ArticleRNA (New York, N.Y.)2001
An early transition state for folding of the P4-P6 RNA domain.
Article in RNA (New York, N.Y.), 2001. 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, 64 citations in OpenAlex.
- Rho (bioRxiv : the preprint server for biology · 2026Article
- Goldilocks and RNA: where Mg2+ concentration is just right.Nucleic acids research · 2023Article
- An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch.Nature communications · 2022Article
- 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
- Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?Journal of the American Chemical Society · 2016Article
- Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting.Journal of the American Chemical Society · 2015Article
- Mg(2+) shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection.Journal of the American Chemical Society · 2015Article
- Role of ion valence in the submillisecond collapse and folding of a small RNA domain.Biochemistry · 2013Article
- Thermodynamic origins of monovalent facilitated RNA folding.Biochemistry · 2012Article
- Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry.Nucleic acids research · 2012Article
- Entropic origin of Mg2+-facilitated RNA folding.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA.The Journal of biological chemistry · 2011Article
- Hinge stiffness is a barrier to RNA folding.Journal of molecular biology · 2008Article
- Topological rearrangement yields structural stabilization and interhelical distance constraints in the Kin.46 self-phosphorylating ribozyme.RNA (New York, N.Y.) · 2006Article
- Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker.Biochemistry · 2006Article
- Fluorescence of covalently attached pyrene as a general RNA folding probe.Nucleic acids research · 2006Article
- Single-molecule transition-state analysis of RNA folding.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- RNA hairpin-folding kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2002Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Tertiary folding of the 160-nt P4-P6 domain of the Tetrahymena group I intron RNA involves burying of substantial surface area, providing a model for the folding of other large RNA domains involved in catalysis. Stopped-flow fluorescence was used to monitor the Mg2+-induced tertiary folding of pyrene-labeled P4-P6. At 35 degrees C with [Mg2+] approximately 10 mM, P4-P6 folds on the tens of milliseconds timescale with k(obs) = 15-31 s(-1). From these values, an activation free energy deltaG(double dagger) of approximately 8-16 kcal/mol is calculated, where the large range for deltaG(double dagger) arises from uncertainty in the pre-exponential factor relating k(obs) and delta G(double dagger). The folding rates of six mutant P4-P6 RNAs were measured and found to be similar to that of the wild-type RNA, in spite of significant thermodynamic destabilization or stabilization. The ratios of the kinetic and thermodynamic free energy changes phi = delta deltaG(double dagger)/delta deltaG(o') are approximately 0, implying a folding transition state in which most of the native-state tertiary contacts are not yet formed (an early folding transition state). The k(obs) depends on the Mg2+ concentration, and the initial slope of k(obs) versus [Mg2+] suggests that only approximately 1 Mg2+ ion is bound in the rate-limiting folding step. This is consistent with an early folding transition state, because folded P4-P6 binds many Mg2+ ions. The observation of a substantial deltaG(double dagger) despite an early folding transition state suggests that a simple two-state folding diagram for Mg2+-induced P4-P6 folding is incomplete. Our kinetic data are some of the first to provide quantitative values for an activation barrier and location of a transition state for tertiary folding of an RNA domain.
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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.