ReviewNucleic acids research2015
New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.
Review 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 37 papers.
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Who cites it
37 citing papers in PubMed.
- Determination of Nucleotide-Nucleotide and Nucleotide-Amino Acid Binding Interactions from All-Atom Potential-of-Mean-Force Calculations.ACS physical chemistry Au · 2026Article
- SARS-CoV-2 reshapes mNAR molecular medicine · 2025Article
- CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation.Nucleic acids research · 2025Article
- Insights into the A-C Mismatch Conformational Ensemble in Duplex DNA and its Role in Genetic Processes through a Structure-based Review.Journal of molecular biology · 2024Review
- Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.Nucleic acids research · 2024Article
- CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation.bioRxiv : the preprint server for biology · 2024Article
- Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix.bioRxiv : the preprint server for biology · 2024Article
- 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
- Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA.The journal of physical chemistry letters · 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
- Sequence dependence of transient Hoogsteen base pairing in DNA.PLoS computational biology · 2022Article
- Bacterial Biofilms Utilize an Underlying Extracellular DNA Matrix Structure That Can Be Targeted for Biofilm Resolution.Microorganisms · 2022Review
- Nucleic Acids and Their Analogues for Biomedical Applications.Biosensors · 2022Review
- Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.Nucleic acids research · 2021Article
- Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy.The journal of physical chemistry. B · 2021Article
- Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks.Journal of chemical theory and computation · 2021Article
- Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms.Nucleic acids research · 2021Article
- Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.The Journal of biological chemistry · 2020Article
- Slow motions in A·T rich DNA sequence.Scientific reports · 2020Article
- Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.Nature communications · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C1' distance across the bp) to search for HG bps in X-ray structures of DNA duplexes in the Protein Data Bank. The survey identifies 106 A•T and 34 G•C HG bps in DNA duplexes, many of which are undocumented in the literature. It also uncovers HG-like bps with syn purines lacking HG hydrogen bonds or constricted C1'-C1' distances that are analogous to conformations that have been proposed to populate the WC-to-HG transition pathway. The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5'-purine. HG bps induce small local perturbations in neighboring bps and, surprisingly, a small but significant degree of DNA bending (∼14°) directed toward the major groove. The survey provides insights into the preferences and structural consequences of HG bps in duplex DNA.
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