ArticleNucleic acids research2007
Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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81 citing papers in PubMed, 152 citations in OpenAlex.
- 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
- Co-transcriptional folding of the glmS ribozyme enables a rapid response to metabolite.Nucleic acids research · 2024Article
- 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
- Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery.ACS chemical biology · 2022Article
- What defines a synthetic riboswitch? - Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials.Nucleic acids research · 2021Article
- Article
- Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy.Frontiers in bioengineering and biotechnology · 2020Article
- Fluorescence-based investigations of RNA-small molecule interactions.Methods (San Diego, Calif.) · 2019Article
- Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana.Scientific reports · 2019Article
- Evaluating riboswitch optimality.Methods in enzymology · 2019Article
- Practical synthesis ofMonatshefte fur chemie · 2019Article
- Riboswitches and Translation Control.Cold Spring Harbor perspectives in biology · 2018Review
- SHAPE probing pictures Mg2+-dependent folding of small self-cleaving ribozymes.Nucleic acids research · 2018Article
- Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- HgII binds to C-T mismatches with high affinity.Nucleic acids research · 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
- Superior cellular activities of azido- over amino-functionalized ligands for engineered preQRNA biology · 2018Article
- Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation.Nucleic acids research · 2017Article
- Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools.Frontiers in genetics · 2017Review
21 more citing papers are in PubMed but not listed here.
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3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are genetic control elements within non-coding regions of mRNA. They consist of a metabolite-sensitive aptamer and an adjoining expression platform. Here, we describe ligand-induced folding of a thiamine pyrophosphate (TPP) responsive riboswitch from Escherichia coli thiM mRNA, using chemically labeled variants. Referring to a recent structure determination of the TPP/aptamer complex, each variant was synthesized with a single 2-aminopurine (AP) nucleobase replacement that was selected to monitor formation of tertiary interactions of a particular region during ligand binding in real time by fluorescence experiments. We have determined the rate constants for conformational adjustment of the individual AP sensors. From the 7-fold differentiation of these constants, it can be deduced that tertiary contacts between the two parallel helical domains (P2/J3-2/P3/L3 and P4/P5/L5) that grip the ligand's ends in two separate pockets, form significantly faster than the function-critical three-way junction with stem P1 fully developed. Based on these data, we characterize the process of ligand binding by an induced fit of the RNA and propose a folding model of the TPP riboswitch aptamer. For the full-length riboswitch domain and for shorter constructs that represent transcriptional intermediates, we have additionally evaluated ligand-induced folding via AP-modified variants and provide insights into the sequential folding pathway that involves a finely balanced equilibrium of secondary structures.
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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.