Repair of oxidatively induced DNA damage by DNA glycosylases: Mechanisms of action, substrate specificities and excision kinetics

Abstract

Endogenous and exogenous reactive species cause oxidatively induced DNA damage in living organisms by a variety of mechanisms. As a result, a plethora of mutagenic and/or cytotoxic products are formed in cellular DNA. This type of DNA damage is repaired by base excision repair, although nucleotide excision repair also plays a limited role. DNA glycosylases remove modified DNA bases from DNA by hydrolyzing the glycosidic bond leaving behind an apurinic/apyrimidinic (AP) site. Some of them also possess an accompanying AP-lyase activity that cleaves the sugar-phosphate chain of DNA. Since the first discovery of a DNA glycosylase, many studies have elucidated the mechanisms of action, substrate specificities and excision kinetics of these enzymes present in all living organisms. For this purpose, most studies used single- or double-stranded oligodeoxynucleotides with a single DNA lesion embedded at a defined position. High-molecular weight DNA with multiple base lesions has been used in other studies with the advantage of the simultaneous investigation of many DNA base lesions as substrates. Differences between the substrate specificities and excision kinetics of DNA glycosylases have been found when these two different substrates were used. Some DNA glycosylases possess varying substrate specificities for either purine-derived lesions or pyrimidine-derived lesions, whereas others exhibit cross-activity for both types of lesions. Laboratory animals with knockouts of the genes of DNA glycosylases have also been used to provide unequivocal evidence for the substrates, which had previously been found in in vitro studies, to be the actual substrates in vivo as well. On the basis of the knowledge gained from the past studies, efforts are being made to discover small molecule inhibitors of DNA glycosylases that may be used as potential drugs in cancer therapy.

Keywords: DNA glycosylases; DNA repair; Excision kinetics; Oxidatively induced DNA damage; Substrate specificities.

Fig. 1.

Structures of oxidatively induced DNA base lesions in DNA.

Fig. 2.

Schematic presentation of short-patch base excision repair X, modified DNA base; α,β-UA, 3’-phospho-α,β-unsaturated aldehyde; P, phosphate. Other abbreviations can be found in the list of abbreviations. It should be noted that NEIL3 is listed with β,δ-elimination activity, although its δ-elimination activity is significantly weaker than its β-elimination activity [261]. (Adapted from [87].)

Fig. 3.

Removal of a modified DNA base by a bifunctional DNA glycosylase followed by β- and δ-eliminations.

Fig. 4.

Mechanism of action of a bifunctional DNA glycosylase. E. coli Fpg and FapyGua are depicted as the DNA glycosylase and the modified DNA base, respectively. Also shown is the trapping of the Schiff base by NaBH₄, leading to a covalent DNA-amino acid cross-link. (For more details of this mechanism see [140,148,150,153].)

Fig. 5.

Experimental scheme for the determination of substrate specificities of DNA glycosylases using the GC-MS methodology and high-molecular weight DNA with multiple lesions.

Fig. 6.

Levels of FapyAde, FapyGua and 8-OH-Gua in livers of wild-type mice (1) and neil1^‒/‒ mice (2). Uncertainties are standard deviations. (Redrawn from the data in [348].)

Fig. 7.

Activities of E. coli Fpg and E. coli FpgΔ213–229 on purine-derived lesions in high-molecular weight DNA with multiple lesions. 1: no enzyme; 2: E. coli Fpg; 3: E. coli FpgΔ213–229. Uncertainties are standard deviations. (Redrawn from the data in [435].)