ArticleProceedings of the National Academy of Sciences of the United States of America2003
Single-molecule transition-state analysis of RNA folding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed.
- High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping.Nucleic acids research · 2024Article
- Single-molecule FRET observes opposing effects of urea and TMAO on structurally similar meso- and thermophilic riboswitch RNAs.Nucleic acids research · 2023Article
- An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch.Nature communications · 2022Article
- Single-Molecular Förster Resonance Energy Transfer Measurement on Structures and Interactions of Biomolecules.Micromachines · 2021Review
- Site-Selective RNA Functionalization via DNA-Induced Structure.Journal of the American Chemical Society · 2020Article
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
- Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts.Nature communications · 2020Article
- Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.The journal of physical chemistry letters · 2018Article
- Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.Journal of molecular biology · 2018Article
- Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway.Journal of the American Chemical Society · 2017Article
- Metals induce transient folding and activation of the twister ribozyme.Nature chemical biology · 2017Article
- Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.Biophysical chemistry · 2017Article
- Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks.Journal of the Royal Society, Interface · 2017Article
- Pressure modulates the self-cleavage step of the hairpin ribozyme.Nature communications · 2017Article
- Single-Molecule FRET Reveals Three Conformations for the TLS Domain of Brome Mosaic Virus Genome.Biophysical journal · 2015Article
- Mg(2+) shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection.Journal of the American Chemical Society · 2015Article
- Native purification and labeling of RNA for single molecule fluorescence studies.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Molecular crowding accelerates ribozyme docking and catalysis.Journal of the American Chemical Society · 2014Article
- Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update.Archives of toxicology · 2014Review
- Probing protein multidimensional conformational fluctuations by single-molecule multiparameter photon stamping spectroscopy.The journal of physical chemistry. B · 2014Article
31 more citing papers are in PubMed but not listed here.
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
How RNA molecules fold into functional structures is a problem of great significance given the expanding list of essential cellular RNA enzymes and the increasing number of applications of RNA in biotechnology and medicine. A critical step toward solving the RNA folding problem is the characterization of the associated transition states. This is a challenging task in part because the rugged energy landscape of RNA often leads to the coexistence of multiple distinct structural transitions. Here, we exploit single-molecule fluorescence spectroscopy to follow in real time the equilibrium transitions between conformational states of a model RNA enzyme, the hairpin ribozyme. We clearly distinguish structural transitions between effectively noninterchanging sets of unfolded and folded states and characterize key factors defining the transition state of an elementary folding reaction where the hairpin ribozyme's two helical domains dock to make several tertiary contacts. Our single-molecule experiments in conjunction with site-specific mutations and metal ion titrations show that the two RNA domains are in a contact or close-to-contact configuration in the transition state even though the native tertiary contacts are at most partially formed. Such a compact transition state without well formed tertiary contacts may be a general property of elementary RNA folding reactions.
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