ArticleJournal of the American Chemical Society2008
Tertiary interactions determine the accuracy of RNA folding.
Article in Journal of the American Chemical Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.Nature communications · 2025Article
- Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS ribozyme.Nucleic acids research · 2024Article
- High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping.Nucleic acids research · 2024Article
- Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time.Nucleic acids research · 2023Article
- General Strategies for RNA X-ray Crystallography.Molecules (Basel, Switzerland) · 2023Review
- In vitro selected GUAA tetraloop-binding receptors with structural plasticity and evolvability towards natural RNA structural modules.Nucleic acids research · 2021Article
- Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.Biophysical journal · 2020Article
- Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Identification and Characterization of New RNA Tetraloop Sequence Families.Biochemistry · 2019Article
- Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.Journal of chemical theory and computation · 2019Article
- Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.The journal of physical chemistry letters · 2018Article
- Article
- Proteins That Chaperone RNA Regulation.Microbiology spectrum · 2018Review
- Cooperativity Principles in Self-Assembled Nanomedicine.Chemical reviews · 2018Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Topological Structure Determination of RNA Using Small-Angle X-Ray Scattering.Journal of molecular biology · 2017Article
- Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.Biophysical journal · 2017Article
- Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization.Biochemistry · 2017Article
- Classification of RNA structure change by 'gazing' at experimental data.Bioinformatics (Oxford, England) · 2017Article
6 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
RNAs must fold into unique three-dimensional structures to function in the cell, but how each polynucleotide finds its native structure is not understood. To investigate whether the stability of the tertiary structure determines the speed and accuracy of RNA folding, docking of a tetraloop with its receptor in a bacterial group I ribozyme was perturbed by site-directed mutagenesis. Disruption of the tetraloop or its receptor destabilizes tertiary interactions throughout the ribozyme by 2-3 kcal/mol, demonstrating that tertiary interactions form cooperatively in the transition from a native-like intermediate to the native state. Nondenaturing PAGE and RNase T1 digestion showed that base pairs form less homogeneously in the mutant RNAs during the transition from the unfolded state to the intermediate. Thus, tertiary interactions between helices bias the ensemble of secondary structures toward native-like conformations. Time-resolved hydroxyl radical footprinting showed that the wild-type ribozyme folds completely within 5-20 ms. By contrast, only 40-60% of a tetraloop mutant ribozyme folds in 30-40 ms, with the remainder folding in 30-200 s via nonnative intermediates. Therefore, destabilization of tetraloop-receptor docking introduces an alternate folding pathway in the otherwise smooth energy landscape of the wild-type ribozyme. Our results show that stable tertiary structure increases the flux through folding pathways that lead directly and rapidly to the native structure.
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