1. Mechanism of translocation of uracil-DNA glycosylase from Escherichia coli between distributed lesions.
- Author
-
Mechetin GV and Zharkov DO
- Subjects
- DNA metabolism, Escherichia coli genetics, Oligonucleotides genetics, Oligonucleotides metabolism, Protein Transport, DNA Damage, DNA Repair, Escherichia coli enzymology, Uracil-DNA Glycosidase metabolism
- 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)., (Copyright © 2011 Elsevier Inc. All rights reserved.)
- Published
- 2011
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