ArticleRNA (New York, N.Y.)2014
A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme.
Article in RNA (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 33 citations in OpenAlex.
- Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches.Journal of molecular biology · 2022Review
- Tolerance of Senecavirus A to Mutations in Its Kissing-Loop or Pseudoknot Structure Computationally Predicted in 3' Untranslated Region.Frontiers in microbiology · 2022Article
- Self-cleaving ribozymes: substrate specificity and synthetic biology applications.RSC chemical biology · 2021Review
- Conformational Ensemble ofThe journal of physical chemistry. B · 2021Article
- Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions.Molecules (Basel, Switzerland) · 2020Review
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation.Nucleic acids research · 2019Article
- An unexpected RNA distal interaction mode found in an essential region of the hepatitis C virus genome.Nucleic acids research · 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
- Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.Biophysical chemistry · 2017Article
- MgBiophysical journal · 2017Article
- Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme.Journal of the American Chemical Society · 2017Article
- Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions.Nucleic acids research · 2016Article
- Discovery and characterization of the first non-coding RNA that regulates gene expression, micF RNA: A historical perspective.World journal of biological chemistry · 2015Article
- Chemistry and Biology of Self-Cleaving Ribozymes.Trends in biochemical sciences · 2015Review
- Crystal structure of the Varkud satellite ribozyme.Nature chemical biology · 2015Article
- Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.The journal of physical chemistry. B · 2015Article
- 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.RNA (New York, N.Y.) · 2015Article
- Fitness Landscapes of Functional RNAs.Life (Basel, Switzerland) · 2015Review
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2 authors at 1 institution in 1 country.
Funding
Abstract
Kissing loops are tertiary structure elements that often play key roles in functional RNAs. In the Neurospora VS ribozyme, a kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain is known to play an important role in substrate recognition. In addition, this I/V kissing-loop interaction is associated with a helix shift in SLI that activates the substrate for catalysis. To better understand the role of this kissing-loop interaction in substrate recognition and activation by the VS ribozyme, we performed a thermodynamic characterization by isothermal titration calorimetry using isolated SLI and SLV stem-loops. We demonstrate that preshifted SLI variants have higher affinity for SLV than shiftable SLI variants, with an energetic cost of 1.8-3 kcal/mol for the helix shift in SLI. The affinity of the preshifted SLI for SLV is remarkably high, the interaction being more stable by 7-8 kcal/mol than predicted for a comparable duplex containing three Watson-Crick base pairs. The structural basis of this remarkable stability is discussed in light of previous NMR studies. Comparative thermodynamic studies reveal that kissing-loop complexes containing 6-7 Watson-Crick base pairs are as stable as predicted from comparable RNA duplexes; however, those with 2-3 Watson-Crick base pairs are more stable than predicted. Interestingly, the stability of SLI/ribozyme complexes is similar to that of SLI/SLV complexes. Thus, the I/V kissing loop interaction represents the predominant energetic contribution to substrate recognition by the trans-cleaving VS ribozyme.
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