Mechanism of translocation of uracil–DNA glycosylase from Escherichia coli between distributed lesions

► Uracil–DNA glycosylase (Ung) excises uracil bases from DNA. ► Ung searches for these lesions by combining diffusion in 3D and random sliding in 1D. ► Mg2+ ions suppress the 1D search by Ung in double-stranded DNA. ► Ung can efficiently search through short single-stranded gaps within double-strand...

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Bibliographic Details
Published in:Biochemical and biophysical research communications 2011-10, Vol.414 (2), p.425-430
Main Authors: Mechetin, Grigory V., Zharkov, Dmitry O.
Format: Article
Language:English
Subjects:
DNA - metabolism
DNA Damage
DNA Repair
Escherichia coli
Escherichia coli - enzymology
Escherichia coli - genetics
Oligonucleotides - genetics
Oligonucleotides - metabolism
One-dimensional diffusion
Processivity
Protein Transport
Random walk
Uracil-DNA Glycosidase - metabolism
Uracil–DNA glycosylase
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Summary:► Uracil–DNA glycosylase (Ung) excises uracil bases from DNA. ► Ung searches for these lesions by combining diffusion in 3D and random sliding in 1D. ► Mg2+ ions suppress the 1D search by Ung in double-stranded DNA. ► Ung can efficiently search through short single-stranded gaps within double-stranded DNA. ► The characteristic Ung 1D search distance is ∼100 nucleotides, and the translocation rate constant is ∼2×106s−1. 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. Mg2+ ions suppressed the search in double-stranded DNA to a higher extent than K+ likely due to tight binding of Mg2+ 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 ∼2×106s−1.
ISSN:0006-291X
1090-2104
DOI:10.1016/j.bbrc.2011.09.106