ArticleNucleic acids research2012
New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed, 36 citations in OpenAlex.
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- Fuzzy RNA recognition by the Trypanosoma brucei editosome.Nucleic acids research · 2022Article
- Visualizing RNA Structures by SAXS-Driven MD Simulations.Frontiers in bioinformatics · 2022Article
- Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction.Nucleic acids research · 2020Article
- RNA Structural Differentiation: Opportunities with Pattern Recognition.Biochemistry · 2019Review
- How the Conformations of an Internal Junction Contribute to Fold an RNA Domain.The journal of physical chemistry. B · 2018Article
- Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.RNA (New York, N.Y.) · 2018Article
- Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges.Biophysical journal · 2018Article
- Tuning RNA folding and function through rational design of junction topology.Nucleic acids research · 2017Article
- Small Molecule-Based Pattern Recognition To Classify RNA Structure.Journal of the American Chemical Society · 2017Article
- Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.Nucleic acids research · 2016Article
- Tuning RNA Flexibility with Helix Length and Junction Sequence.Biophysical journal · 2015Article
- Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.Journal of the American Chemical Society · 2015Article
- Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.The journal of physical chemistry. B · 2015Article
- Dynamic motions of the HIV-1 frameshift site RNA.Biophysical journal · 2015Article
- From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function.Current opinion in structural biology · 2015Review
- Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore.Nucleic acids research · 2014Article
- Insights into domain-domain motions in proteins and RNA from solution NMR.Accounts of chemical research · 2014Review
- Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.Nucleic acids research · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Recent studies have shown that topological constraints encoded at the RNA secondary structure level involving basic steric and stereochemical forces can significantly restrict the orientations sampled by helices across two-way RNA junctions. Here, we formulate these topological constraints in greater quantitative detail and use this topological framework to rationalize long-standing but poorly understood observations regarding the basic behavior of RNA two-way junctions. Notably, we show that the asymmetric nature of the A-form helix and the finite length of a bulge provide a physical basis for the experimentally observed directionality and bulge-length amplitude dependence of bulge induced inter-helical bends. We also find that the topologically allowed space can be modulated by variations in sequence, particularly with the addition of non-canonical GU base pairs at the junction, and, surprisingly, by the length of the 5' and 3' helices. A survey of two-way RNA junctions in the protein data bank confirms that junction residues have a strong preference to adopt looped-in, non-canonically base-paired conformations, providing a route for extending our bulge-directed framework to internal loop motifs and implying a simplified link between secondary and tertiary structure. Finally, our results uncover a new simple mechanism for coupling junction-induced topological constraints with tertiary interactions.
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.