ArticleNucleic acids research2013
Single-molecule chemical denaturation of riboswitches.
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 19 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
19 citing papers in PubMed, 32 citations in OpenAlex.
- Aptamers in Ocular Disease Therapy and Drug Delivery: Current Progress and Future Opportunities.Current therapeutic research, clinical and experimental · 2026Review
- Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases.Nature communications · 2024Article
- Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.Communications biology · 2022Article
- Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag.Nature chemical biology · 2022Article
- Article
- Monitoring RNA dynamics in native transcriptional complexes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Thermal adaptation of structural dynamics and regulatory function of adenine riboswitch.RNA biology · 2021Article
- A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition.Nucleic acids research · 2021Article
- Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations.Nucleic acids research · 2019Article
- Unprecedented tunability of riboswitch structure and regulatory function by sub-millimolar variations in physiological Mg2.Nucleic acids research · 2019Article
- Real-time observation of conformational switching in single conjugated polymer chains.Science advances · 2018Article
- Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy.Nucleic acids research · 2017Article
- Applications of PLOR in labeling large RNAs at specific sites.Methods (San Diego, Calif.) · 2016Article
- Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes.Frontiers in chemistry · 2016Review
- A kissing loop is important for btuB riboswitch ligand sensing and regulatory control.The Journal of biological chemistry · 2015Article
- Synthesis and applications of RNAs with position-selective labelling and mosaic composition.Nature · 2015Article
- Article
- Single-molecule studies of riboswitch folding.Biochimica et biophysica acta · 2014Review
- Nanomanipulation of single RNA molecules by optical tweezers.Journal of visualized experiments : JoVE · 2014Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation to observe and manipulate RNA dynamics. We demonstrate that the competing interplay between metal ions and denaturant agents provides a platform to extract information that otherwise will remain hidden with current methods. Using the adenine-sensing riboswitch aptamer as a model, we provide strong evidence for a rate-limiting folding step of the aptamer domain being modulated through ligand binding, a feature that is important for regulation of the controlled gene. In the absence of ligand, the rate-determining step is dominated by the formation of long-range key tertiary contacts between peripheral stem-loop elements. In contrast, when the adenine ligand interacts with partially folded messenger RNAs, the aptamer requires specifically bound Mg(2+) ions, as those observed in the crystal structure, to progress further towards the native form. Moreover, despite that the ligand-free and ligand-bound states are indistinguishable by FRET, their different stability against urea-induced denaturation allowed us to discriminate them, even when they coexist within a single FRET trajectory; a feature not accessible by existing methods.
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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.