title: Two glycosylase families diffusively scan DNA using a wedge residue to probe for and identify oxidatively damaged bases.
abstract: DNA glycosylases are enzymes that perform the initial steps of base excision repair, the principal repair mechanism that identifies and removes endogenous damages that occur in an organism's DNA. We characterized the motion of single molecules of three bacterial glycosylases that recognize oxidized bases, Fpg, Nei, and Nth, as they scan for damages on tightropes of λ DNA. We find that all three enzymes use a key "wedge residue" to scan for damage because mutation of this residue to an alanine results in faster diffusion. Moreover, all three enzymes bind longer and diffuse more slowly on DNA that contains the damages they recognize and remove. Using a sliding window approach to measure diffusion constants and a simple chemomechanical simulation, we demonstrate that these enzymes diffuse along DNA, pausing momentarily to interrogate random bases, and when a damaged base is recognized, they stop to evert and excise it.
authors.affiliation: Department of Molecular Physiology and Biophysics, The University of Vermont, Burlington, VT 05405-0075; and.
authors.forename: Shane R
authors.initials: SR
authors.lastname: Nelson
authors.affiliation: Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, VT 05405-0084.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Dunn
authors.affiliation: Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, VT 05405-0084.
authors.forename: Scott D
authors.initials: SD
authors.lastname: Kathe
authors.affiliation: Department of Molecular Physiology and Biophysics, The University of Vermont, Burlington, VT 05405-0075; and susan.wallace@uvm.edu david.warshaw@uvm.edu.
authors.forename: David M
authors.initials: DM
authors.lastname: Warshaw
authors.affiliation: Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, VT 05405-0084 susan.wallace@uvm.edu david.warshaw@uvm.edu.
authors.forename: Susan S
authors.initials: SS
authors.lastname: Wallace
mesh_terms: D000409:Alanine / Q000235:genetics; D020134:Catalytic Domain; D004249:DNA Damage; D004252:DNA Mutational Analysis; D004260:DNA Repair; D004269:DNA, Bacterial / Q000737:chemistry; D043382:DNA-Formamidopyrimidine Glycosylase / Q000378:metabolism*; D043224:Deoxyribonuclease (Pyrimidine Dimer) / Q000378:metabolism*; D004058:Diffusion; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism*; D008968:Molecular Conformation; D009154:Mutation; D010100:Oxygen / Q000737:chemistry*; D011485:Protein Binding; D013314:Stress, Mechanical
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D043224:Deoxyribonuclease (Pyrimidine Dimer); C106403:NTH protein, E coli; C468346:Nei protein, E coli; D043382:DNA-Formamidopyrimidine Glycosylase; C468610:DNA-formamidopyrimidine glycosylase, E coli; D000409:Alanine; D010100:Oxygen
keywords: DNA repair; search mechanisms