ArticleNucleic acids research2013
Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed, 98 citations in OpenAlex.
- Conformational landscape of 2-aminopurine-substituted RNA oligonucleotides from machine-learning-driven enhanced sampling.Physical chemistry chemical physics : PCCP · 2026Article
- A Standardized Prism-Based TIRF Platform for Quantitative Single-Molecule Fluorescence Studies of Biomolecular Dynamics.Biosensors · 2026Article
- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.Nucleic acids research · 2026Article
- Alternative probe chemistries for single-molecule analysis of long noncoding RNA.The Journal of biological chemistry · 2026Article
- Alternative probe chemistries for single-molecule analysis of long non-coding RNA.bioRxiv : the preprint server for biology · 2026Article
- SHAPE-Based Chemical Probes for Studying preQACS chemical biology · 2025Article
- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.bioRxiv : the preprint server for biology · 2025Article
- High-throughput competitive binding assay for targeting RNA tertiary structures with small molecules: application to pseudoknots and G-quadruplexes.Nucleic acids research · 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
- Ligand binding characteristics of an NAD+ riboswitch revealed by FRET and biolayer interferometry.bioRxiv : the preprint server for biology · 2024Article
- Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression.Nature communications · 2024Article
- Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages.Microbiology and molecular biology reviews : MMBR · 2024Review
- Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression.bioRxiv : the preprint server for biology · 2024Article
- Single-molecule FRET observes opposing effects of urea and TMAO on structurally similar meso- and thermophilic riboswitch RNAs.Nucleic acids research · 2023Article
- Advances in RNA Labeling with Trifluoromethyl Groups.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- Structure and function analysis of a type III preQThe Journal of biological chemistry · 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
- Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets.Antibiotics (Basel, Switzerland) · 2022Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
Riboswitches are structural elements in the 5' untranslated regions of many bacterial messenger RNAs that regulate gene expression in response to changing metabolite concentrations by inhibition of either transcription or translation initiation. The preQ1 (7-aminomethyl-7-deazaguanine) riboswitch family comprises some of the smallest metabolite sensing RNAs found in nature. Once ligand-bound, the transcriptional Bacillus subtilis and translational Thermoanaerobacter tengcongensis preQ1 riboswitch aptamers are structurally similar RNA pseudoknots; yet, prior structural studies have characterized their ligand-free conformations as largely unfolded and folded, respectively. In contrast, through single molecule observation, we now show that, at near-physiological Mg(2+) concentration and pH, both ligand-free aptamers adopt similar pre-folded state ensembles that differ in their ligand-mediated folding. Structure-based Gō-model simulations of the two aptamers suggest that the ligand binds late (Bacillus subtilis) and early (Thermoanaerobacter tengcongensis) relative to pseudoknot folding, leading to the proposal that the principal distinction between the two riboswitches lies in their relative tendencies to fold via mechanisms of conformational selection and induced fit, respectively. These mechanistic insights are put to the test by rationally designing a single nucleotide swap distal from the ligand binding pocket that we find to predictably control the aptamers' pre-folded states and their ligand binding affinities.
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