ArticleJournal of molecular biology2008
Hinge stiffness is a barrier to RNA folding.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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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.
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Who cites it
35 citing papers in PubMed, 50 citations in OpenAlex.
- Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis.Methods in enzymology · 2022Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- Millisecond timescale reactions observed via X-ray spectroscopy in a 3D microfabricated fused silica mixer.Journal of synchrotron radiation · 2021Article
- Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs.Biochemistry · 2019Article
- Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations.Biophysical journal · 2019Article
- How the Conformations of an Internal Junction Contribute to Fold an RNA Domain.The journal of physical chemistry. B · 2018Article
- Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.The journal of physical chemistry letters · 2018Article
- Revealing the distinct folding phases of an RNA three-helix junction.Nucleic acids research · 2018Article
- Predicting Ion Effects in an RNA Conformational Equilibrium.The journal of physical chemistry. B · 2017Article
- 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
- Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations.Journal of chemical theory and computation · 2016Article
- Understanding the kinetic mechanism of RNA single base pair formation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Tuning RNA Flexibility with Helix Length and Junction Sequence.Biophysical journal · 2015Article
- Prostate-specific RNA aptamer: promising nucleic acid antibody-like cancer detection.Scientific reports · 2015Article
- Article
- Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions.Biochemistry · 2013Article
- Understanding the role of three-dimensional topology in determining the folding intermediates of group I introns.Biophysical journal · 2013Article
- Role of ion valence in the submillisecond collapse and folding of a small RNA domain.Biochemistry · 2013Article
- Ion-mediated RNA structural collapse: effect of spatial confinement.Biophysical journal · 2012Article
- Predicting ion-nucleic acid interactions by energy landscape-guided sampling.Journal of chemical theory and computation · 2012Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Cation-mediated RNA folding from extended to compact, biologically active conformations relies on a temporal balance of forces. The Mg2 +-mediated folding of the Tetrahymena thermophila ribozyme is characterized by rapid nonspecific collapse followed by tertiary-contact-induced compaction. This article focuses on an autonomously folding portion of the Tetrahymena ribozyme, its P4-P6 domain, in order to probe one facet of the rapid collapse: chain flexibility. The time evolution of P4-P6 folding was followed by global and local measures as a function of Mg2 + concentration. While all concentrations of Mg2 + studied are sufficient to screen the charge on the helices, the rates of compaction and tertiary contact formation diverge as the concentration of Mg2 + increases; collapse is greatly accelerated by Mg2 +, while tertiary contact formation is not. These studies highlight the importance of chain stiffness to RNA folding; at 10 mM Mg2 +, a stiff hinge limits the rate of P4-P6 folding. At higher magnesium concentrations, the rate-limiting step shifts from hinge bending to tertiary contact formati
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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.