ArticleBiochemistry2011
Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- An efficient algorithm for exploring RNA branching conformations under the nearest-neighbor thermodynamic model.Algorithms for molecular biology : AMB · 2026Article
- Can geometric combinatorics improve RNA branching predictions?BMC bioinformatics · 2025Article
- The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.Biochemistry · 2022Article
- A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including NJournal of molecular biology · 2022Article
- VfoldMCPX: predicting multistrand RNA complexes.RNA (New York, N.Y.) · 2022Article
- Fluorescence-Based Binding Characterization of Small Molecule Ligands Targeting CUG RNA Repeats.International journal of molecular sciences · 2022Article
- Review
- Article
- Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding.The journal of physical chemistry. B · 2021Article
- Determining parameters for non-linear models of multi-loop free energy change.Bioinformatics (Oxford, England) · 2019Article
- Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.RNA (New York, N.Y.) · 2018Article
- A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction.Nucleic acids research · 2017Article
- Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA.RNA (New York, N.Y.) · 2017Article
- Blind tests of RNA nearest-neighbor energy prediction.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Bridging the gap between in vitro and in vivo RNA folding.Quarterly reviews of biophysics · 2016Article
- The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective.RNA biology · 2013Article
- A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.RNA (New York, N.Y.) · 2012Article
- Thermodynamically stable RNA three-way junction for constructing multifunctional nanoparticles for delivery of therapeutics.Nature nanotechnology · 2011Article
- Understanding the transcriptome through RNA structure.Nature reviews. Genetics · 2011Review
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.
Funding
Abstract
Three-way multibranch loops (junctions) are common in RNA secondary structures. Computer algorithms such as RNAstructure and MFOLD do not consider the identity of unpaired nucleotides in multibranch loops when predicting secondary structure. There is limited experimental data, however, to parametrize this aspect of these algorithms. In this study, UV optical melting and a fluorescence competition assay are used to measure stabilities of multibranch loops containing up to five unpaired adenosines or uridines or a loop E motif. These results provide a test of our understanding of the factors affecting multibranch loop stability and provide revised parameters for predicting stability. The results should help to improve predictions of RNA secondary structure.
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.