ArticleProceedings of the National Academy of Sciences of the United States of America2016
Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 26 citations in OpenAlex.
- Rho (bioRxiv : the preprint server for biology · 2026Article
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing.bioRxiv : the preprint server for biology · 2026Article
- Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations.The journal of physical chemistry. B · 2023Article
- Goldilocks and RNA: where Mg2+ concentration is just right.Nucleic acids research · 2023Article
- Measurement of the specific and non-specific binding energies of MgBiophysical journal · 2022Article
- Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch.Frontiers in molecular biosciences · 2022Article
- FRETraj: integrating single-molecule spectroscopy with molecular dynamics.Bioinformatics (Oxford, England) · 2021Article
- High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Cooperativity and Allostery in RNA Systems.Methods in molecular biology (Clifton, N.J.) · 2021Review
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
- Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch.Nucleic acids research · 2019Article
- How the Conformations of an Internal Junction Contribute to Fold an RNA Domain.The journal of physical chemistry. B · 2018Article
- The Story of RNA Folding, as Told in Epochs.Cold Spring Harbor perspectives in biology · 2018Review
- Revealing the distinct folding phases of an RNA three-helix junction.Nucleic acids research · 2018Article
- Hidden Structural Modules in a Cooperative RNA Folding Transition.Cell reports · 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
- 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
- A magnesium-induced triplex pre-organizes the SAM-II riboswitch.PLoS computational biology · 2017Article
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6 authors at 1 institution in 1 country.
Funding
Abstract
The past decade has seen a wealth of 3D structural information about complex structured RNAs and identification of functional intermediates. Nevertheless, developing a complete and predictive understanding of the folding and function of these RNAs in biology will require connection of individual rate and equilibrium constants to structural changes that occur in individual folding steps and further relating these steps to the properties and behavior of isolated, simplified systems. To accomplish these goals we used the considerable structural knowledge of the folded, unfolded, and intermediate states of P4-P6 RNA. We enumerated structural states and possible folding transitions and determined rate and equilibrium constants for the transitions between these states using single-molecule FRET with a series of mutant P4-P6 variants. Comparisons with simplified constructs containing an isolated tertiary contact suggest that a given tertiary interaction has a stereotyped rate for breaking that may help identify structural transitions within complex RNAs and simplify the prediction of folding kinetics and thermodynamics for structured RNAs from their parts. The preferred folding pathway involves initial formation of the proximal tertiary contact. However, this preference was only ∼10 fold and could be reversed by a single point mutation, indicating that a model akin to a protein-folding contact order model will not suffice to describe RNA folding. Instead, our results suggest a strong analogy with a modified RNA diffusion-collision model in which tertiary elements within preformed secondary structures collide, with the success of these collisions dependent on whether the tertiary elements are in their rare binding-competent conformations.
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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.