ArticleProceedings of the National Academy of Sciences of the United States of America2012
Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Mechanism underlying the high regulatory performance of the doxycycline riboswitch G12.Nature communications · 2026Article
- Specific Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein Deduced from Hairpin Unfolding.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Functional analysis of thiamine pyrophosphate-responsive riboswitches in human bacterial pathogens of the ESKAPE group using a dual-luciferase reporter gene assay.Journal of bacteriology · 2025Article
- Roquin exhibits opposing effects on RNA stem-loop stability through its two ROQ domain binding sites.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Recent Advancements in the Technologies Detecting Food Spoiling Agents.Journal of functional biomaterials · 2021Review
- 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
- Mechanical strength of RNA knot in Zika virus protects against cellular defenses.Nature chemical biology · 2021Article
- Article
- Significant Differences in RNA Structure Destabilization by HIV-1 GagDp6 and NCp7 Proteins.Viruses · 2020Article
- Alternate RNA Structures.Cold Spring Harbor perspectives in biology · 2020Review
- A glassy carbon electrode modified with reduced graphene oxide and gold nanoparticles for electrochemical aptasensing of lipopolysaccharides from Escherichia coli bacteria.Mikrochimica acta · 2019Article
- Article
- Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana.Scientific reports · 2019Article
- Conformation and mechanical property of rpoS mRNA inhibitory stem studied by optical tweezers and X-ray scattering.PloS one · 2019Article
- Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching.RNA (New York, N.Y.) · 2018Article
- Self-cleavage of theProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Single-molecule FRET studies on the cotranscriptional folding of a thiamine pyrophosphate riboswitch.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Real-time observation of polymerase-promoter contact remodeling during transcription initiation.Nature communications · 2017Article
- Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches.Molecules (Basel, Switzerland) · 2017Review
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4 authors.
Funding
Abstract
Riboswitches are motifs in the untranslated regions (UTRs) of RNA transcripts that sense metabolite levels and modulate the expression of the corresponding genes for metabolite import, export, synthesis, or degradation. All riboswitches contain an aptamer: an RNA structure that, upon binding ligand, folds to expose or sequester regulatory elements in the adjacent sequence through alternative nucleotide pairing. The coupling between ligand binding and aptamer folding is central to the regulatory mechanisms of thiamine pyrophosphate (TPP) riboswitches and has not been fully characterized. Here, we show that TPP aptamer folding can be decomposed into ligand-independent and -dependent steps that correspond to the formation of secondary and tertiary structures, respectively. We reconstructed the full energy landscape for folding of the wild-type (WT) aptamer and measured perturbations of this landscape arising from mutations or ligand binding. We show that TPP binding proceeds in two steps, from a weakly to a strongly bound state. Our data imply a hierarchical folding sequence, and provide a framework for understanding molecular mechanism throughout the TPP riboswitch family.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.