title: Dynamic opening of DNA during the enzymatic search for a damaged base.
abstract: Uracil DNA glycosylase (UDG) removes uracil from U.A or U.G base pairs in genomic DNA by extruding the aberrant uracil from the DNA base stack. A question in enzymatic DNA repair is whether UDG and related glycosylases also use an extrahelical recognition mechanism to inspect the integrity of undamaged base pairs. Using NMR imino proton exchange measurements we find that UDG substantially increases the equilibrium constant for opening of T-A base pairs by almost two orders of magnitude relative to free B-DNA. This increase is brought about by enzymatic stabilization of an open state of the base pair without increasing the rate constant for spontaneous base pair opening. These findings indicate a passive search mechanism in which UDG uses the spontaneous opening dynamics of DNA to inspect normal base pairs in a rapid genome-wide search for uracil in DNA.
authors.affiliation: Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.
authors.forename: Chunyang
authors.initials: C
authors.lastname: Cao
authors.forename: Yu Lin
authors.initials: YL
authors.lastname: Jiang
authors.forename: James T
authors.initials: JT
authors.lastname: Stivers
authors.forename: Fenhong
authors.initials: F
authors.lastname: Song
mesh_terms: D001483:Base Sequence; D002384:Catalysis; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004249:DNA Damage; D045647:DNA Glycosylases / Q000378:metabolism*; D004260:DNA Repair; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008280:Magnetics; D009690:Nucleic Acid Conformation; D011522:Protons; D013379:Substrate Specificity; D013816:Thermodynamics; D051981:Uracil-DNA Glycosidase; D014867:Water
chemical_list: D011522:Protons; D014867:Water; D004247:DNA; D045647:DNA Glycosylases; D051981:Uracil-DNA Glycosidase