ArticleNucleic acids research2021
Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 27 citations in OpenAlex.
- Contrasting effects of different molecular crowding environments on base-pair opening/closing dynamics of DNA triplex structures.The FEBS journal · 2026Article
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- DNA Mechanical Strain Steers Transcription Factor Recognition.Research square · 2026Article
- Systematic DNA nicking reveals the structural logic of protein recognition.bioRxiv : the preprint server for biology · 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
- 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
- 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
- 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
- Solution Structure of Poly(UG) RNA.Journal of molecular biology · 2023Article
- Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism.Nucleic acids research · 2023Article
- Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements.Frontiers in molecular biosciences · 2023Article
- Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1.Nature communications · 2022Article
- Alchemical Free-Energy Calculations of Watson-Crick and Hoogsteen Base Pairing Interconversion in DNA.Journal of chemical theory and computation · 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
- 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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Watson-Crick base pairs (bps) are the fundamental unit of genetic information and the building blocks of the DNA double helix. However, A-T and G-C can also form alternative 'Hoogsteen' bps, expanding the functional complexity of DNA. We developed 'Hoog-finder', which uses structural fingerprints to rapidly screen Hoogsteen bps, which may have been mismodeled as Watson-Crick in crystal structures of protein-DNA complexes. We uncovered 17 Hoogsteen bps, 7 of which were in complex with 6 proteins never before shown to bind Hoogsteen bps. The Hoogsteen bps occur near mismatches, nicks and lesions and some appear to participate in recognition and damage repair. Our results suggest a potentially broad role for Hoogsteen bps in stressed regions of the genome and call for a community-wide effort to identify these bps in current and future crystal structures of DNA and its complexes.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.