ArticleJournal of the American Chemical Society2005
Determining the Mg2+ stoichiometry for folding an RNA metal ion core.
Article in Journal of the American Chemical Society, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 96 citations in OpenAlex.
- Quantifying MgbioRxiv : the preprint server for biology · 2026Article
- Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems.The journal of physical chemistry. B · 2024Article
- Structural Basis for Fluorescence Activation by Pepper RNA.ACS chemical biology · 2022Article
- Dynamics of Cations around DNA and Protein as Revealed byAnalytical chemistry · 2022Article
- Experimental approaches for investigating ion atmospheres around nucleic acids and proteins.Computational and structural biotechnology journal · 2021Review
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution.Nature communications · 2020Article
- Predicting Monovalent Ion Correlation Effects in Nucleic Acids.ACS omega · 2019Article
- Article
- Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems.Journal of the American Chemical Society · 2018Article
- The Story of RNA Folding, as Told in Epochs.Cold Spring Harbor perspectives in biology · 2018Review
- 8-Hydroxyquinoline Functionalized Graphene Oxide: an Efficient Fluorescent Nanosensor for ZnJournal of fluorescence · 2018Article
- Hidden Structural Modules in a Cooperative RNA Folding Transition.Cell reports · 2018Article
- 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
- RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly.Journal of molecular biology · 2016Article
- 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
- Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme.RNA (New York, N.Y.) · 2016Article
- Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting.Journal of the American Chemical Society · 2015Article
- Mechanistic Analysis of Activation of the Innate Immune Sensor PKR by Bacterial RNA.Journal of molecular biology · 2015Article
Corrections and comments
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4 authors at 1 institution in 1 country.
Funding
Abstract
The folding and catalytic function of RNA molecules depend on their interactions with divalent metal ions, such as magnesium. As with every molecular process, the most basic knowledge required for understanding the close relationship of an RNA with its metal ions is the stoichiometry of the interaction. Unfortunately, inventories of the numbers of divalent ions associated with unfolded and folded RNA states have been unattainable. A common approach has been to interpret Hill coefficients fit to folding equilibria as the number of metal ions bound upon folding. However, this approach is vitiated by the presence of diffusely associated divalent ions in a dynamic ion atmosphere and by the likelihood of multiple transitions along a folding pathway. We demonstrate that the use of molar concentrations of background monovalent salt can alleviate these complications. These simplifying solution conditions allow a precise determination of the stoichiometry of the magnesium ions involved in folding the metal ion core of the P4-P6 domain of the Tetrahymena group I ribozyme. Hill analysis of hydroxyl radical footprinting data suggests that the P4-P6 RNA core folds cooperatively upon the association of two metal ions. This unexpectedly small stoichiometry is strongly supported by counting magnesium ions associated with the P4-P6 RNA via fluorescence titration and atomic emission spectroscopy. By pinpointing the metal ion stoichiometry, these measurements provide a critical but previously missing step in the thermodynamic dissection of the coupling between metal ion binding and RNA folding.
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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.