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Single-molecule chemical denaturation of riboswitches

To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation t...

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Autores principales: Dalgarno, Paul A., Bordello, Jorge, Morris, Rhodri, St-Pierre, Patrick, Dubé, Audrey, Samuel, Ifor D. W., Lafontaine, Daniel A., Penedo, J. Carlos
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627600/
https://www.ncbi.nlm.nih.gov/pubmed/23446276
http://dx.doi.org/10.1093/nar/gkt128
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author Dalgarno, Paul A.
Bordello, Jorge
Morris, Rhodri
St-Pierre, Patrick
Dubé, Audrey
Samuel, Ifor D. W.
Lafontaine, Daniel A.
Penedo, J. Carlos
author_facet Dalgarno, Paul A.
Bordello, Jorge
Morris, Rhodri
St-Pierre, Patrick
Dubé, Audrey
Samuel, Ifor D. W.
Lafontaine, Daniel A.
Penedo, J. Carlos
author_sort Dalgarno, Paul A.
collection PubMed
description To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation to observe and manipulate RNA dynamics. We demonstrate that the competing interplay between metal ions and denaturant agents provides a platform to extract information that otherwise will remain hidden with current methods. Using the adenine-sensing riboswitch aptamer as a model, we provide strong evidence for a rate-limiting folding step of the aptamer domain being modulated through ligand binding, a feature that is important for regulation of the controlled gene. In the absence of ligand, the rate-determining step is dominated by the formation of long-range key tertiary contacts between peripheral stem-loop elements. In contrast, when the adenine ligand interacts with partially folded messenger RNAs, the aptamer requires specifically bound Mg(2+) ions, as those observed in the crystal structure, to progress further towards the native form. Moreover, despite that the ligand-free and ligand-bound states are indistinguishable by FRET, their different stability against urea-induced denaturation allowed us to discriminate them, even when they coexist within a single FRET trajectory; a feature not accessible by existing methods.
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spelling pubmed-36276002013-04-17 Single-molecule chemical denaturation of riboswitches Dalgarno, Paul A. Bordello, Jorge Morris, Rhodri St-Pierre, Patrick Dubé, Audrey Samuel, Ifor D. W. Lafontaine, Daniel A. Penedo, J. Carlos Nucleic Acids Res RNA To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation to observe and manipulate RNA dynamics. We demonstrate that the competing interplay between metal ions and denaturant agents provides a platform to extract information that otherwise will remain hidden with current methods. Using the adenine-sensing riboswitch aptamer as a model, we provide strong evidence for a rate-limiting folding step of the aptamer domain being modulated through ligand binding, a feature that is important for regulation of the controlled gene. In the absence of ligand, the rate-determining step is dominated by the formation of long-range key tertiary contacts between peripheral stem-loop elements. In contrast, when the adenine ligand interacts with partially folded messenger RNAs, the aptamer requires specifically bound Mg(2+) ions, as those observed in the crystal structure, to progress further towards the native form. Moreover, despite that the ligand-free and ligand-bound states are indistinguishable by FRET, their different stability against urea-induced denaturation allowed us to discriminate them, even when they coexist within a single FRET trajectory; a feature not accessible by existing methods. Oxford University Press 2013-04 2013-02-27 /pmc/articles/PMC3627600/ /pubmed/23446276 http://dx.doi.org/10.1093/nar/gkt128 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Dalgarno, Paul A.
Bordello, Jorge
Morris, Rhodri
St-Pierre, Patrick
Dubé, Audrey
Samuel, Ifor D. W.
Lafontaine, Daniel A.
Penedo, J. Carlos
Single-molecule chemical denaturation of riboswitches
title Single-molecule chemical denaturation of riboswitches
title_full Single-molecule chemical denaturation of riboswitches
title_fullStr Single-molecule chemical denaturation of riboswitches
title_full_unstemmed Single-molecule chemical denaturation of riboswitches
title_short Single-molecule chemical denaturation of riboswitches
title_sort single-molecule chemical denaturation of riboswitches
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627600/
https://www.ncbi.nlm.nih.gov/pubmed/23446276
http://dx.doi.org/10.1093/nar/gkt128
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