title: Fluorescence tools to investigate riboswitch structural dynamics.
abstract: Riboswitches are novel regulatory elements that respond to cellular metabolites to control gene expression. They are constituted of highly conserved domains that have evolved to recognize specific metabolites. Such domains, so-called aptamers, are folded into intricate structures to enable metabolite recognition. Over the years, the development of ensemble and single-molecule fluorescence techniques has allowed to probe most of the mechanistic aspects of aptamer folding and ligand binding. In this review, we summarize the current fluorescence toolkit available to study riboswitch structural dynamics. We fist describe those methods based on fluorescent nucleotide analogues, mostly 2-aminopurine (2AP), to investigate short-range conformational changes, including some key steady-state and time-resolved examples that exemplify the versatility of fluorescent analogues as structural probes. The study of long-range structural changes by Förster resonance energy transfer (FRET) is mostly discussed in the context of single-molecule studies, including some recent developments based on the combination of single-molecule FRET techniques with controlled chemical denaturation methods. This article is part of a Special Issue entitled: Riboswitches.
authors.affiliation: RNA Group, Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
authors.forename: Patrick
authors.initials: P
authors.lastname: St-Pierre
authors.affiliation: SUPA, School of Physics and Astronomy University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom.
authors.forename: Kaley
authors.initials: K
authors.lastname: McCluskey
authors.affiliation: SUPA, School of Physics and Astronomy University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom.
authors.forename: Euan
authors.initials: E
authors.lastname: Shaw
authors.affiliation: SUPA, School of Physics and Astronomy University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom; Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom. Electronic address: jcp10@st-andrews.ac.uk.
authors.forename: J C
authors.initials: JC
authors.lastname: Penedo
authors.affiliation: RNA Group, Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada. Electronic address: daniel.lafontaine@usherbrooke.ca.
authors.forename: D A
authors.initials: DA
authors.lastname: Lafontaine
keywords: Fluorescence; Forster resonance energy transfer; RNA conformational change; Riboswitch; Single-molecule FRET