ArticleRNA (New York, N.Y.)2005
Fast formation of the P3-P7 pseudoknot: a strategy for efficient folding of the catalytically active ribozyme.
Article in RNA (New York, N.Y.), 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed, 20 citations in OpenAlex.
- Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time.Nucleic acids research · 2023Article
- RNA catalysis as a probe for chaperone activity of DEAD-box helicases.Methods in enzymology · 2012Article
- The Azoarcus group I intron ribozyme misfolds and is accelerated for refolding by ATP-dependent RNA chaperone proteins.The Journal of biological chemistry · 2011Article
- Enhancing the prebiotic relevance of a set of covalently self-assembling, autorecombining RNAs through in vitro selection.Journal of molecular evolution · 2010Article
- Slow formation of a pseudoknot structure is rate limiting in the productive co-transcriptional folding of the self-splicing Candida intron.RNA (New York, N.Y.) · 2009Article
- Structural rearrangements linked to global folding pathways of the Azoarcus group I ribozyme.Journal of molecular biology · 2009Article
- A phage RNA-binding protein binds to a non-cognate structured RNA and stabilizes its core structure.Biochemical and biophysical research communications · 2009Article
- Coordination of two sequential ester-transfer reactions: exogenous guanosine binding promotes the subsequent omegaG binding to a group I intron.Nucleic acids research · 2008Article
- Splicing and evolution of an unusually small group I intron.Current genetics · 2008Article
- Tertiary interactions determine the accuracy of RNA folding.Journal of the American Chemical Society · 2008Article
- Monovalent cations use multiple mechanisms to resolve ribozyme misfolding.RNA (New York, N.Y.) · 2006Article
- Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup.Nucleic acids research · 2005Article
- A peripheral element assembles the compact core structure essential for group I intron self-splicing.Nucleic acids research · 2005Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Formation of the P3-P7 pseudoknot structure, the core of group I ribozymes, requires long-range base pairing. Study of the Tetrahymena ribozyme appreciates the hierarchical folding of the large, multidomain RNA, in which the P3-P7 core folds significantly slower than do the other domains. Here we explored the formation of the P3-P7 pseudoknot of the Candida ribozyme that has been reported to concertedly fold to the catalytically active structure with a rate constant of 2 min(-1). We demonstrate that pseudoknot formation occurs during the rapid ribozyme compaction, coincident with formation of many tertiary interactions of the ribozyme. A low physiological concentration of magnesium (1.5 mM) is sufficient to fully support the pseudoknot formation. The presence of nonnative intermediates containing an unfolded P3-P7 region is evident. However, catalysis-based analysis shows these nonnative intermediates are stable and fail to convert to the catalytically active structure, suggesting that rapid pseudoknot formation is essential for folding of the active ribozyme. Interestingly, RNAstructure predicts no stable Alt P3 structure for the Candida ribozyme, but two stable Alt P3s for the Tetrahymena ribozyme, explaining the dramatic difference in folding of the P3-P7 core of these two ribozymes. We propose that rapid formation of the P3-P7 pseudoknot represents a folding strategy ensuring efficient production of the catalytically active structure of group I ribozymes, which sheds new light on the mechanism of effective ribozyme folding in vivo.
Indexed as
Identifiers
What OpenQuestion holds
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.