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Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting

We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5′-end that are complementary to nucleotides at the 3′-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more...

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Autores principales: Miranda, André, Santos, Tiago, Largy, Eric, Cruz, Carla
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7916057/
https://www.ncbi.nlm.nih.gov/pubmed/33557379
http://dx.doi.org/10.3390/ph14020121
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author Miranda, André
Santos, Tiago
Largy, Eric
Cruz, Carla
author_facet Miranda, André
Santos, Tiago
Largy, Eric
Cruz, Carla
author_sort Miranda, André
collection PubMed
description We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5′-end that are complementary to nucleotides at the 3′-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more conformations, one of which allows NCL binding. We found a decrease of polymorphism of G-quadruplex (G4)-forming sequences comparing to AS1411 and the G4 formation in presence of K(+) promotes the duplex folding. We also studied the binding properties of ligands TMPyP4, PhenDC3, PDS, 360A, and BRACO-19 in terms of stability, binding, topology maintenance of AS1411-N6, and NCL recognition. The melting experiments revealed promising stabilizer effects of PhenDC3, 360A, and TMPyP4, and the affinity calculations showed that 360A is the most prominent affinity ligand for AS1411-N6 and AS1411. The affinity determined between AS1411-N6 and NCL denoting a strong interaction and complex formation was assessed by PAGE in which the electrophoretic profile of AS1411-N6 showed bands of the dimeric form in the presence of the ligands and NCL.
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spelling pubmed-79160572021-03-01 Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting Miranda, André Santos, Tiago Largy, Eric Cruz, Carla Pharmaceuticals (Basel) Article We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5′-end that are complementary to nucleotides at the 3′-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more conformations, one of which allows NCL binding. We found a decrease of polymorphism of G-quadruplex (G4)-forming sequences comparing to AS1411 and the G4 formation in presence of K(+) promotes the duplex folding. We also studied the binding properties of ligands TMPyP4, PhenDC3, PDS, 360A, and BRACO-19 in terms of stability, binding, topology maintenance of AS1411-N6, and NCL recognition. The melting experiments revealed promising stabilizer effects of PhenDC3, 360A, and TMPyP4, and the affinity calculations showed that 360A is the most prominent affinity ligand for AS1411-N6 and AS1411. The affinity determined between AS1411-N6 and NCL denoting a strong interaction and complex formation was assessed by PAGE in which the electrophoretic profile of AS1411-N6 showed bands of the dimeric form in the presence of the ligands and NCL. MDPI 2021-02-04 /pmc/articles/PMC7916057/ /pubmed/33557379 http://dx.doi.org/10.3390/ph14020121 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Miranda, André
Santos, Tiago
Largy, Eric
Cruz, Carla
Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting
title Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting
title_full Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting
title_fullStr Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting
title_full_unstemmed Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting
title_short Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting
title_sort locking up the as1411 aptamer with a flanking duplex: towards an improved nucleolin-targeting
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7916057/
https://www.ncbi.nlm.nih.gov/pubmed/33557379
http://dx.doi.org/10.3390/ph14020121
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