ArticleNucleic acids research2017
Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Article
- Assessing the contribution of rare DNA states to cancer mutational signatures using sequence-specific conformational fingerprinting.Nature communications · 2026Article
- Assessing the contribution of rare DNA states to cancer mutational signatures using sequence-specific conformational fingerprinting.Research square · 2025Article
- An A-T Hoogsteen Base Pair in a Naked DNA Hairpin Motif: A Protein-Recognized Conformation.Angewandte Chemie (International ed. in English) · 2025Article
- Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.Journal of chemical information and modeling · 2025Article
- Optimising in-cell NMR acquisition for nucleic acids.Journal of biomolecular NMR · 2024Article
- Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.Nucleic acids research · 2024Article
- Direct Measurement of 8OG Syn-Anti Flips in Mutagenic 8OG·A and Long-Range Damage-Dependent Hoogsteen Breathing Dynamics UsingThe journal of physical chemistry. B · 2024Article
- Direct Measurement of 8OGbioRxiv : the preprint server for biology · 2024Article
- Experimental detection of conformational transitions between forms of DNA: problems and prospects.Biophysical reviews · 2023Review
- Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements.Frontiers in molecular biosciences · 2023Article
- Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA.Journal of chemical information and modeling · 2022Article
- Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism.Nucleic acids research · 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
- Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes.The journal of physical chemistry. B · 2022Article
- Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.Nucleic acids research · 2021Article
- Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.Current opinion in structural biology · 2021Review
- Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy.The journal of physical chemistry. B · 2021Article
- Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell.International journal of molecular sciences · 2021Article
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7 authors.
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Abstract
In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair.
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