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Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides

G-quadruplexes (GQs), a non-canonical form of DNA, are receiving a huge interest as target sites for potential applications in antiviral and anticancer drug treatments. The biological functions of GQs can be controlled by specifically binding proteins known as GQs binding proteins. Some of the GQs b...

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Autores principales: Patra, Satyajit, Claude, Jean-Benoît, Naubron, Jean-Valère, Wenger, Jérome
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8643622/
https://www.ncbi.nlm.nih.gov/pubmed/34791437
http://dx.doi.org/10.1093/nar/gkab1002
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author Patra, Satyajit
Claude, Jean-Benoît
Naubron, Jean-Valère
Wenger, Jérome
author_facet Patra, Satyajit
Claude, Jean-Benoît
Naubron, Jean-Valère
Wenger, Jérome
author_sort Patra, Satyajit
collection PubMed
description G-quadruplexes (GQs), a non-canonical form of DNA, are receiving a huge interest as target sites for potential applications in antiviral and anticancer drug treatments. The biological functions of GQs can be controlled by specifically binding proteins known as GQs binding proteins. Some of the GQs binding proteins contain an arginine and glycine-rich sequence known as RGG peptide. Despite the important role of RGG, the GQs-RGG interaction remains poorly understood. By single molecule measurements, the interaction dynamics can be determined in principle. However, the RGG–GQs interaction occurs at micromolar concentrations, making conventional single-molecule experiments impossible with a diffraction-limited confocal microscope. Here, we use a 120 nm zero-mode waveguide (ZMW) nanoaperture to overcome the diffraction limit. The combination of dual-color fluorescence cross-correlation spectroscopy (FCCS) with FRET is used to unveil the interaction dynamics and measure the association and dissociation rates. Our data show that the RGG–GQs interaction is predominantly driven by electrostatics but that a specific affinity between the RGG sequence and the GQs structure is preserved. The single molecule approach at micromolar concentration is the key to improve our understanding of GQs function and develop its therapeutic applications by screening a large library of GQs-targeting peptides and proteins.
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spelling pubmed-86436222021-12-06 Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides Patra, Satyajit Claude, Jean-Benoît Naubron, Jean-Valère Wenger, Jérome Nucleic Acids Res Molecular Biology G-quadruplexes (GQs), a non-canonical form of DNA, are receiving a huge interest as target sites for potential applications in antiviral and anticancer drug treatments. The biological functions of GQs can be controlled by specifically binding proteins known as GQs binding proteins. Some of the GQs binding proteins contain an arginine and glycine-rich sequence known as RGG peptide. Despite the important role of RGG, the GQs-RGG interaction remains poorly understood. By single molecule measurements, the interaction dynamics can be determined in principle. However, the RGG–GQs interaction occurs at micromolar concentrations, making conventional single-molecule experiments impossible with a diffraction-limited confocal microscope. Here, we use a 120 nm zero-mode waveguide (ZMW) nanoaperture to overcome the diffraction limit. The combination of dual-color fluorescence cross-correlation spectroscopy (FCCS) with FRET is used to unveil the interaction dynamics and measure the association and dissociation rates. Our data show that the RGG–GQs interaction is predominantly driven by electrostatics but that a specific affinity between the RGG sequence and the GQs structure is preserved. The single molecule approach at micromolar concentration is the key to improve our understanding of GQs function and develop its therapeutic applications by screening a large library of GQs-targeting peptides and proteins. Oxford University Press 2021-11-17 /pmc/articles/PMC8643622/ /pubmed/34791437 http://dx.doi.org/10.1093/nar/gkab1002 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Molecular Biology
Patra, Satyajit
Claude, Jean-Benoît
Naubron, Jean-Valère
Wenger, Jérome
Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides
title Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides
title_full Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides
title_fullStr Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides
title_full_unstemmed Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides
title_short Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides
title_sort fast interaction dynamics of g-quadruplex and rgg-rich peptides unveiled in zero-mode waveguides
topic Molecular Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8643622/
https://www.ncbi.nlm.nih.gov/pubmed/34791437
http://dx.doi.org/10.1093/nar/gkab1002
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