Removal of oxidatively generated DNA damage by overlapping repair pathways

Abstract

It is generally believed that the mammalian nucleotide excision repair pathway removes DNA helix-distorting bulky DNA lesions, while small non-bulky lesions are repaired by base excision repair (BER). However, recent work demonstrates that the oxidativly generated guanine oxidation products, spiroimininodihydantoin (Sp), 5-guanidinohydantoin (Gh), and certain intrastrand cross-linked lesions, are good substrates of NER and BER pathways that compete with one another in human cell extracts. The oxidation of guanine by peroxynitrite is known to generate 5-guanidino-4-nitroimidazole (NIm) which is structurally similar to Gh, except that the 4-nitro group in NIm is replaced by a keto group in Gh. However, unlike Gh, NIm is an excellent substrate of BER, but not of NER. These and other related results are reviewed and discussed in this article.

Keywords: Base excision repair; DNA damage; Nucleotide excision repair; Oxidative stress; Reactive oxygen species.

Fig. 1

Excision of damaged nucleobases by (A) BER, (B) NIR (the lesion is not excised in this pathway), and (C) NER mechanisms.

Fig. 2

Representative two-electron (blue) and four-electron (green) oxidation products of guanine produced by ROS and RNS. Abbreviations: cdG, 5′,8-cyclo-2′-deoxyguanosine; NIm, 5-guanidino-4-nitroimidazole; FapyG, 2,6-diamino-4-hydroxy-5-formamidopyrimidine; 8-oxoG, 8-oxo-7,8-dihydroguanine; G*–T*, intrastrand guanine(C8)-thymine(N3) cross-link; Sp, spiroiminodihydantoin; Gh, 5-guanidinohydantoin; Ia, iminoallantoin.

Fig. 3

Denaturing polyacrylamide gel electrophoresis analysis of the cleavage patterns generated by DNA glycosylases/AP lyases (BER) and NIR-AP endonucleases (NIR) in duplexes containing G*CT* and G*T* lesions. Panels A and D: duplexes constructed from either 5′-³²P-labeled 17 mer G*CT* (A), or G*T* (D) strands hybridized with their natural complementary strands. Panel B: size marker 8-mer oligonucleotide standards with 5′-³²P-labled 8-mer containing 3′-hydroxyl (3′-OH), or 3′-phosphoaldehyde (3′-PUA), or 3′-phosphate (3′-P) ends are shown in lanes 3, 5, and 7, respectively. These standards were derived from the parent 17-mer strands containing uracil. Panels C and E: duplexes constructed from cordycepin 3′-³²P-endlabeled 18 mer G*CT* (C) or G*T* (E) strands hybridized with their complementary 17-mer complementary strands. UT indicates untreated oligonucleotide. (Reproduced from Talhaoui et al., J. Biol. Chem. 290 (2015) 4610-14617 [101]).

Fig. 4

A denaturing polyacrylamide gel showing the appearance of excision (BER) and dual incision (NER) products obtained by incubating, as a function of time, 135-mer duplexes with single Gh, S-Sp, or NIm lesions in HeLa cell extracts. The lesions were positioned at the 67^th nucleotide counted from the 5′-end of the modified strand. The 10R (+)-cis-anti-B[a]P-N²-dG adducts, a bulky DNA lesion derived from the binding of a diol epoxide metabolite of benzo[a]pyrene, was used as positive control of NER activity in these cell extracts [88, 89]. Lane 1: oligonucleotide size markers. The apparent size range of the NER dual incision products is shown by the dotted lines (red). (Reproduced from Shafirovich et al., J. Biol. Chem. 291 (2016) 5309-5319 [108]).