ArticleNature communications2016
The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Alternative probe chemistries for single-molecule analysis of long noncoding RNA.The Journal of biological chemistry · 2026Article
- Functional characterization of dynamic nascent RNA folding ensembles in real time.Science advances · 2026Article
- Alternative probe chemistries for single-molecule analysis of long non-coding RNA.bioRxiv : the preprint server for biology · 2026Article
- Peptide Nucleic Acids (PNAs) in Antimicrobial Therapy: A Next Generation Strategy.International journal of molecular sciences · 2026Review
- Coexistence of virome-encoded health-associated genes and pathogenic genes in global habitats.Applied and environmental microbiology · 2025Article
- A unifying model for microRNA-guided silencing of messenger RNAs.Nature communications · 2025Article
- Tiny but multi-stable: four distinct conformational states govern the ligand-free state of the preQ1 riboswitch from a thermophilic bacterium.Nucleic acids research · 2025Article
- Molecular basis of mRNA delivery to the bacterial ribosome.Science (New York, N.Y.) · 2024Article
- A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration.Nature communications · 2024Article
- Structure and function analysis of a type III preQThe Journal of biological chemistry · 2023Article
- Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level.Nucleic acids research · 2023Article
- Bursting translation on single mRNAs in live cells.Molecular cell · 2023Article
- Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution.Nature communications · 2023Article
- A riboswitch separated from its ribosome-binding site still regulates translation.Nucleic acids research · 2023Article
- Probing Transient Riboswitch Structures via Single Molecule Accessibility Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Using Single-Molecule FRET to Evaluate DNA Nanodevices at Work.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Precise tuning of bacterial translation initiation by non-equilibrium 5'-UTR unfolding observed in single mRNAs.Nucleic acids research · 2022Article
- A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.Nature communications · 2022Article
- Incoherent dual regulation by a SAM-II riboswitch controlling translation at a distance.RNA biology · 2022Article
- Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
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4 authors.
Funding
Abstract
In response to intracellular signals in Gram--negative bacteria, translational riboswitches--commonly embedded in messenger RNAs (mRNAs)-regulate gene expression through inhibition of translation initiation. It is generally thought that this regulation originates from occlusion of the Shine-Dalgarno (SD) sequence upon ligand binding; however, little direct evidence exists. Here we develop Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) to investigate the ligand-dependent accessibility of the SD sequence of an mRNA hosting the 7-aminomethyl-7-deazaguanine (preQ1)-sensing riboswitch. Spike train analysis reveals that individual mRNA molecules alternate between two conformational states, distinguished by 'bursts' of probe binding associated with increased SD sequence accessibility. Addition of preQ1 decreases the lifetime of the SD's high-accessibility (bursting) state and prolongs the time between bursts. In addition, ligand-jump experiments reveal imperfect riboswitching of single mRNA molecules. Such complex ligand sensing by individual mRNA molecules rationalizes the nuanced ligand response observed during bulk mRNA translation.
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