Single-molecule chemical denaturation of riboswitches

Paul A Dalgarno, Jorge Bordello, Rhodri Morris, Patrick St-Pierre, Audrey Dubé, Ifor D W Samuel, Daniel A Lafontaine, J Carlos Penedo

Research output: Contribution to journalArticle

Abstract

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.
LanguageEnglish
JournalNucleic Acids Research
Early online date27 Feb 2013
DOIs
Publication statusPublished - 2013

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Riboswitch
Ligands
Energy Transfer
Adenine
RNA
Ions
Metals
Nucleotide Aptamers
Urea
Messenger RNA
Genes

Cite this

Dalgarno, P. A., Bordello, J., Morris, R., St-Pierre, P., Dubé, A., Samuel, I. D. W., ... Penedo, J. C. (2013). Single-molecule chemical denaturation of riboswitches. Nucleic Acids Research. https://doi.org/10.1093/nar/gkt128
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. In: Nucleic Acids Research. 2013.
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Dalgarno, PA, Bordello, J, Morris, R, St-Pierre, P, Dubé, A, Samuel, IDW, Lafontaine, DA & Penedo, JC 2013, 'Single-molecule chemical denaturation of riboswitches', Nucleic Acids Research. https://doi.org/10.1093/nar/gkt128

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.

In: Nucleic Acids Research, 2013.

Research output: Contribution to journalArticle

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AU - Bordello, Jorge

AU - Morris, Rhodri

AU - St-Pierre, Patrick

AU - Dubé, Audrey

AU - Samuel, Ifor D W

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