ArticleJournal of molecular biology2006
Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes.
Article in Journal of molecular biology, 2006. 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, 40 citations in OpenAlex.
- Mechanistic Insights of miRNA Hybridization with ssDNA Self Assembled Monolayers on Gold Electrodes: An Electrochemical and Computational Study.Sensors and actuators. B, Chemical · 2026Article
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- VfoldMCPX: predicting multistrand RNA complexes.RNA (New York, N.Y.) · 2022Article
- Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.Journal of chemical theory and computation · 2022Article
- Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions.Computational and structural biotechnology journal · 2022Review
- Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions.Biophysical journal · 2018Article
- A Method to Predict the Structure and Stability of RNA/RNA Complexes.Methods in molecular biology (Clifton, N.J.) · 2016Article
- Spliceosome assembly in the absence of stable U4/U6 RNA pairing.RNA (New York, N.Y.) · 2015Article
- Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing.RNA (New York, N.Y.) · 2014Article
- Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA complex.RNA (New York, N.Y.) · 2013Article
- Free energy cost of stretching mRNA hairpin loops inhibits small RNA binding.Biophysical journal · 2013Article
- Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity.Nucleic acids research · 2012Article
- RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.RNA (New York, N.Y.) · 2012Article
- Structure of the yeast U2/U6 snRNA complex.RNA (New York, N.Y.) · 2012Article
- Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal.RNA (New York, N.Y.) · 2011Article
- Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling.Nucleic acid therapeutics · 2011Article
- Physics-based de novo prediction of RNA 3D structures.The journal of physical chemistry. B · 2011Article
- Computing the conformational entropy for RNA folds.The Journal of chemical physics · 2010Article
- Predicting structures and stabilities for H-type pseudoknots with interhelix loops.RNA (New York, N.Y.) · 2009Article
- Salt dependence of nucleic acid hairpin stability.Biophysical journal · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
We develop a statistical mechanical model for RNA/RNA complexes with both intramolecular and intermolecular interactions. As an application of the model, we compute the free energy landscapes, which give the full distribution for all the possible conformations, for U4/U6 and U2/U6 in major spliceosome and U4atac/U6atac and U12/U6atac in minor spliceosome. Different snRNA experiments found contrasting structures, our free energy landscape theory shows why these structures emerge and how they compete with each other. For yeast U2/U6, the model predicts that the two distinct experimental structures, the four-helix junction structure and the helix Ib-containing structure, can actually coexist and specifically compete with each other. In addition, the energy landscapes suggest possible mechanisms for the conformational switches in splicing. For instance, our calculation shows that coaxial stacking is essential for stabilizing the four-helix junction in yeast U2/U6. Therefore, inhibition of the coaxial stacking possibly by protein-binding may activate the conformational switch from the four-helix junction to the helix Ib-containing structure. Moreover, the change of the energy landscape shape gives information about the conformational changes. We find multiple (native-like and misfolded) intermediates formed through base-pairing rearrangements in snRNA complexes. For example, the unfolding of the U2/U6 undergoes a transition to a misfolded state which is functional, while in the unfolding of U12/U6atac, the functional helix Ib is found to be the last one to unfold and is thus the most stable structural component. Furthermore, the energy landscape gives the stabilities of all the possible (functional) intermediates and such information is directly related to splicing efficiency.
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.