ArticleNucleic acids research2015
Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition.
Article 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 22 papers.
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Who cites it
22 citing papers in PubMed, 54 citations in OpenAlex.
- Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides.International journal of molecular sciences · 2024Article
- Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells.Nucleic acids research · 2023Article
- Article
- Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket.Journal of the American Chemical Society · 2021Article
- Automated AFM analysis of DNA bending reveals initial lesion sensing strategies of DNA glycosylases.Scientific reports · 2020Article
- The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase.Nature communications · 2020Article
- The Role of Active-Site Residues Phe98, His239, and Arg243 in DNA Binding and in the Catalysis of Human Uracil-DNA Glycosylase SMUG1.Molecules (Basel, Switzerland) · 2019Article
- Substrate specificity of human apurinic/apyrimidinic endonuclease APE1 in the nucleotide incision repair pathway.Nucleic acids research · 2018Article
- A conserved loop-wedge motif moderates reaction site search and recognition by FEN1.Nucleic acids research · 2018Article
- Article
- Hide and seek: How do DNA glycosylases locate oxidatively damaged DNA bases amidst a sea of undamaged bases?Free radical biology & medicine · 2017Review
- Mutational and Kinetic Analysis of Lesion Recognition by Escherichia coli Endonuclease VIII.Genes · 2017Article
- Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase.BMC structural biology · 2017Article
- Probing the activity of NTHL1 orthologs by targeting conserved amino acid residues.DNA repair · 2017Article
- DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase.Journal of the American Chemical Society · 2017Article
- Visualizing the Search for Radiation-damaged DNA Bases in Real Time.Radiation physics and chemistry (Oxford, England : 1993) · 2016Article
- Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion.Journal of molecular biology · 2016Article
- A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine-DNA glycosylase.Nucleic acids research · 2016Article
- A human transcription factor in search mode.Nucleic acids research · 2016Article
- Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion.Biochemistry · 2015Article
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
Abstract
Formamidopyrimidine-DNA glycosylase (Fpg) excises 8-oxoguanine (oxoG) from DNA but ignores normal guanine. We combined molecular dynamics simulation and stopped-flow kinetics with fluorescence detection to track the events in the recognition of oxoG by Fpg and its mutants with a key phenylalanine residue, which intercalates next to the damaged base, changed to either alanine (F110A) or fluorescent reporter tryptophan (F110W). Guanine was sampled by Fpg, as evident from the F110W stopped-flow traces, but less extensively than oxoG. The wedgeless F110A enzyme could bend DNA but failed to proceed further in oxoG recognition. Modeling of the base eversion with energy decomposition suggested that the wedge destabilizes the intrahelical base primarily through buckling both surrounding base pairs. Replacement of oxoG with abasic (AP) site rescued the activity, and calculations suggested that wedge insertion is not required for AP site destabilization and eversion. Our results suggest that Fpg, and possibly other DNA glycosylases, convert part of the binding energy into active destabilization of their substrates, using the energy differences between normal and damaged bases for fast substrate discrimination.
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Registered trials
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