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Hydration of DNA-binding biological active compounds: EHF dielectrometry and molecular modeling results

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Abstract

We report hydration properties of several DNA-binding ligands (pharmaceutical drug caffeine; mutagens proflavine, ethidium bromide, propidium iodide; polyamines putrescine, spermine), which are able to interact with DNA in different modes via external binding, intercalation or minor groove binding. We show that the detection of the bound water molecules and the estimation of their amount in aqueous solutions of ligands can be efficiently carried out using the measurements of complex dielectric permittivity of the solutions in the millimeter range of radio waves. Our dielectrometric data are combined with the results of the molecular modeling including quantum chemical calculations and Monte Carlo simulations. We show that number of water molecules able to form hydrogen bonds with donor–acceptor groups of ligands correlates with hydration numbers taken from the literature or obtained in EHF dielectrometry experiment. The latter indicates that the EHF dielectrometry method is sensitive for the tightly bound water molecules.

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Acknowledgments

The study was supported in part by the SCST Programme of Implementation and Usage of GRID technologies for 2009–2013. The calculations were carried out using clusters of Institute for Scintillation Materials NASU and Institute for Radiophysics and Electronics NASU. The research which results are presented in the present paper was fulfilled due to the collaboration with Prof. O. Shishkin. The authors also thank Roman Zubatyuk (ISMA NASU) for the assistance in quantum chemical calculations.

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  1. Usikov Institute for Radiophysics and Electronics of National Academy of Sciences of Ukraine, 12 Ak. Proskura Str., Kharkiv, 61085, Ukraine

    Anna Victorovna Shestopalova, Daryna A. Pesina, Vsevolod A. Kashpur & Olga V. Khorunzhaya

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  1. Anna Victorovna Shestopalova
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  2. Daryna A. Pesina
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Correspondence to Anna Victorovna Shestopalova.

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Shestopalova, A.V., Pesina, D.A., Kashpur, V.A. et al. Hydration of DNA-binding biological active compounds: EHF dielectrometry and molecular modeling results. Struct Chem 27, 159–173 (2016). https://doi.org/10.1007/s11224-015-0695-4

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