ArticleRNA (New York, N.Y.)2014
Building a stable RNA U-turn with a protonated cytidine.
Article in RNA (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- 5-Formylcytosine is not a prevalent RNA modification in mammalian cells.Nature communications · 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
- Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA.RNA (New York, N.Y.) · 2023Article
- Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection.Frontiers in molecular biosciences · 2021Article
- Coarse-grained dynamic RNA titration simulations.Interface focus · 2019Article
- Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides.Nucleic acids research · 2018Article
- Adenine protonation enables cyclic-di-GMP binding to cyclic-GAMP sensing riboswitches.RNA (New York, N.Y.) · 2018Article
- An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch.Nucleic acids research · 2018Article
- NMR experiments for the rapid identification of P=O···H-X type hydrogen bonds in nucleic acids.Journal of biomolecular NMR · 2017Article
- The crystal structure of the 5΄ functional domain of the transcription riboregulator 7SK.Nucleic acids research · 2017Article
- Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.RNA (New York, N.Y.) · 2017Article
- Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.Journal of molecular biology · 2016Article
- Watson-Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation.RNA (New York, N.Y.) · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone.
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.