ArticleRNA (New York, N.Y.)1999
Quantifying the energetic interplay of RNA tertiary and secondary structure interactions.
Article in RNA (New York, N.Y.), 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 59 citations in OpenAlex.
- Rho (bioRxiv : the preprint server for biology · 2026Article
- Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs.RNA (New York, N.Y.) · 2024Article
- Making target sites in large structured RNAs accessible to RNA-cleaving DNAzymes through hybridization with synthetic DNA oligonucleotides.Nucleic acids research · 2024Article
- Catalytic RNA Oligomers Formed by Co-Oligomerization of a Pair of Bimolecular RNase P Ribozymes.Molecules (Basel, Switzerland) · 2022Article
- Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems.Journal of the American Chemical Society · 2018Article
- The Story of RNA Folding, as Told in Epochs.Cold Spring Harbor perspectives in biology · 2018Review
- Hidden Structural Modules in a Cooperative RNA Folding Transition.Cell reports · 2018Article
- Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme.Journal of the American Chemical Society · 2017Article
- RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly.Journal of molecular biology · 2016Article
- Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.Nature communications · 2016Article
- Ribosome assembly factors Pwp1 and Nop12 are important for folding of 5.8S rRNA during ribosome biogenesis in Saccharomyces cerevisiae.Molecular and cellular biology · 2014Article
- Role of ion valence in the submillisecond collapse and folding of a small RNA domain.Biochemistry · 2013Article
- Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures.Nucleic acids research · 2012Article
- Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding.RNA (New York, N.Y.) · 2012Article
- SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA.Biochemistry · 2008Article
- Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.RNA (New York, N.Y.) · 2008Article
- Direct measurement of tertiary contact cooperativity in RNA folding.Journal of the American Chemical Society · 2008Article
- Deletion of the P5abc peripheral element accelerates early and late folding steps of the Tetrahymena group I ribozyme.Biochemistry · 2007Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
To understand the RNA-folding problem, we must know the extent to which RNA structure formation is hierarchical (tertiary folding of preformed secondary structure). Recently, nuclear magnetic resonance (NMR) spectroscopy was used to show that Mg2+-dependent tertiary interactions force secondary structure rearrangement in the 56-nt tP5abc RNA, a truncated subdomain of the Tetrahymena group I intron. Here we combine mutagenesis with folding computations, nondenaturing gel electrophoresis, high-resolution NMR spectroscopy, and chemical-modification experiments to probe further the energetic interplay of tertiary and secondary interactions in tP5abc. Point mutations predicted to destabilize the secondary structure of folded tP5abc greatly disrupt its Mg2+-dependent folding, as monitored by nondenaturing gels. Imino proton assignments and sequential NOE walks of the two-dimensional NMR spectrum of one of the tP5abc mutants confirm the predicted secondary structure, which does not change in the presence of Mg2+. In contrast to these data on tP5abc, the same point mutations in the context of the P4-P6 domain (of which P5abc is a subdomain) shift the Mg2+ dependence of P4-P6 folding only moderately, and dimethyl sulfate (DMS) modification experiments demonstrate that Mg2+ does cause secondary structure rearrangement of the P4-P6 mutants' P5abc subdomains. Our data provide experimental support for two simple conclusions: (1) Even single point mutations at bases involved only in secondary structure can be enough to tip the balance between RNA tertiary and secondary interactions. (2) Domain context must be considered in evaluating the relative importance of tertiary and secondary contributions. This tertiary/secondary interplay is likely relevant to the folding of many large RNA and to bimolecular snRNA-snRNA and snRNA-intron RNA interactions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.