Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics

Abstract This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) coval...

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Autores principales:	Athika Darumas Putri, Bayu Tri Murti, Suvardhan Kanchi, Myalowenkosi I. Sabela, Krishna Bisetty, Ashutosh Tiwari, Inamuddin, Abdullah M. Asiri
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/bfef183e2b5943489928e03a5faf1ef3
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spelling	oai:doaj.org-article:bfef183e2b5943489928e03a5faf1ef32021-12-02T15:09:28ZComputational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics10.1038/s41598-019-44378-x2045-2322https://doaj.org/article/bfef183e2b5943489928e03a5faf1ef32019-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-44378-xhttps://doaj.org/toc/2045-2322Abstract This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an “on/off”-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system’s π-π interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.Athika Darumas PutriBayu Tri MurtiSuvardhan KanchiMyalowenkosi I. SabelaKrishna BisettyAshutosh TiwariInamuddinAbdullah M. AsiriNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-14 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Athika Darumas Putri Bayu Tri Murti Suvardhan Kanchi Myalowenkosi I. Sabela Krishna Bisetty Ashutosh Tiwari Inamuddin Abdullah M. Asiri Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics
description	Abstract This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an “on/off”-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system’s π-π interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.
format	article
author	Athika Darumas Putri Bayu Tri Murti Suvardhan Kanchi Myalowenkosi I. Sabela Krishna Bisetty Ashutosh Tiwari Inamuddin Abdullah M. Asiri
author_facet	Athika Darumas Putri Bayu Tri Murti Suvardhan Kanchi Myalowenkosi I. Sabela Krishna Bisetty Ashutosh Tiwari Inamuddin Abdullah M. Asiri
author_sort	Athika Darumas Putri
title	Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics
title_short	Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics
title_full	Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics
title_fullStr	Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics
title_full_unstemmed	Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics
title_sort	computational studies on the molecular insights of aptamer induced poly(n-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/bfef183e2b5943489928e03a5faf1ef3
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Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics

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