title: Mechanism of translocation of uracil-DNA glycosylase from Escherichia coli between distributed lesions.
abstract: Uracil-DNA glycosylase (Ung) is a DNA repair enzyme that excises uracil bases from DNA, where they appear through deamination of cytosine or incorporation from a cellular dUTP pool. DNA repair enzymes often use one-dimensional diffusion along DNA to accelerate target search; however, this mechanism remains poorly investigated mechanistically. We used oligonucleotide substrates containing two uracil residues in defined positions to characterize one-dimensional search of DNA by Escherichia coli Ung. Mg(2+) ions suppressed the search in double-stranded DNA to a higher extent than K(+) likely due to tight binding of Mg(2+) to DNA phosphates. Ung was able to efficiently overcome short single-stranded gaps within double-stranded DNA. Varying the distance between the lesions and fitting the data to a theoretical model of DNA random walk, we estimated the characteristic one-dimensional search distance of ~100 nucleotides and translocation rate constant of ~2×10(6) s(-1).
authors.affiliation: SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia.
authors.forename: Grigory V
authors.initials: GV
authors.lastname: Mechetin
authors.forename: Dmitry O
authors.initials: DO
authors.lastname: Zharkov
mesh_terms: D004247:DNA / Q000378:metabolism; D004249:DNA Damage; D004260:DNA Repair; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics; D009841:Oligonucleotides / Q000235:genetics / Q000378:metabolism; D021381:Protein Transport; D051981:Uracil-DNA Glycosidase / Q000378:metabolism*
chemical_list: D009841:Oligonucleotides; D004247:DNA; D051981:Uracil-DNA Glycosidase