ReviewWiley interdisciplinary reviews. RNA
Recognition modes of RNA tetraloops and tetraloop-like motifs by RNA-binding proteins.
Review in Wiley interdisciplinary reviews. RNA. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 77 citations in OpenAlex.
- A large-scale cryo-EM RNA motif dataset and benchmark for machine learning-based structure modeling.Computational biology and chemistry · 2026Article
- Zα and Zβ domains of ADAR1 and ZBP1 bind G-quadruplexes with nanomolar affinities, establishing Zβ as a G-quadruplex-specific domain.Nucleic acids research · 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
- Mini-Hairpin DNA: Extraordinarily Stable Structure and Its Applications.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Identification of conserved RNA secondary structures in human respiratory syncytial virus A (hRSV A).NAR genomics and bioinformatics · 2025Article
- Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures.Scientific reports · 2025Article
- DynaRNA: accurate dynamic RNA conformation ensemble generation with diffusion model.Communications biology · 2025Article
- Unraveling unbreakable hairpins: characterizing RNA secondary structures that are persistent after dinucleotide shuffling.RNA (New York, N.Y.) · 2025Article
- Deaminase-based RNA recording enables high throughput mutational profiling of protein-RNA interactions.bioRxiv : the preprint server for biology · 2025Article
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2.Journal of the American Chemical Society · 2024Article
- Major-groove sequence-specific RNA recognition by LoaP, a paralog of transcription elongation factor NusG.Structure (London, England : 1993) · 2024Article
- Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.Journal of chemical information and modeling · 2024Article
- Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop.The journal of physical chemistry. B · 2024Article
- Structural basis for cloverleaf RNA-initiated viral genome replication.Nucleic acids research · 2023Article
- Conserved Sequences in the 5' and 3' Untranslated Regions of Jingmenvirus Group Representatives.Viruses · 2023Article
- Characterizing the Conformational Free-Energy Landscape of RNA Stem-Loops Using Single-Molecule Field-Effect Transistors.Journal of the American Chemical Society · 2023Article
- Acylation probing of "generic" RNA libraries reveals critical influence of loop constraints on reactivity.Cell chemical biology · 2022Article
- Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases.ACS chemical biology · 2022Article
- Sequence-specific RNA recognition by an RGG motif connects U1 and U2 snRNP for spliceosome assembly.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
RNA hairpins are the most commonly occurring secondary structural elements in RNAs and serve as nucleation sites for RNA folding, RNA-RNA, and RNA-protein interactions. RNA hairpins are frequently capped by tetraloops, and based on sequence similarity, three broad classes of RNA tetraloops have been defined: GNRA, UNCG, and CUYG. Other classes such as the UYUN tetraloop in histone mRNAs, the UGAA in 16S rRNA, the AUUA tetraloop from the MS2 bacteriophage, and the AGNN tetraloop that binds RNase III have also been characterized. The tetraloop structure is compact and is usually characterized by a paired interaction between the first and fourth nucleotides. The two unpaired nucleotides in the loop are usually involved in base-stacking or base-phosphate hydrogen bonding interactions. Several structures of RNA tetraloops, free and complexed to other RNAs or proteins, are now available and these studies have increased our understanding of the diverse mechanisms by which this motif is recognized. RNA tetraloops can mediate RNA-RNA contacts via the tetraloop-receptor motif, kissing hairpin loops, A-minor interactions, and pseudoknots. While these RNA-RNA interactions are fairly well understood, how RNA-binding proteins recognize RNA tetraloops and tetraloop-like motifs remains unclear. In this review, we summarize the structures of RNA tetraloop-protein complexes and the general themes that have emerged on sequence- and structure-specific recognition of RNA tetraloops. We highlight how proteins achieve molecular recognition of this nucleic acid motif, the structural adaptations observed in the tetraloop to accommodate the protein-binding partner, and the role of dynamics in recognition.
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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.