ArticleRNA (New York, N.Y.)2002
Metal ion binding and the folding of the hairpin ribozyme.
Article in RNA (New York, N.Y.), 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 53 citations in OpenAlex.
- Quantifying MgbioRxiv : the preprint server for biology · 2026Article
- Enhanced Ribozyme-Catalyzed Recombination and Oligonucleotide Assembly in Peptide-RNA Condensates.Angewandte Chemie (International ed. in English) · 2021Article
- Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.Biophysical chemistry · 2017Article
- Pressure modulates the self-cleavage step of the hairpin ribozyme.Nature communications · 2017Article
- Molecular crowding accelerates ribozyme docking and catalysis.Journal of the American Chemical Society · 2014Article
- Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis.RNA biology · 2013Article
- The importance of peripheral sequences in determining the metal selectivity of an in vitro-selected Co(2+) -dependent DNAzyme.Chembiochem : a European journal of chemical biology · 2012Article
- Metal-ion-dependent folding of a uranyl-specific DNAzyme: insight into function from fluorescence resonance energy transfer studies.Chemistry (Weinheim an der Bergstrasse, Germany) · 2011Article
- Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data.RNA (New York, N.Y.) · 2011Article
- Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions.Journal of the American Chemical Society · 2009Article
- Site-specific variations in RNA folding thermodynamics visualized by 2-aminopurine fluorescence.Biochemistry · 2007Article
- Dissecting metal ion-dependent folding and catalysis of a single DNAzyme.Nature chemical biology · 2007Article
- A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control.RNA (New York, N.Y.) · 2007Article
- Nucleobase catalysis in the hairpin 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
- Determining the Mg2+ stoichiometry for folding an RNA metal ion core.Journal of the American Chemical Society · 2005Article
- Investigation of Mg2+- and temperature-dependent folding of the hairpin ribozyme by photo-crosslinking: effects of photo-crosslinker tether length and chemistry.Nucleic acids research · 2005Article
- The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure.Nucleic acids research · 2005Article
- Tris-borate is a poor counterion for RNA: a cautionary tale for RNA folding studies.Nucleic acids research · 2004Article
- Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2004Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The hairpin ribozyme comprises two formally unpaired loops carried on two arms of a four-way helical RNA junction. Addition of divalent metal ions brings about a conformational transition into an antiparallel structure in which there is an intimate association between the loops to generate the active form of the ribozyme. In this study, we have used fluorescence resonance energy transfer to analyze the global folding of the complete ribozyme, and the simple four-way junction derived from it, over a wide concentration range of divalent and monovalent metal ions. The simple junction undergoes an ion-induced rotation into an antiparallel form. In the presence of a constant background concentration of sodium ions, the magnesium-ion-induced transition is characterized by noncooperative binding with a Hill coefficient n = 1. By contrast, the magnesium-ion-induced folding of the complete ribozyme is more complex, involving two distinct binding phases. The first phase occurs in the micromolar range, and involves the cooperative binding of at least three magnesium ions. This can also be achieved by high concentrations of sodium ions, and is therefore likely to be due to diffuse binding of cations at the junction and the interface of the loop-loop interaction. The second phase occurs in the millimolar range, and can only be induced by divalent metal ions. This transition occurs in response to the noncooperative, site-specific binding of magnesium ions. We observe a good correlation between the extent of ion-induced folding and cleavage activity.
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