Aberrant repair of 8-oxoguanine in short DNA bulges

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Abstract

The presence of DNA damage can increase the likelihood of DNA replication errors and promote mutations. In particular, pauses of DNA polymerase at the site of damage can lead to polymerase slippage and the formation of 1–2 nucleotide bulges. Repair of such structures using an undamaged DNA template leads to small deletions. One of the most abundant oxidative DNA lesions, 8-oxoguanine (oxoG), has been shown to induce small deletions but the mechanism of this phenomenon is currently unknown. We have studied the aberrant repair of oxoG, located in one- and two-nucleotide bulges, by the Escherichia coli and human base excision repair systems. Our results indicate that the repair in such substrates can serve as a mechanism for fixing small deletions in bacteria but not in humans.

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About the authors

D. A. Eroshenko

Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk State University

Email: dzharkov@niboch.nsc.ru
Russian Federation, Novosibirsk; Novosibirsk

E. A. Diatlova

Institute of Chemical Biology and Fundamental Medicine SB RAS

Email: dzharkov@niboch.nsc.ru
Russian Federation, Novosibirsk

V. M. Golyshev

Institute of Chemical Biology and Fundamental Medicine SB RAS

Email: dzharkov@niboch.nsc.ru
Russian Federation, Novosibirsk

A. V. Endutkin

Institute of Chemical Biology and Fundamental Medicine SB RAS

Email: dzharkov@niboch.nsc.ru
Russian Federation, Novosibirsk

D. O. Zharkov

Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk State University

Author for correspondence.
Email: dzharkov@niboch.nsc.ru

Corresponding Member

Russian Federation, Novosibirsk; Novosibirsk

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2. Fig. 1. Scheme of the formation of microdeletions during DNA polymerase slippage (a); diagram of the structure of the DNA substrates used in the work (b); graphs of the dependence of the initial reaction rate on the initial substrate concentration [S] for the enzyme Fpg (4.2 nM) (reaction conditions: 25 mM Tris–HCl pH 7.5, 50 mM NaCl, 1 mM EDTA, 1 mM DTT, 37 °C) (c) ; kinetic curves of substrate cleavage by the OGG1 enzyme in the same buffer at [E]0 = 5 µM, [S]0 = 20 nM (d) and [E]0 = 10 nM, [S]0 = 100 nM (d). For substrates X.2.1 and X.2.2, the splitting in (e) is not observed. After reaction with OGG1, the mixtures were heated with 100 mM NaOH (5 min, 95°C). In all cases, reaction products were separated by electrophoresis on a 20% polyacrylamide gel in the presence of 7 M urea and analyzed using a Typhoon 9500 radioluminescence scanning unit (GE Healthcare). The graphs show the means and standard deviations from three independent experiments.

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3. Fig. 2. Representative fluorescent images after electrophoretic separation in a denaturing 20% polyacrylamide gel of reaction products in the reconstructed system for the repair of substrates X.0 (a), X.1 (b), X.2.1 (c) and X.2.2 (d) . Reaction conditions: 50 mM Tris–HCl (pH 7.5), 10 mM MgCl2, 10 mM DTT, 1 mM ATP, 25 μg/ml bovine serum albumin, 50 nM DNA substrate, 0.5 units. act./μl DNA ligase, 200 nM other enzymes, 250 μM dNTP, 30 min at 37 °C. The structures of the cleaved DNA strand and repair intermediates are indicated in Roman numerals: (i) the original damaged DNA strand, (iia) the product of cleavage by the Fpg enzyme, (iib) the product of cleavage by the OGG1 enzyme, (iii) the product of cleavage by AP endonucleases, (iv) the product of the incorporation of a single nucleotide by DNA polymerases. X – oxoG, Y – C or T, B – C, G or T, asterisk indicates 5′-terminal fluorescent tag (Cy3).

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