ArticleRNA (New York, N.Y.)2000
The folding of the hairpin ribozyme: dependence on the loops and the junction.
Article in RNA (New York, N.Y.), 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 55 citations in OpenAlex.
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- Characterization of the glmS Ribozymes from Listeria Monocytogenes and Clostridium Difficile.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- Enhanced Ribozyme-Catalyzed Recombination and Oligonucleotide Assembly in Peptide-RNA Condensates.Angewandte Chemie (International ed. in English) · 2021Article
- Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs.Nucleic acids research · 2021Article
- Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.RNA (New York, N.Y.) · 2017Article
- Tuning RNA folding and function through rational design of junction topology.Nucleic acids research · 2017Article
- Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.Journal of the American Chemical Society · 2015Article
- Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.Nucleic acids research · 2014Article
- 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
- Clustering to identify RNA conformations constrained by secondary structure.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Exploring ribozyme conformational changes with X-ray crystallography.Methods (San Diego, Calif.) · 2009Review
- Mutational inhibition of ligation in the hairpin ribozyme: substitutions of conserved nucleobases A9 and A10 destabilize tertiary structure and selectively promote cleavage.RNA (New York, N.Y.) · 2008Article
- Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.RNA (New York, N.Y.) · 2006Article
- Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Characterization of a native hammerhead ribozyme derived from schistosomes.RNA (New York, N.Y.) · 2005Article
- Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements.RNA (New York, N.Y.) · 2004Article
- Modifications and deletions of helices within the hairpin ribozyme-substrate complex: an active ribozyme lacking helix 1.RNA (New York, N.Y.) · 2004Article
- A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Structural basis for a lethal mutation in U6 RNA.Biochemistry · 2003Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
In its natural context, the hairpin ribozyme is constructed around a four-way helical junction. This presents the two loops that interact to form the active site on adjacent arms, requiring rotation into an antiparallel structure to bring them into proximity. In the present study we have compared the folding of this form of the ribozyme and subspecies lacking either the loops or the helical junction using fluorescence resonance energy transfer. The complete ribozyme as a four-way junction folds into an antiparallel structure by the cooperative binding of magnesium ions, requiring 20-40 microM for half-maximal extent of folding ([Mg2+]1/2) and a Hill coefficient n = 2. The isolated junction (lacking the loops) also folds into a corresponding antiparallel structure, but does so noncooperatively (n = 1) at a higher magnesium ion concentration ([Mg2+]1/2 = 3 mM). Introduction of a G + 1A mutation into loop A of the ribozyme results in a species with very similar folding to the simple junction, and complete loss of ribozyme activity. Removal of the junction from the ribozyme, replacing it either with a strand break (serving as a hinge) or a GC5 bulge, results in greatly impaired folding, with [Mg2+]1/2 > 20 mM. The results indicate that the natural form of the ribozyme undergoes ion-induced folding by the cooperative formation of an antiparallel junction and loop-loop interaction to generate the active form of the ribozyme. The four-way junction thus provides a scaffold in the natural RNA that facilitates the folding of the ribozyme into the active form.
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