ArticleNucleic acids research2012
Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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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.
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Who cites it
28 citing papers in PubMed, 40 citations in OpenAlex.
- Uncovering hidden druggable sites: computational approaches to allosteric and cryptic pocket discovery-from molecular dynamics to AI.Journal of computer-aided molecular design · 2026Review
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- Computer aided design of inhibitor molecules against Vpr protein from different HIV-1 subtypes.In silico pharmacology · 2025Article
- 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
- The CDR3 region as the major driver of TREM-1 interaction with its ligands, anComputational and structural biotechnology journal · 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
- A cryptic pocket in Ebola VP35 allosterically controls RNA binding.Nature communications · 2022Article
- Targeting Oncogene Promoters and Ribosomal RNA Biogenesis by G-Quadruplex Binding Ligands Translate to Anticancer Activity.ACS bio & med chem Au · 2022Article
- SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights.International journal of molecular sciences · 2022Article
- Molecular modelling of the HCMV IL-10 protein isoforms and analysis of their interaction with the human IL-10 receptor.PloS one · 2022Article
- Review
- Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.The Journal of biological chemistry · 2020Article
- Competition Between Phenothiazines and BH3 Peptide for the Binding Site of the Antiapoptotic BCL-2 Protein.Frontiers in chemistry · 2020Article
- Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA.Nucleic acids research · 2019Article
- Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick А·Т DNA base pairs into the Hoogsteen and reverse Hoogsteen forms.Scientific reports · 2018Article
- Dual Labeling of the CBP/p300 KIX Domain forChembiochem : a European journal of chemical biology · 2018Article
- Structural Dynamics of DPP-4 and Its Influence on the Projection of Bioactive Ligands.Molecules (Basel, Switzerland) · 2018Article
- Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs.Frontiers in chemistry · 2018Article
- Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
Formaldehyde has long been recognized as a hazardous environmental agent highly reactive with DNA. Recently, it has been realized that due to the activity of histone demethylation enzymes within the cell nucleus, formaldehyde is produced endogenously, in direct vicinity of genomic DNA. Should it lead to extensive DNA damage? We address this question with the aid of a computational mapping method, analogous to X-ray and nuclear magnetic resonance techniques for observing weakly specific interactions of small organic compounds with a macromolecule in order to establish important functional sites. We concentrate on the leading reaction of formaldehyde with free bases: hydroxymethylation of cytosine amino groups. Our results show that in B-DNA, cytosine amino groups are totally inaccessible for the formaldehyde attack. Then, we explore the effect of recently discovered transient flipping of Watson-Crick (WC) pairs into Hoogsteen (HG) pairs (HG breathing). Our results show that the HG base pair formation dramatically affects the accessibility for formaldehyde of cytosine amino nitrogens within WC base pairs adjacent to HG base pairs. The extensive literature on DNA interaction with formaldehyde is analyzed in light of the new findings. The obtained data emphasize the significance of DNA HG breathing.
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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.