ArticleRNA (New York, N.Y.)2007
Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined induced fit mechanism.
Article in RNA (New York, N.Y.), 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Conjugation of hydrophobic drugs to motile pRNA 4WJ nanoparticles for spontaneous tumor targeting and undetectable toxicity.Nature protocols · 2026Review
- Exploring functional transitions of the 2'-dG riboswitch aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning.Nature communications · 2026Article
- Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements.RNA (New York, N.Y.) · 2024Article
- Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The dynamic, motile and deformative properties of RNA nanoparticles facilitate the third milestone of drug development.Advanced drug delivery reviews · 2022Review
- The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements.Nucleic acids research · 2021Article
- Evaluating riboswitch optimality.Methods in enzymology · 2019Article
- Small-Molecule-Binding Riboswitches.Microbiology spectrum · 2018Review
- Comprehensive profiling of the ligand binding landscapes of duplexed aptamer families reveals widespread induced fit.Nature communications · 2018Article
- Long-Range Interactions in Riboswitch Control of Gene Expression.Annual review of biophysics · 2017Review
- Measuring RNA structure transcriptome-wide with icSHAPE.Methods (San Diego, Calif.) · 2017Review
- Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools.Frontiers in genetics · 2017Review
- Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.PloS one · 2017Article
- Cotranscriptional folding of a riboswitch at nucleotide resolution.Nature structural & molecular biology · 2016Article
- RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly.Journal of molecular biology · 2016Article
- Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model.The Journal of chemical physics · 2016Article
- An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.RNA (New York, N.Y.) · 2016Article
- Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes.PloS one · 2016Article
- Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch.Journal of the American Chemical Society · 2014Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
All known guanine-sensing riboswitches regulate gene expression by specifically binding to guanine (G) or related analogs with high affinity to switch off transcription. The aptamers of this class of riboswitches are characterized by three helices (P1-P3), surrounding a central core of phylogenetically conserved nucleotides and a long-range loop-loop interaction. To gain more insight into the switching mechanism, we present here a comparison between the solution-state structures of the G-free and G-bound forms of the guanine aptamer from the xpt-pbuX operon of Bacillus subtilis, as derived from NMR chemical shifts and magnetic-field-induced residual dipolar couplings. The high-resolution NMR analysis shows the G-free aptamer is highly structured with parallel P2 and P3 helices and the long-range loop-loop interaction already present, implying that the structure is largely preformed to bind the ligand. Structural changes upon guanine binding are found to be localized to the central core. In the free state, the G-quadruple interaction and two base pairs of the P1 stem flanking the central core appear to be largely disordered. The ligand thus binds via a combined predetermined-induced fit mechanism, involving a previously unstructured five-residue loop of the J2-3 junction that folds over the ligand. These limited additional interactions within a preorganized setting possibly explain how the aptamer rapidly responds to ligand binding, which is necessary to switch the structural state of the expression platform within a narrow time frame before the RNA polymerase escapes the 5'-UTR.
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