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In Vitro and Computational Approaches to Untangle the Binding Mechanism of Galangin with Calf Thymus DNA

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Abstract

Flavonoids have potential applications in the nutraceutical, medicinal, pharmaceutical and cosmetic fields. The binding of flavonoids with DNA could unravel essential information required for the design of novel and effective chemical agents. The present paper describes the interaction of a flavonoid and a potent anticancer drug, galangin (GAL) with calf thymus DNA (ct-DNA) by fluorescence, UV absorption, melting studies, viscosity measurements and molecular docking studies. A hyperchromic effect was noticed in the absorption spectra of ct-DNA in the presence of the GAL system, indicating the presence of a groove mode of binding. Furthermore, GAL persuaded the minor changes in ct-DNA viscosity, indicating a non-intercalative mode of binding. Fluorescence studies revealed that the GAL quenched the fluorescence intensity of ct-DNA-Hoechst, thereby indicating the interaction between GAL and ct-DNA. Fluorescence results obtained at 298, 308 and 318 K revealed that the fluorescence quenching of ct-DNA-Hoechst-GAL occurred through the static quenching mechanism. Thermodynamic parameters for ct-DNA-Hoechst-GAL were computed and suitable conclusions were drawn. The changes noticed in the conformation of ct-DNA upon interaction with GAL were evaluated in terms of molar ellipticity. It indicated a plausible interaction between ct-DNA and GAL. The molecular docking studies also confirmed the groove mode of binding in the ct-DNA-GAL system. Thus, this work helped to unravel the binding mechanism between GAL and ct-DNA.

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Data Availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

The authors thank the authorities of USIC, Karnatak University, Dharwad for providing the necessary facilities to carry out this research work. The authors also thank the UPE-FAR I, DST-PURSE-II program for providing the facility of Schrodinger software suit to perform the molecular docking studies.

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Authors and Affiliations

  1. Department of Chemistry, Karnatak University, Dharwad, 580003, Karnataka, India

    Roopa Naik & J. Seetharamappa

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  1. Roopa Naik
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Contributions

Contributed Authors–Roopa Naik and J. Seetharamappa. All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by Roopa Naik. The first draft of the manuscript was written by Roopa Naik. Manuscript revision and experimental platform was contributed by J. Seetharamappa. All authors read and approved the final manuscript.

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Correspondence to J. Seetharamappa.

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Highlights

• The exposure of bases pairs of ct-DNA to GAL was due to non-covalent interaction

• Fluorescence intensity of ct-DNA-Hoechst was quenched upon binding with GAL

• GAL interacted to ct-DNA by static quenching mechanism

• Viscosity, melting, probe binding assay, CD and docking studies confirmed the interaction and ruled out the intercalative mode of binding

• Molecular and biological processes of ct-DNA-GAL system was studied in vitro by theoretical and experimental methods

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Naik, R., Seetharamappa, J. In Vitro and Computational Approaches to Untangle the Binding Mechanism of Galangin with Calf Thymus DNA. J Fluoresc 33, 13–24 (2023). https://doi.org/10.1007/s10895-022-03033-x

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