ArticleRNA (New York, N.Y.)2013
Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides.
Article in RNA (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 113 citations in OpenAlex.
- Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.bioRxiv : the preprint server for biology · 2026Article
- Structural analysis of uridine modifications in solved RNA structures.NAR genomics and bioinformatics · 2026Article
- A method for estimating energy parameters of RNAs by differentiating base-pairing probabilities.NAR genomics and bioinformatics · 2025Article
- Pseudouridine residues as substrates for serum ribonucleases.RNA (New York, N.Y.) · 2025Article
- Functions and therapeutic applications of pseudouridylation.Nature reviews. Molecular cell biology · 2025Review
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Article
- RNA modifications: emerging players in the regulation of reproduction and development.Acta biochimica et biophysica Sinica · 2024Review
- RluA is the major mRNA pseudouridine synthase in Escherichia coli.PLoS genetics · 2024Article
- Structure and sequence at an RNA template 5' end influence insertion of transgenes by an R2 retrotransposon protein.RNA (New York, N.Y.) · 2024Article
- Exploring the challenges of RNAi-based strategies for crop protection.Advanced biotechnology · 2024Review
- Decoding the 'Fifth' Nucleotide: Impact of RNA Pseudouridylation on Gene Expression and Human Disease.Molecular biotechnology · 2024Review
- Review
- Pseudouridine andRSC chemical biology · 2024Review
- Why U matters: detection and functions of pseudouridine modifications in mRNAs.Trends in biochemical sciences · 2024Review
- Global RNA modifications to the MALAT1 triple helix differentially affect thermostability and weaken binding to METTL16.The Journal of biological chemistry · 2024Article
- Modified RNAs and predictions with the ViennaRNA Package.Bioinformatics (Oxford, England) · 2023Article
- RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life.Science advances · 2023Article
- Translation ofFrontiers in molecular biosciences · 2023Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Pseudouridine (Ψ) is the most common noncanonical nucleotide present in naturally occurring RNA and serves a variety of roles in the cell, typically appearing where structural stability is crucial to function. Ψ residues are isomerized from native uridine residues by a class of highly conserved enzymes known as pseudouridine synthases. In order to quantify the thermodynamic impact of pseudouridylation on U-A base pairs, 24 oligoribonucleotides, 16 internal and eight terminal Ψ-A oligoribonucleotides, were thermodynamically characterized via optical melting experiments. The thermodynamic parameters derived from two-state fits were used to generate linearly independent parameters for use in secondary structure prediction algorithms using the nearest-neighbor model. On average, internally pseudouridylated duplexes were 1.7 kcal/mol more stable than their U-A counterparts, and terminally pseudouridylated duplexes were 1.0 kcal/mol more stable than their U-A equivalents. Due to the fact that Ψ-A pairs maintain the same Watson-Crick hydrogen bonding capabilities as the parent U-A pair in A-form RNA, the difference in stability due to pseudouridylation was attributed to two possible sources: the novel hydrogen bonding capabilities of the newly relocated imino group as well as the novel stacking interactions afforded by the electronic configuration of the Ψ residue. The newly derived nearest-neighbor parameters for Ψ-A base pairs may be used in conjunction with other nearest-neighbor parameters for accurately predicting the most likely secondary structure of A-form RNA containing Ψ-A base pairs.
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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.