133. doi:10.1002/cbdv.201700133
- Kocharyan, G. H., Minasyan, S. H., and Tavadyan, L. A. (2016). Interaction of flavonoids: morin, quercetin and rutin, with DNA. Proceedings of Yerevan state University, Chemistry and Biology, 1, 49-54.
- Tu, B., Liu, Z. J., Chen, Z. F., Ouyang, Y., and Hu, Y. J. (2015). Understanding the structure-activity relationship between quercetin and naringenin: in vitro. RSC Advances, 5, 106171-106181. doi:10.1039/C5RA22551E
- Bhattacharjee S., Sengupta P. K., and Bhowmik S. (2017). Exploring the preferential interaction of quercetin with VEGF promoter G-quadruplex DNA and construction of a pH-dependent DNA-based logic gate. RSC Advances, 7, 37230-37240. doi:10.1039/C7RA05930B
- Marinić, M., Piantanida, I., Rusak, G., and Žinić, M. (2006). Interactions of quercetin and its lanthanide complex with double stranded DNA/RNA and single stranded RNA: Spectrophotometric sensing of poly G. Journal of Inorganic Biochemistry, 100(2): 288-298. doi:10.1016/j.jinorgbio.2005.11.013
- Ashraf, A. El-Bindary, Zeinab, M. Anwar, Taissir, El-Shafaie. (2021). Effect of some amino acids on the binding of quercetin and rutin flavonoids with DNA. Journal of Molecular Liquids, 334, 116131, 1-17. doi:10.1016/j.molliq.2021.116131
- Janjua N. K., Siddiq A., Yaqub A., Sabahat S., Qureshi R., and Haque S. (2009). Spectrophotometric analysis of flavonoid-DNA binding interactions at physiological conditions. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 74, 1135-1137. doi:10.1016/j.saa.2009.09.022
- Kanakis, C. D., Nafisi, S., Rajabi, M., Shadaloi, A., Tarantilis, P. A., Polissiou, M. G., Bariyanga J., and Tajmir-Riahi H. A. (2009). Structural analysis of DNA and RNA interactions with antioxidant flavonoids. Spectroscopy, 23(1), 29-43. doi:10.1155/2009/154321
- Hegde, A. H., Prashanth, S. N., and Seetharamappa, J. (2012). Interaction of antioxidant flavonoids with calf thymus DNA analyzed by spectroscopic and electrochemical methods. Journal of Pharmaceutical and Biomedical Analysis, 63, 40-46. doi:10.1016/j.jpba.2012.01.034
- Kanakis, C. D., Tarantilis, P. A., Polissiou, M. G., Diamantoglou, S., and Tajmir-Riahi, H. A. (2005). DNA interaction with naturally occurring antioxidant flavonoids quercetin, kaempferol, and delphinidin. Journal of Biomolecular Structure and Dynamics, 22(6), 719-724. doi:10.1080/07391102.2005.10507038
- Plaper, A., Golob, M., Hafner, I., Oblak, M., Solmajer, T., and Jerala, R. (2003). Characterization of quercetin binding site on DNA gyrase. Biochemical and Biophysical Research Communications, 306, 530-536. doi:10.1016/S0006-291X(03)01006-4
- Guaman Ortiz, L. M., Lombardi, P., Tillhon, M. and Scovassi, A. I. (2014). Berberine, an epiphany against cancer. Molecules, 19(8), 12349-12367. doi:10.3390/molecules190812349
- Seo, Y.-S., Yim, M.-J., Kim, B.-H., Kang, K.-R., Lee, S.-Y, Oh, J.-S., You, J.-S., Kim, S.-G., Yu, S.-J., Lee, G.-J., Kim, D.K., Kim, C.S., Kim, J.-S., Kim, J.-S. (2015). Berberine-induced anticancer activities in FaDu head and neck squamous cell carcinoma cells. Oncology Reports, 34(6), 3025-3034. doi:10.3892/or.2015.4312
- Grebinyk, A., Yashchuk, V., Bashmakova, N., Gryn, D., Hagemann, T., Naumenko, A., Kutsevol, N., Dandekar, T., Frohme M. (2019). A new triple system DNA-Nanosilver-Berberine for cancer therapy. Applied Nanoscience, 9(6), 945-956. doi:10.1007/s13204-018-0688-x
- Fu Ch., Guiping G., and Wang H. (2018). The Anticancer Effect of Sanguinarine: A Review. Current Pharmaceutical Design, 24(24), 2760-2764. doi:10.2174/1381612824666180829100601
- Ai X.,,Yu P., Peng L., Luo L., Liu J., Li S., Lai, X., Luan, F., Meng X. (2021). Berberine: A Review of its Pharmacokinetics Properties and Therapeutic Potentials in Diverse Vascular Diseases. Frontiers in Pharmacology, 12(Article 762654). doi:10.3389/fphar.2021.762654
- Maiti, M., and Kumar, G. S. (2010). Polymorphic Nucleic Acid Binding of Bioactive Isoquinoline Alkaloids and Their Role in Cancer. Review Article. Journal of Nucleic Acids, 2010 (Article ID 593408), 23 pages. doi:10.4061/2010/593408
- Bashmakova, N., Kutovyy, S., Yashchuk, V., Hovorun, D., Losytskyy, V., and Zaika, L. (2009). Optical spectroscopy studies of the interaction between a number of plant alkaloids and the DNA double helix in an aqueous solution. Ukrainian Journal of Physics, 54(5), 471-479.
- Gumenyuk V. G., Bashmakova N. V., Kutovyy S. Y., Yashchuk V. M., and Zaika L. A. (2011). Binding parameters of alkaloids berberine and sanguinarine to DNA. Ukrainian Journal of Physics, 56(6), 525-534. doi:10.15407/ujpe56.6.524
- Kutovyy S. Y., Savchuk R. S., Bashmakova N. V. (2014). Binding parameters of alkaloid sanguinarine with DNA. Bulletin of Taras Shevchenko National University of Kyiv. Series: Physics & Mathematics, No.3, 265-272.
- Gumenyuk, V., Kutovyy, S., Sych, T., Savchuk, R., and Bashmakova, N. (2014). Peculiarities of the binding of some small ligands to DNA. Molecular Crystals and Liquid Crystals, 589, 242-250. doi:10.1080/15421406.2013.872856
- Kutovyy, S. Y., Sych, T. P., and Zaika, L. A. (2014). Features of ethydium bromide and acridine orange binding to DNA. Bulletin of Taras Shevchenko National University of Kyiv. Series: Physics & Mathematics, No.3, 273-278.
- Kutovyy, S. Y., Savchuk, R. S., Bashmakova, N. V., Hovorun, D. M. and Zaika, L. A. (2018). Mechanisms and Parameters of the Binding of Amitozinoberamid to DNA in the Aqueous Solution, Ukrainian Journal of Physics, 63(8), 709-720. doi:10.15407/ujpe63.8.709
- Drugbank. https://www.drugbank.ca/drugs/DB04216.
- Domagała, S., Munshi, P., Ahmed, M., Guillot, B., and Jelsch, C. (2010). Structural analysis and multipole modelling of quercetin monohydrate - a quantitative and comparative study. Acta Crystallographica B, 67, 63-78. doi:10.1107/S0108768110041996
- Filip X., Grosu I.-G., Miclăuş M., and Filip C. (2013). NMR crystallography methods to probe complex hydrogen bonding networks: application to structure elucidation of anhydrous quercetin. CrystEngComm, 15, 4131−4142. doi:10.1039/c3ce40299a
- Filip, X. and Filip, C. (2015). Can the conformation of flexible hydroxyl groups be constrained by simple NMR crystallography approaches? The case of the quercetin solid forms. Solid State Nuclear Magnetic Resonance, 65, 21-28. doi:10.1016/j.ssnmr.2014.10.006
- Aparicio, S. A. (2010). Systematic computational study on flavonoids. International Journal of Molecular Sciences, 11, 2017−2038. doi:10.3390/ijms11052017
- Brovarets', O. O., and Hovorun, D. M. (2020). Conformational diversity of the quercetin molecule: a quantum-chemical view. Journal of Biomolecular Structures and Dynamics, 38, 2817−2836. doi:10.1080/07391102.2019.1656671
- Kutovyy, S., Savchuk, R., Bashmakova, N., Stanovyi, О., and Palchykivska, L. (2021). Vibrational spectra of quercetin and their interpretation with quantum-mechanical density-functional method. Ukrainian Journal of Physical Optics, 22, 181-197. doi:10.3116/16091833/22/4/181/2021
- Dall'Acqua, S., Miolo, G., Innocenti, G., and Caffieri, S. (2012). The Photodegradation of Quercetin: Relation to Oxidation. Molecules, 17(8), 8898-8907. doi:10.3390/molecules17088898
- Buchweitz, M., Kroon, P. A., Rich, G. T., and Wilde, P. J. (2016). Quercetin solubilisation in bile salts: A comparison with sodium dodecyl sulphate. Food Chemistry, 211, 356-364. doi:10.1016/j.foodchem.2016.05.034
- Raza, A., Xu, X., Xia, L., Xia, C., Tang, J., and Ouyang, Z. (2016). Quercetin-iron complex: synthesis, characterization, antioxidant, DNA binding, DNA cleavage, and antibacterial activity studies. Journal of Fluorescence, 26, 2023−2031. doi:10.1007/s10895-016-1896-y
- Momić, T., Savić, J. Z., Cernigoj, U., Trebše, P., and Vasić, V. M. (2007). Protolytic equilibria and photodegradation of quercetin in aqueous solution. Collections of Czechoslovak Chemical Communications, 72, 1447-60. doi:10.1135/cccc20071447
- Jurasekova, Z., Domingo, C., Garcia-Ramos, J. V., and Sanchez-Cortes, S. (2014). Effect of pH on the chemical modification of quercetin and structurally related flavonoids characterized by optical (UV-visible and Raman) spectroscopy. Physical Chemistry Chemical Physics, 16(25), 12802-12811. doi:10.1039/C4CP00864B
- Cornard, J. P., Dangleterre, L., and Lapouge, C. (2005). Computational and Spectroscopic Characterization of the Molecular and Electronic Structure of the Pb(II)-Quercetin Complex. The Journal of Physical Chemistry A, 109(44), 10044-10051. doi:10.1021/jp053506i
- Scatchard, G. (1949). The Attractions of Proteins for Small Molecules an Ions. Annals of the New York Academy of Sciences, 51, 660-672. doi:10.1111/j.1749-6632.1949.tb27297.x
- McGhee, J. D., and von Hippel, P. H. (1974). Theoretical Aspects of DNA-Protein Interactions: Co-operative and Non-co-operative Binding of Large Ligands to a One-dimensional Homogeneous Lattice. Journal of Molecular Biology, 86, 469-489. doi:10.1016/0022-2836(74)90031-X
-
Взаємодію флавоноїду кверцетину з макромолекулою ДНК у водному розчині досліджено методами оптичної спектроскопії – електронного поглинання та флуоресценції. На основі отриманих результатів побудовано залежності спектральних характеристик від відношення концентрацій N/c між парами основ ДНК і молекулами ліганду. За допомогою системи модифікованих рівнянь Скетчарда і МакГі-фон Гіппеля визначено параметри зв'язування кверцетину з ДНК. Користуючись системою модифікованих рівнянь Скетчарда та МакГі-фон Хіппеля, визначено параметри зв'язування кверцетину з ДНК. Для порівняння наведено параметри зв'язування з ДНК інших досліджених нами раніше молекул.
Ключові слова: ДНК, кверцетин, рівняння зв’язування МакГі - фон Хіппеля, спектри поглинання, спектри флуоресценції.
Ключові слова: ДНК, кверцетин, рівняння зв’язування МакГі - фон Хіппеля, спектри поглинання, спектри флуоресценції.
© Ukrainian Journal of Physical Optics ©