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Fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus DNA


Citation

Jumbri, Khairulazhar and Kassim, Mohd Azlan and Mohamad Yunus, Normawati and Abdul Rahman, Mohd Basyaruddin and Ahmad, Haslina and Abdul Wahab, Roswanira (2020) Fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus DNA. Processes, 8 (1). art. no. 13. pp. 1-17. ISSN 2227-9717

Abstract

This work presents a molecular level investigation on the nature and mode of binding between imidazolium-based ionic liquids (ILs) ([Cnbim]Br where n = 2, 4, 6) with calf thymus DNA. This investigation offers valuable insight into the mechanisms of interactions that can affect the structural features of DNA and possibly cause the alteration or inhibition of DNA function. To expedite analysis, the study resorted to using molecular docking and COnductor like Screening MOdel for Real Solvents (COSMO-RS) in conjunction with fluorescence spectroscopic data for confirmation and validation of computational results. Both the fluorescence and docking studies consistently revealed a weak interaction between the two molecules, which corresponded to the binding energy of a stable docking conformation in the range of −5.19 to −7.75 kcal mol−1. As predicted, the rod-like structure of imidazolium-based ILs prefers to bind to the double-helix DNA through a minor groove. Interestingly, the occurrence of T-shape π-π stacking was observed between the amine group in adenine that faces the aromatic ring of imidazole. In addition, data of COSMO-RS for the interaction of individual nucleic acid bases to imidazolium-based ILs affirmed that ILs showed a propensity to bind to different bases, the highest being guanine followed by cytosine, thymine, uracil, and adenine.


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Additional Metadata

Item Type: Article
Divisions: Faculty of Science
DOI Number: https://doi.org/10.3390/pr8010013
Publisher: MDPI
Keywords: COSMO-RS; Docking; Ionic liquids; DNA; Binding energy
Depositing User: Nabilah Mustapa
Date Deposited: 04 May 2020 15:52
Last Modified: 04 May 2020 15:52
Altmetrics: http://www.altmetric.com/details.php?domain=psasir.upm.edu.my&doi=10.3390/pr8010013
URI: http://psasir.upm.edu.my/id/eprint/38200
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