ArticleNucleic acids research2018
Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?
Article in Nucleic acids research, 2018. 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, 38 citations in OpenAlex.
- How Binding Affinity and Binding Specificity Map to Sequence Space.Journal of molecular evolution · 2026Article
- Thermodynamic and kinetic considerations in DNA triplex formation revealed by ITC.European biophysics journal : EBJ · 2026Article
- Revealing hidden protonated conformational states in RNA dynamic ensembles.Nucleic acids research · 2025Article
- An A-T Hoogsteen Base Pair in a Naked DNA Hairpin Motif: A Protein-Recognized Conformation.Angewandte Chemie (International ed. in English) · 2025Article
- Kinetic Dissection of Proton-Coupled Conformational Transitions in Nucleic Acids by Integrating pH-Dependent NMR and Chemical Modifications.Journal of the American Chemical Society · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs.Journal of chemical information and modeling · 2023Article
- Nucleobases in Meteorites to Nucleobases in RNA and DNA?Journal of molecular evolution · 2022Article
- Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- 1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis.Journal of the American Chemical Society · 2022Article
- Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.Nucleic acids research · 2021Article
- A quantitative model predicts how mNature communications · 2021Article
- Unnatural bases for recognition of noncoding nucleic acid interfaces.Biopolymers · 2021Review
- Structural Insights Into Tautomeric Dynamics in Nucleic Acids and in Antiviral Nucleoside Analogs.Frontiers in molecular biosciences · 2021Review
- Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE iminoMagnetic resonance (Gottingen, Germany) · 2021Article
- Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.The Journal of biological chemistry · 2020Article
- Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.Nature communications · 2020Article
- Article
- Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA.Biophysical journal · 2020Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
A(syn)-U/T and G(syn)-C+ Hoogsteen (HG) base pairs (bps) are energetically more disfavored relative to Watson-Crick (WC) bps in A-RNA as compared to B-DNA by >1 kcal/mol for reasons that are not fully understood. Here, we used NMR spectroscopy, optical melting experiments, molecular dynamics simulations and modified nucleotides to identify factors that contribute to this destabilization of HG bps in A-RNA. Removing the 2'-hydroxyl at single purine nucleotides in A-RNA duplexes did not stabilize HG bps relative to WC. In contrast, loosening the A-form geometry using a bulge in A-RNA reduced the energy cost of forming HG bps at the flanking sites to B-DNA levels. A structural and thermodynamic analysis of purine-purine HG mismatches reveals that compared to B-DNA, the A-form geometry disfavors syn purines by 1.5-4 kcal/mol due to sugar-backbone rearrangements needed to sterically accommodate the syn base. Based on MD simulations, an additional penalty of 3-4 kcal/mol applies for purine-pyrimidine HG bps due to the higher energetic cost associated with moving the bases to form hydrogen bonds in A-RNA versus B-DNA. These results provide insights into a fundamental difference between A-RNA and B-DNA duplexes with important implications for how they respond to damage and post-transcriptional modifications.
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