ArticleBiophysical journal2017
Mapping the Universe of RNA Tetraloop Folds.
Article in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops.RNA (New York, N.Y.) · 2026Article
- Structure and sequence characteristics of 5'-stem-loop 1 modulate the escape from nsp1-mediated repression in SARS-CoV-2 variants.Nucleic acids research · 2026Article
- A Two-Step Purification Strategy for RNA and RNA-Protein Complexes for Crystallization.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures.Scientific reports · 2025Article
- RNA adapts its flexibility to efficiently fold and resist unfolding.Nucleic acids research · 2025Article
- Unique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA.Nucleic acids research · 2025Article
- Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.Journal of chemical information and modeling · 2025Article
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.Nucleic acids research · 2024Article
- Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops.Journal of chemical theory and computation · 2024Article
- Identification and characterization of RNA pentaloop sequence families.NAR genomics and bioinformatics · 2023Article
- Zika virus RNA structure controls its unique neurotropism by bipartite binding to Musashi-1.Nature communications · 2023Article
- Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones.Nature communications · 2022Article
- Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field.Journal of computational biophysics and chemistry · 2022Article
- RR3DD: an RNA global structure-based RNA three-dimensional structural classification database.RNA biology · 2021Article
- The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity.Nucleic acids research · 2021Article
- In vitro selected GUAA tetraloop-binding receptors with structural plasticity and evolvability towards natural RNA structural modules.Nucleic acids research · 2021Article
- A unified dinucleotide alphabet describing both RNA and DNA structures.Nucleic acids research · 2020Article
- Integrating NMR and simulations reveals motions in the UUCG tetraloop.Nucleic acids research · 2020Article
- RNA CoSSMos 2.0: an improved searchable database of secondary structure motifs in RNA three-dimensional structures.Database : the journal of biological databases and curation · 2020Article
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2 authors.
Funding
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Abstract
We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the relationship among the different folds. The cluster analysis also identifies 20 novel tetraloop folds that are peculiar to specific positions in ribosomal RNAs and that are stabilized by tertiary interactions. In our RNA tetraloop database we find a significant number of non-GNRA and non-UNCG sequences adopting the canonical GNRA and UNCG folds. Conversely, we find a significant number of GNRA and UNCG sequences adopting non-GNRA and non-UNCG folds. Our analysis demonstrates that there is not a simple one-to-one, but rather a many-to-many mapping between tetraloop sequence and tetraloop fold.
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