title: Isolating contributions from intersegmental transfer to DNA searching by alkyladenine DNA glycosylase.
abstract: Large genomes pose a challenge to DNA repair pathways because rare sites of damage must be efficiently located from among a vast excess of undamaged sites. Human alkyladenine DNA glycosylase (AAG) employs nonspecific DNA binding interactions and facilitated diffusion to conduct a highly redundant search of adjacent sites. This ensures that every site is searched, but could be a detriment if the protein is trapped in a local segment of DNA. Intersegmental transfer between DNA segments that are transiently in close proximity provides an elegant solution that balances global and local searching processes. It has been difficult to detect intersegmental transfer experimentally; therefore, we developed biochemical assays that allowed us to observe and measure the rates of intersegmental transfer by AAG. AAG has a flexible amino terminus that tunes its affinity for nonspecific DNA, but we find that it is not required for intersegmental transfer. As AAG has only a single DNA binding site, this argues against the bridging model for intersegmental transfer. The rates of intersegmental transfer are strongly dependent on the salt concentration, supporting a jumping mechanism that involves microscopic dissociation and capture by a proximal DNA site. As many DNA-binding proteins have only a single binding site, jumping may be a common mechanism for intersegmental transfer.
authors.affiliation: Department of Biological Chemistry and the Chemical Biology Doctoral Program, the University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Hedglin
authors.forename: Yaru
authors.initials: Y
authors.lastname: Zhang
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: O'Brien
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D045647:DNA Glycosylases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D011485:Protein Binding; D017434:Protein Structure, Tertiary
chemical_list: D004247:DNA; C021565:3-methyladenine-DNA glycosylase; D045647:DNA Glycosylases
keywords: Base Excision Repair; DNA Glycosylase; DNA Repair; Enzyme Kinetics; Enzyme Mechanisms; Facilitated Diffusion; Intersegmental Transfer; Mutagenesis Mechanisms