ArticleNucleic acids research2015
Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Continuous UV irradiation played an inconclusive role in selecting the canonical genetic alphabet.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Synthesis and Hybridization Properties of RNA Oligomers Containing Biologically Relevant 5-Aminomethyl-2-thiouridines (xnmCurrent medicinal chemistry · 2026Article
- From U to mnm⁵Se²U: tuning base pairing preferences through 2-chalcogen and 5-methylaminomethyl modifications.Scientific reports · 2025Article
- A Geranylated Natural Product Simamycin Disrupts the Allosteric Catalysis of tRNA-2-selenouridine Synthase SelU.Biochemistry · 2025Article
- Nonenzymatic RNA copying with a potentially primordial genetic alphabet.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Recent Update on siRNA Therapeutics.International journal of molecular sciences · 2025Review
- Loss of both wobbleUFrontiers in plant science · 2025Article
- Cross-Effects in Folding and Phase Transitions of hnRNP A1 and C9Orf72 RNA G4 In Vitro.Molecules (Basel, Switzerland) · 2024Article
- Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying.Journal of the American Chemical Society · 2024Article
- Review
- Kinetic explanations for the sequence biases observed in the nonenzymatic copying of RNA templates.Nucleic acids research · 2022Article
- Sequencing the origins of life.BBA advances · 2022Review
- Sulfur modification in natural RNA and therapeutic oligonucleotides.RSC chemical biology · 2021Review
- Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension.Nucleic acids research · 2021Article
- Article
- Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea.RNA (New York, N.Y.) · 2020Article
- Naturally occurring modified ribonucleosides.Wiley interdisciplinary reviews. RNA · 2020Review
- C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3' Synonymous mRNA Codons.International journal of molecular sciences · 2020Article
- A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides.Journal of the American Chemical Society · 2020Article
- Alanine tRNAs Translate Environment Into Behavior inFrontiers in cell and developmental biology · 2020Article
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Authors and funding
5 authors.
Funding
Abstract
Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s(2)U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s(2)U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s(2)U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s(2)U:A and s(2)U:U pairs and their native counterparts. These results indicate that s(2)U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s(2)U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s(2)U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s(2)U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using (1)H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying.
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