PMID:21971549

Citation	Mechetin, GV and Zharkov, DO (2011) Mechanism of translocation of uracil-DNA glycosylase from Escherichia coli between distributed lesions. Biochem. Biophys. Res. Commun. 414:425-30
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).
Links	PubMed PMC3249333 Online version:10.1016/j.bbrc.2011.09.106
Keywords	DNA/metabolism; DNA Damage; DNA Repair; Escherichia coli/enzymology; Escherichia coli/genetics; Oligonucleotides/genetics; Oligonucleotides/metabolism; Protein Transport; Uracil-DNA Glycosidase/metabolism
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