ArticleJournal of molecular biology2009
Analysis of four-way junctions in RNA structures.
Article in Journal of molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
What it found
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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
76 citing papers in PubMed.
- R3J-AGNN: GNN-Based Prediction of Inter-Branch Angles in RNA Three-Way Junctions from Secondary Structure.Biology · 2026Article
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- Comprehensive datasets for RNA design, machine learning, and beyond.Scientific reports · 2025Article
- Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer.Nucleic acids research · 2025Article
- Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets.RNA (New York, N.Y.) · 2025Article
- Porphyrins as Chiroptical Conformational Probes for Biomolecules.Molecules (Basel, Switzerland) · 2025Review
- Structural basis for tRNA mimicry by mascRNA and menRNA.Cell discovery · 2025Article
- A Glimpse of Noncoding RNAs: Secondary Structure, Emerging Trends, and Potential Applications in Human Diseases.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST.Nature communications · 2024Article
- Recognition of the tRNA structure: Everything everywhere but not all at once.Cell chemical biology · 2024Review
- When will RNA get its AlphaFold moment?Nucleic acids research · 2023Article
- Structural basis for cloverleaf RNA-initiated viral genome replication.Nucleic acids research · 2023Article
- Intricate 3D architecture of a DNA mimic of GFP.Nature · 2023Article
- RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.Nucleic acids research · 2023Article
- Avidity-based bright and photostable light-up aptamers for single-molecule mRNA imaging.Nature chemical biology · 2023Article
- Article
- A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript.Nucleic acids research · 2022Article
- rRNA expansion segment 7 in eukaryotes: from Signature Fold to tentacles.Nucleic acids research · 2022Article
- Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication.Microbiology and molecular biology reviews : MMBR · 2022Review
- Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.International journal of molecular sciences · 2022Article
16 more citing papers are in PubMed but not listed here.
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.
Funding
Abstract
RNA secondary structures can be divided into helical regions composed of canonical Watson-Crick and related base pairs, as well as single-stranded regions such as hairpin loops, internal loops, and junctions. These elements function as building blocks in the design of diverse RNA molecules with various fundamental functions in the cell. To better understand the intricate architecture of three-dimensional (3D) RNAs, we analyze existing RNA four-way junctions in terms of base-pair interactions and 3D configurations. Specifically, we identify nine broad junction families according to coaxial stacking patterns and helical configurations. We find that helices within junctions tend to arrange in roughly parallel and perpendicular patterns and stabilize their conformations using common tertiary motifs such as coaxial stacking, loop-helix interaction, and helix packing interaction. Our analysis also reveals a number of highly conserved base-pair interaction patterns and novel tertiary motifs such as A-minor-coaxial stacking combinations and sarcin/ricin motif variants. Such analyses of RNA building blocks can ultimately help in the difficult task of RNA 3D structure prediction.
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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.