ArticleMethods (San Diego, Calif.)2015
Conformational flexibility of viral RNA switches studied by FRET.
Article in Methods (San Diego, Calif.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket).bioRxiv : the preprint server for biology · 2026Article
- DNA to RNA Tuning of a Pyrrolidine-Derived Quinoxaline Scaffold: Magnesium Induces Binding and Inhibition of Internal Ribosomal Entry Site RNA-Mediated Translational of Hepatitis C Virus.ACS pharmacology & translational science · 2025Article
- Structure-based virtual screening of unbiased and RNA-focused libraries to identify new ligands for the HCV IRES model system.RSC medicinal chemistry · 2024Article
- Review
- Target-Directed Approaches for Screening Small Molecules against RNA Targets.SLAS discovery : advancing life sciences R & D · 2020Review
- Optimization and characterization of position-selective labelling of RNA (PLOR) for diverse RNA and DNA sequences.RNA biology · 2020Article
- Fluorescence-based investigations of RNA-small molecule interactions.Methods (San Diego, Calif.) · 2019Article
- Ensemble and single-molecule FRET studies of protein synthesis.Methods (San Diego, Calif.) · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The function of RNA switches involved in the regulation of transcription and translation relies on their ability to adopt different, structurally well-defined states. A new class of ligand-responsive RNA switches, which we recently discovered in positive strand RNA viruses, are distinct from conventional riboswitches. The viral switches undergo large conformational changes in response to ligand binding while retaining the same secondary structure in their free and ligand-bound forms. Here, we describe FRET experiments to study folding and ligand binding of the viral RNA switches. In addition to reviewing previous approaches involving RNA model constructs which were directly conjugated with fluorescent dyes, we outline the design and application of new modular constructs for FRET experiments, in which dye labeling is achieved by hybridization of a core RNA switch module with universal DNA fluorescent probes. As an example, folding and ligand binding of the RNA switch from the internal ribosome entry site of hepatitis C virus is studied comparatively with conventional and modular FRET constructs.
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