ArticleNucleic acids research2007
Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Cooperativity and Allostery in RNA Systems.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch.Nature chemical biology · 2017Article
- Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy.Nucleic acids research · 2017Article
- A magnesium-induced triplex pre-organizes the SAM-II riboswitch.PLoS computational biology · 2017Article
- Fluorescence Resonance Energy Transfer Characterization of DNA Wrapping in Closed and Open Escherichia coli RNA Polymerase-λP(R) Promoter Complexes.Biochemistry · 2016Article
- Nucleic acid catalysis: metals, nucleobases, and other cofactors.Chemical reviews · 2014Review
- Complex RNA folding kinetics revealed by single-molecule FRET and hidden Markov models.Journal of the American Chemical Society · 2014Article
- Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures.Algorithms for molecular biology : AMB · 2014Article
- Microscale thermophoresis provides insights into mechanism and thermodynamics of ribozyme catalysis.RNA biology · 2013Article
- Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA.RNA (New York, N.Y.) · 2013Article
- Three critical hydrogen bonds determine the catalytic activity of the Diels-Alderase ribozyme.Nucleic acids research · 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
- Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA.The Journal of biological chemistry · 2011Article
- Radioactive phosphorylation of alcohols to monitor biocatalytic Diels-Alder reactions.PloS one · 2011Article
- Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations.RNA (New York, N.Y.) · 2010Article
- DNA as a versatile chemical component for catalysis, encoding, and stereocontrol.Angewandte Chemie (International ed. in English) · 2010Review
- Selection of RNA aptamers imported into yeast and human mitochondria.RNA (New York, N.Y.) · 2010Article
- Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine.Biochemistry · 2010Article
- Single-molecule Förster resonance energy transfer studies of RNA structure, dynamics and function.Biophysical reviews · 2009Review
- Ligand-regulated oligomerization of beta(2)-adrenoceptors in a model lipid bilayer.The EMBO journal · 2009Article
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5 authors.
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Abstract
Here, we report a single-molecule fluorescence resonance energy transfer (FRET) study of a Diels-Alderase (DAse) ribozyme, a 49-mer RNA with true catalytic properties. The DAse ribozyme was labeled with Cy3 and Cy5 as a FRET pair of dyes to observe intramolecular folding, which is a prerequisite for its recognition and turnover of two organic substrate molecules. FRET efficiency histograms and kinetic data were taken on a large number of surface-immobilized ribozyme molecules as a function of the Mg(2+) concentration in the buffer solution. From these data, three separate states of the DAse ribozyme can be distinguished, the unfolded (U), intermediate (I) and folded (F) states. A thermodynamic model was developed to quantitatively analyze the dependence of these states on the Mg(2+) concentration. The FRET data also provide information on structural properties. The I state shows a strongly cooperative compaction with increasing Mg(2+) concentration that arises from association with several Mg(2+) ions. This transition is followed by a second Mg(2+)-dependent cooperative transition to the F state. The observation of conformational heterogeneity and continuous fluctuations between the I and F states on the approximately 100 ms timescale offers insight into the folding dynamics of this ribozyme.
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