ArticleRNA (New York, N.Y.)2017
Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.
Article in RNA (New York, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 46 citations in OpenAlex.
- Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops.RNA (New York, N.Y.) · 2026Article
- Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures.Scientific reports · 2025Article
- Selective Nonenzymatic Formation of Biologically Common RNA Hairpins.Angewandte Chemie (International ed. in English) · 2025Article
- The pseudoknot structure of a viral RNA reveals a conserved mechanism for programmed exoribonuclease resistance.bioRxiv : the preprint server for biology · 2024Article
- High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR.Nucleic acids research · 2023Article
- Conserved Structure Associated with Different 3'CITEs Is Important for Translation of Umbraviruses.Viruses · 2023Article
- Sequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy.The journal of physical chemistry. B · 2023Article
- Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules.Nucleic acids research · 2022Article
- Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.Molecules (Basel, Switzerland) · 2022Article
- Importance of Anion-π Interactions in RNA GAAA and GGAG Tetraloops: A Combined MD and QM Study.Journal of chemical theory and computation · 2021Article
- Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals.Crystals · 2021Article
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- Polysomes Bypass a 50-Nucleotide Coding Gap Less Efficiently Than Monosomes Due to Attenuation of a 5' mRNA Stem-Loop and Enhanced Drop-off.Journal of molecular biology · 2020Article
- Integrating NMR and simulations reveals motions in the UUCG tetraloop.Nucleic acids research · 2020Article
- A unified dinucleotide alphabet describing both RNA and DNA structures.Nucleic acids research · 2020Article
- Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs.Nucleic acids research · 2020Article
- Identification and Characterization of New RNA Tetraloop Sequence Families.Biochemistry · 2019Article
- Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing.Nucleic acids research · 2019Article
- Conformational adaptation of UNCG loops upon crowding.RNA (New York, N.Y.) · 2019Article
- Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA.Nucleic acids research · 2018Article
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its "natural" fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion may occur for loops with UNCG sequences, for instance within tRNA anticodon loops. Hence, we show that some structured tetranucleotide sequences starting with G or U can adopt either of these folds. The underlying structural basis that defines these two fold types is the mutually exclusive stacking of a backbone oxygen on either the first (in GNRA) or the last nucleobase (in UNCG), generating an oxygen-π contact. We thereby propose to refrain from using sequences to distinguish between loop conformations. Instead, we suggest using descriptors such as U-turn (for "GNRA-type" folds) and a newly described Z-turn (for "UNCG-type" folds). Because tetraloops adopt for the largest part only two (inter)convertible turns, we are better able to interpret from a structural perspective loop interchangeability occurring in ribosomes and viral RNA. In this respect, we propose a general view on the inclination for a given sequence to adopt (or not) a specific fold. We also suggest how long-noncoding RNAs may adopt discrete but transient structures, which are therefore hard to predict.
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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.