ArticleScientific reports2019
Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 48 citations in OpenAlex.
- CRISPR technologies for detecting DNA and RNA methylation: Mechanisms, platforms, and translational opportunities.Bioengineering & translational medicine · 2026Review
- Engineering polymeric RNA scaffolds as programmable combinatorial innate immune agonists.Nucleic acids research · 2026Article
- Functions and therapeutic applications of pseudouridylation.Nature reviews. Molecular cell biology · 2025Review
- RluA is the major mRNA pseudouridine synthase in Escherichia coli.PLoS genetics · 2024Article
- Decoding the 'Fifth' Nucleotide: Impact of RNA Pseudouridylation on Gene Expression and Human Disease.Molecular biotechnology · 2024Review
- Pseudouridine andRSC chemical biology · 2024Review
- Why U matters: detection and functions of pseudouridine modifications in mRNAs.Trends in biochemical sciences · 2024Review
- Epitranscriptomics as a New Layer of Regulation of Gene Expression in Skeletal Muscle: Known Functions and Future Perspectives.International journal of molecular sciences · 2023Review
- Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA.RNA (New York, N.Y.) · 2023Article
- How does precursor RNA structure influence RNA processing and gene expression?Bioscience reports · 2023Review
- In Vitro Reconstitution of Pseudouridylation Catalyzed by Human Box H/ACA Ribonucleoprotein Particles.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- RNase H-based analysis of synthetic mRNA 5' cap incorporation.RNA (New York, N.Y.) · 2022Article
- Translational recoding by chemical modification of non-AUG start codon ribonucleotide bases.Science advances · 2022Article
- Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives.Journal of computer-aided molecular design · 2022Article
- Structure Characterization ofFrontiers in microbiology · 2022Article
- Pseudouridines in RNAs: switching atoms means shifting paradigms.FEBS letters · 2021Review
- The Importance of the Epi-Transcriptome in Translation Fidelity.Non-coding RNA · 2021Review
- Long Non-Coding RNA Epigenetics.International journal of molecular sciences · 2021Review
- Development of effective potassium acetate extractant.RSC advances · 2021Article
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pseudouridine (Ψ) is the most common chemical modification present in RNA. In general, Ψ increases the thermodynamic stability of RNA. However, the degree of stabilization depends on the sequence and structural context. To explain experimentally observed sequence dependence of the effect of Ψ on the thermodynamic stability of RNA duplexes, we investigated the structure, dynamics and hydration of RNA duplexes with an internal Ψ-A base pair in different nearest-neighbor sequence contexts. The structures of two RNA duplexes containing 5'-GΨC/3'-CAG and 5'-CΨG/3'-GAC motifs were determined using NMR spectroscopy. To gain insight into the effect of Ψ on duplex dynamics and hydration, we performed molecular dynamics (MD) simulations of RNA duplexes with 5'-GΨC/3'-CAG, 5'-CΨG/3'-GAC, 5'-AΨU/3'-UAA and 5'-UΨA/3'-AAU motifs and their unmodified counterparts. Our results showed a subtle impact from Ψ modification on the structure and dynamics of the RNA duplexes studied. The MD simulations confirmed the change in hydration pattern when U is replaced with Ψ. Quantum chemical calculations showed that the replacement of U with Ψ affected the intrinsic stacking energies at the base pair steps depending on the sequence context. The calculated intrinsic stacking energies help to explain the experimentally observed sequence dependent changes in the duplex stability from Ψ modification.
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