ArticleProceedings of the National Academy of Sciences of the United States of America2013
Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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72 citing papers in PubMed.
- Mechanism underlying the high regulatory performance of the doxycycline riboswitch G12.Nature communications · 2026Article
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- Site-Selective Ligand Selection by Mutational Profiling for Covalent RNA Targeting.Angewandte Chemie (International ed. in English) · 2026Article
- Structural basis for Mg²⁺-glycine synergy in the tandem glycine riboswitch revealed by cryo-EM.Npj structural biology · 2026Article
- Critical Role of MgThe journal of physical chemistry. B · 2025Article
- Deciphering ligand and metal ion dependent intricate folding landscape of Vc2 c-di-GMP riboswitch aptamer.Nucleic acids research · 2025Article
- Nexus between RNA conformational dynamics and functional versatility.Current opinion in structural biology · 2024Review
- Opportunities for Riboswitch Inhibition by Targeting Co-Transcriptional RNA Folding Events.International journal of molecular sciences · 2024Review
- A transient intermediate RNA structure underlies the regulatory function of theRNA (New York, N.Y.) · 2023Article
- Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state.Structure (London, England : 1993) · 2023Article
- Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution.Nature communications · 2023Article
- Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.Nucleic acids research · 2022Article
- Long-read single-molecule RNA structure sequencing using nanopore.Nucleic acids research · 2022Article
- Precise tuning of bacterial translation initiation by non-equilibrium 5'-UTR unfolding observed in single mRNAs.Nucleic acids research · 2022Article
- Key players in regulatory RNA realm of bacteria.Biochemistry and biophysics reports · 2022Review
- Article
- Monitoring RNA dynamics in native transcriptional complexes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches.The journal of physical chemistry. B · 2021Article
- A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition.Nucleic acids research · 2021Article
- Article
12 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Thiamine pyrophosphate (TPP)-sensitive mRNA domains are the most prevalent riboswitches known. Despite intensive investigation, the complex ligand recognition and concomitant folding processes in the TPP riboswitch that culminate in the regulation of gene expression remain elusive. Here, we used single-molecule fluorescence resonance energy transfer imaging to probe the folding landscape of the TPP aptamer domain in the absence and presence of magnesium and TPP. To do so, distinct labeling patterns were used to sense the dynamics of the switch helix (P1) and the two sensor arms (P2/P3 and P4/P5) of the aptamer domain. The latter structural elements make interdomain tertiary contacts (L5/P3) that span a region immediately adjacent to the ligand-binding site. In each instance, conformational dynamics of the TPP riboswitch were influenced by ligand binding. The P1 switch helix, formed by the 5' and 3' ends of the aptamer domain, adopts a predominantly folded structure in the presence of Mg(2+) alone. However, even at saturating concentrations of Mg(2+) and TPP, the P1 helix, as well as distal regions surrounding the TPP-binding site, exhibit an unexpected degree of residual dynamics and disperse kinetic behaviors. Such plasticity results in a persistent exchange of the P3/P5 forearms between open and closed configurations that is likely to facilitate entry and exit of the TPP ligand. Correspondingly, we posit that such features of the TPP aptamer domain contribute directly to the mechanism of riboswitch-mediated translational regulation.
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