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

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• 作者：Grigory V. Mechetin^a ; Dmitry O. Zharkov^a ;   ; ^b ;   ; ^{dzharkov@niboch.nsc.ru}
• 关键词：DNA repair ; Uracil&ndash ; DNA glycosylase ; One-dimensional diffusion ; Random walk ; Processivity
• 刊名：Biochemical and Biophysical Research Communications
• 出版年：2011
• 出版时间：22 October 2011
• 年：2011
• 卷：414
• 期：2
• 页码：425-430
• 全文大小：315 K
• ISSN：S0006291X11017219

文摘

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 ?00 nucleotides and translocation rate constant of ? × 10⁶ s^?.