ArticleActa crystallographica. Section D, Structural biology2017
Mismodeled purines: implicit alternates and hidden Hoogsteens.
Article in Acta crystallographica. Section D, Structural biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Article
- Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM.bioRxiv : the preprint server for biology · 2024Article
- Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements.Frontiers in molecular biosciences · 2023Article
- 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
- Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.Nucleic acids research · 2021Article
- Infrared Spectroscopic Observation of a G-CAngewandte Chemie (International ed. in English) · 2019Article
- Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-SpecificallyBiochemistry · 2019Article
- Modulation of Hoogsteen dynamics on DNA recognition.Nature communications · 2018Article
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3 authors.
Funding
Abstract
Hoogsteen base pairs are seen in DNA crystal structures, but only rarely. This study tests whether Hoogsteens or other syn purines are either under-modeled or over-modeled, which are known problems for rare conformations. Candidate purines needing a syn/anti 180° flip were identified by diagnostic patterns of difference electron-density peaks. Manual inspection narrowed 105 flip candidates to 20 convincing cases, all at ≤2.7 Å resolution. Rebuilding and refinement confirmed that 14 of these were authentic purine flips. Seven examples are modeled as Watson-Crick base pairs but should be Hoogsteens (commonest at duplex termini), and three had the opposite issue. Syn/anti flips were also needed for some single-stranded purines. Five of the 20 convincing cases arose from an unmodeled alternate duplex running in the opposite direction. These are in semi-palindromic DNA sequences bound by a homodimeric protein and show flipped-purine-like difference peaks at residues where the palindrome is imperfect. This study documents types of incorrect modeling which are worth avoiding. However, the primary conclusions are that such mistakes are infrequent, the bias towards fitting anti purines is very slight, and the occurrence rate of Hoogsteen base pairs in DNA crystal structures remains unchanged from earlier estimates at ∼0.3%.
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