Formation and processing of DNA damage substrates for the hNEIL enzymes

Abstract

Reactive oxygen species (ROS) are harnessed by the cell for signaling at the same time as being detrimental to cellular components such as DNA. The genome and transcriptome contain instructions that can alter cellular processes when oxidized. The guanine (G) heterocycle in the nucleotide pool, DNA, or RNA is the base most prone to oxidation. The oxidatively-derived products of G consistently observed in high yields from hydroxyl radical, carbonate radical, or singlet oxygen oxidations under conditions modeling the cellular reducing environment are discussed. The major G base oxidation products are 8-oxo-7,8-dihydroguanine (OG), 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), spiroiminodihydantoin (Sp), and 5-guanidinohydantoin (Gh). The yields of these products show dependency on the oxidant and the reaction context that includes nucleoside, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and G-quadruplex DNA (G4-DNA) structures. Upon formation of these products in cells, they are recognized by the DNA glycosylases in the base excision repair (BER) pathway. This review focuses on initiation of BER by the mammalian Nei-like1-3 (NEIL1-3) glycosylases for removal of 2Ih, Sp, and Gh. The unique ability of the human NEILs to initiate removal of the hydantoins in ssDNA, bulge-DNA, bubble-DNA, dsDNA, and G4-DNA is outlined. Additionally, when Gh exists in a G4 DNA found in a gene promoter, NEIL-mediated repair is modulated by the plasticity of the G4-DNA structure provided by additional G-runs flanking the sequence. On the basis of these observations and cellular studies from the literature, the interplay between DNA oxidation and BER to alter gene expression is discussed.

Sequencing the Mouse Genome for the Oxidatively Modified Base 8-Oxo-7,8-dihydroguanine by OG-Seq

“…To identify the best enrichment protocol, control experiments were conducted with synthetic OG-containing oligomers of known sequence and secondary structure. The controls were also spiked with duplex oligomers devoid of OG to determine the impact that the non-OG-containing strands from the genomic sample (∼10 4 –10 5 more) will have on the enrichment efficiency. A commercially available OG antibody was titrated from 10–7000 equiv.…”

“…S2). 5,14 Oxidation of OG yields an electrophilic intermediate that can be trapped with a primary-amine nucleophile to furnish a stable amine-conjugated product. 15,16 Greenberg and co-workers harnessed this approach to synthesize biotin-terminated polyamines for labeling OG in the genomic context and quantify its concentrations.…”

“…The present results provide genome-level results supporting the many in vitro studies that predicted oxidation of 5′-GG-3′ sequences would dominate in vivo. 3-5 Lastly, one hypothesis for this non-random chromosome-level distribution of OG-enriched peaks may reside in the non-random spatial distribution of interphase chromosomes in the nucleus. 12 Interphase chromosomes bias regions for interacting with the nuclear envelope causing these regions to be preferentially exposed to more oxidants diffusing into the nucleus, while other regions are protected from oxidation because they are toward the interior of the nucleus.…”

“…These findings support many decades of in vitro studies aimed at understanding oxidative damage to cellular DNA. 3-5 …”

Genotoxicity of ortho-quinones: reactive oxygen species versus covalent modification

“…61 A separate group of glycosylases, NEIL 1 and NEIL 2 repair the spiroiminohydantoin and 5-guandionhydantoin lesions. 62,63 …”