ArticleJournal of molecular biology2011
Conformation effects of base modification on the anticodon stem-loop of Bacillus subtilis tRNA(Tyr).
Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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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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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.
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Who cites it
24 citing papers in PubMed, 37 citations in OpenAlex.
- Determining the effects of pseudouridine incorporation on human tRNAs.The EMBO journal · 2025Article
- tRNA Modifications and Dysregulation: Implications for Brain Diseases.Brain sciences · 2024Review
- Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers.Chemical reviews · 2024Review
- Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop.The journal of physical chemistry. B · 2024Article
- Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons.Nucleic acids research · 2024Article
- The life and times of a tRNA.RNA (New York, N.Y.) · 2023Review
- Structural and functional characterization of TrmM in mProtein science : a publication of the Protein Society · 2022Article
- Review
- Posttranscriptional modifications at the 37th position in the anticodon stem-loop of tRNA: structural insights from MD simulations.RNA (New York, N.Y.) · 2021Article
- NAngewandte Chemie (International ed. in English) · 2020Article
- A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.Journal of molecular biology · 2020Article
- Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.Scientific reports · 2019Article
- To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs.IUBMB life · 2019Review
- The chemical diversity of RNA modifications.The Biochemical journal · 2019Review
- mRNA pseudouridylation affects RNA metabolism in the parasiteRNA (New York, N.Y.) · 2017Article
- Structural landscape of base pairs containing post-transcriptional modifications in RNA.RNA (New York, N.Y.) · 2017Article
- tRNA Modifications: Impact on Structure and Thermal Adaptation.Biomolecules · 2017Review
- Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function.Biomolecules · 2017Review
- Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations.Nucleic acids research · 2014Article
- Pseudouridine: still mysterious, but never a fake (uridine)!RNA biology · 2014Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
tRNA molecules contain 93 chemically unique nucleotide base modifications that expand the chemical and biophysical diversity of RNA and contribute to the overall fitness of the cell. Nucleotide modifications of tRNA confer fidelity and efficiency to translation and are important in tRNA-dependent RNA-mediated regulatory processes. The three-dimensional structure of the anticodon is crucial to tRNA-mRNA specificity, and the diverse modifications of nucleotide bases in the anticodon region modulate this specificity. We have determined the solution structures and thermodynamic properties of Bacillus subtilis tRNA(Tyr) anticodon arms containing the natural base modifications N(6)-dimethylallyl adenine (i(6)A(37)) and pseudouridine (ψ(39)). UV melting and differential scanning calorimetry indicate that the modifications stabilize the stem and may enhance base stacking in the loop. The i(6)A(37) modification disrupts the hydrogen bond network of the unmodified anticodon loop including a C(32)-A(38)(+) base pair and an A(37)-U(33) base-base interaction. Although the i(6)A(37) modification increases the dynamic nature of the loop nucleotides, metal ion coordination reestablishes conformational homogeneity. Interestingly, the i(6)A(37) modification and Mg(2+) are sufficient to promote the U-turn fold of the anticodon loop of Escherichia coli tRNA(Phe), but these elements do not result in this signature feature of the anticodon loop in tRNA(Tyr).
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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.