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...

Full description

Saved in:
Bibliographic Details
Main Authors: Jumbri, Khairulazhar, Kassim, Mohd. Azlan, M. Yunus, Normawati, Abdul Rahman, Mohd. Basyaruddin, Ahmad, Haslina, Abdul Wahab, Roswanira
Format: Article
Language:English
Published: MDPI AG 2020
Subjects:
Online Access: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
Tags: Add Tag
No Tags, Be the first to tag this record!
Institution: Universiti Teknologi Malaysia
Language: English
id my.utm.90336
record_format eprints
spelling 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
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
language English
topic QD Chemistry
spellingShingle 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
description 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.
format 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
_version_ 1698696921245286400