ArticleRNA (New York, N.Y.)2015
The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 19 citations in OpenAlex.
- RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions.RNA (New York, N.Y.) · 2024Article
- An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme.Nucleic acids research · 2021Article
- A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation.Nucleic acids research · 2019Article
- Principles for targeting RNA with drug-like small molecules.Nature reviews. Drug discovery · 2018Review
- Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges.Biophysical journal · 2018Article
- Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme.Wiley interdisciplinary reviews. RNA · 2017Review
- Mapping the Universe of RNA Tetraloop Folds.Biophysical journal · 2017Article
- NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions.The journal of physical chemistry letters · 2016Article
- Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions.Nucleic acids research · 2016Article
- Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations.Nucleic acids research · 2016Article
- Ribozymes: How RNA catalyzes cyclization.Nature chemical biology · 2015Article
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4 authors at 2 institutions in 1 country.
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Abstract
As part of an effort to structurally characterize the complete Neurospora VS ribozyme, NMR solution structures of several subdomains have been previously determined, including the internal loops of domains I and VI, the I/V kissing-loop interaction and the III-IV-V junction. Here, we expand this work by determining the NMR structure of a 62-nucleotide RNA (J236) that encompasses the VS ribozyme II-III-VI three-way junction and its adjoining stems. In addition, we localize Mg(2+)-binding sites within this structure using Mn(2+)-induced paramagnetic relaxation enhancement. The NMR structure of the J236 RNA displays a family C topology with a compact core stabilized by continuous stacking of stems II and III, a cis WC/WC G•A base pair, two base triples and two Mg(2+) ions. Moreover, it reveals a remote tertiary interaction between the adenine bulges of stems II and VI. Additional NMR studies demonstrate that both this bulge-bulge interaction and Mg(2+) ions are critical for the stable folding of the II-III-VI junction. The NMR structure of the J236 RNA is consistent with biochemical studies on the complete VS ribozyme, but not with biophysical studies performed with a minimal II-III-VI junction that does not contain the II-VI bulge-bulge interaction. Together with previous NMR studies, our findings provide important new insights into the three-dimensional architecture of this unique ribozyme.
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