Journal
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Volume 414, Issue 2, Pages 425-430Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.bbrc.2011.09.106
Keywords
DNA repair; Uracil-DNA glycosylase; One-dimensional diffusion; Random walk; Processivity
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Funding
- Russian Foundation for Basic Research [10-04-91058-PICS_a, 11-04-00807-a]
- Russian Ministry of Education and Science [NSh-3185.2010.4, 14.740.12.0819]
- Presidium of the Russian Academy of Sciences [6.14]
- National Cancer Institute [CA017395-33]
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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 similar to 100 nucleotides and translocation rate constant of similar to 2 x 10(6) s(-1). (C) 2011 Elsevier Inc. All rights reserved.
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