Fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus DNA
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 feature...
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my.utm.903362021-04-30T14:48:37Z http://eprints.utm.my/id/eprint/90336/ Fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus DNA Jumbri, Khairulazhar Kassim, Mohd. Azlan M. Yunus, Normawati Abdul Rahman, Mohd. Basyaruddin Ahmad, Haslina Abdul Wahab, Roswanira QD Chemistry 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 ofDNAand possibly cause the alteration or inhibition ofDNAfunction. 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. MDPI AG 2020-01-01 Article PeerReviewed application/pdf en http://eprints.utm.my/id/eprint/90336/1/RoswaniraAbdulWahab2020_FluorescenceandMolecularSimulationStudies.pdf Jumbri, Khairulazhar and Kassim, Mohd. Azlan and M. 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). pp. 1-17. ISSN 2227-9717 http://dx.doi.org/10.3390/pr8010013 DOI:10.3390/pr8010013 |
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QD Chemistry Jumbri, Khairulazhar Kassim, Mohd. Azlan M. Yunus, Normawati Abdul Rahman, Mohd. Basyaruddin Ahmad, Haslina Abdul Wahab, Roswanira Fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus DNA |
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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 ofDNAand possibly cause the alteration or inhibition ofDNAfunction. 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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Article |
author |
Jumbri, Khairulazhar Kassim, Mohd. Azlan M. Yunus, Normawati Abdul Rahman, Mohd. Basyaruddin Ahmad, Haslina Abdul Wahab, Roswanira |
author_facet |
Jumbri, Khairulazhar Kassim, Mohd. Azlan M. Yunus, Normawati Abdul Rahman, Mohd. Basyaruddin Ahmad, Haslina Abdul Wahab, Roswanira |
author_sort |
Jumbri, Khairulazhar |
title |
Fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus DNA |
title_short |
Fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus DNA |
title_full |
Fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus DNA |
title_fullStr |
Fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus DNA |
title_full_unstemmed |
Fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus DNA |
title_sort |
fluorescence and molecular simulation studies on the interaction between imidazolium-based ionic liquids and calf thymus dna |
publisher |
MDPI AG |
publishDate |
2020 |
url |
http://eprints.utm.my/id/eprint/90336/1/RoswaniraAbdulWahab2020_FluorescenceandMolecularSimulationStudies.pdf http://eprints.utm.my/id/eprint/90336/ http://dx.doi.org/10.3390/pr8010013 |
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1698696921245286400 |