ArticleACS chemical biology2012
Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding.
Article in ACS chemical biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
34 citing papers in PubMed, 64 citations in OpenAlex.
- Deciphering ligand and metal ion dependent intricate folding landscape of Vc2 c-di-GMP riboswitch aptamer.Nucleic acids research · 2025Article
- Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble.Nature communications · 2023Article
- DeepFRET, a software for rapid and automated single-molecule FRET data classification using deep learning.eLife · 2020Article
- The Vc2 Cyclic di-GMP-Dependent Riboswitch of Vibrio cholerae Regulates Expression of an Upstream Putative Small RNA by Controlling RNA Stability.Journal of bacteriology · 2019Article
- Article
- Unprecedented tunability of riboswitch structure and regulatory function by sub-millimolar variations in physiological Mg2.Nucleic acids research · 2019Article
- Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.ACS chemical biology · 2019Review
- Finely tuned conformational dynamics regulate the protective function of the lncRNA MALAT1 triple helix.Nucleic acids research · 2019Article
- Monitoring co-transcriptional folding of riboswitches through helicase unwinding.Methods in enzymology · 2019Article
- Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World.Chemical reviews · 2018Review
- Cyclic di-GMP Regulates TfoY in Vibrio cholerae To Control Motility by both Transcriptional and Posttranscriptional Mechanisms.Journal of bacteriology · 2018Article
- Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.RNA (New York, N.Y.) · 2017Article
- Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR.ACS chemical biology · 2016Article
- Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin.Journal of molecular biology · 2016Article
- Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes.Frontiers in chemistry · 2016Review
- Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes.Nature communications · 2015Article
- Collapse and hybridization of RNA: view from replica technique approach.The European physical journal. E, Soft matter · 2015Article
- Consistent global structures of complex RNA states through multidimensional chemical mapping.eLife · 2015Article
- The Globular State of the Single-Stranded RNA: Effect of the Secondary Structure Rearrangements.Journal of nucleic acids · 2015Article
- Native purification and labeling of RNA for single molecule fluorescence studies.Methods in molecular biology (Clifton, N.J.) · 2015Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Cyclic diguanylate (c-di-GMP) is a bacterial second messenger important for physiologic adaptation and virulence. Class-I c-di-GMP riboswitches are phylogenetically widespread and thought to mediate pleiotropic genetic responses to the second messenger. Previous studies suggest that the RNA aptamer domain switches from an extended free state to a compact, c-di-GMP-bound conformation in which two helical stacks dock side-by-side. Single molecule fluorescence resonance energy transfer (smFRET) experiments now reveal that the free RNA exists in four distinct populations that differ in dynamics in the extended and docked conformations. In the presence of c-di-GMP and Mg(2+), a stably docked population (>30 min) becomes predominant. smFRET mutant analysis demonstrates that tertiary interactions distal to the c-di-GMP binding site strongly modulate the RNA population structure, even in the absence of c-di-GMP. These allosteric interactions accelerate ligand recognition by preorganizing the RNA, favoring rapid c-di-GMP binding.
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Registered trials
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.