Introduction
Overview of Direct Repair of DNA Alkylation DamageCellular DNA is constantly subjected to modifications by intracellular and extracellular chemicals, which can result in covalent changes. 1,2 Alkylating agents are one group of such chemicals that can lead to DNA damage. 3 These agents are prevalent in the environment and are used as anticancer compounds in the clinical setting. 4-10 Alkylating agents also exist endogenously inside cells; for instance, S-adenosylmethionine, a methyl donor for many cellular reactions, has been shown to produce methylation damage. 11,12 The attack on DNA by these alkylating agents can lead to various types of lesions on the heterocyclic bases or backbone. 3,13-15 Most of these resulting adducts are mutagenic or toxic, and cells have evolved various proteins to detect and repair them. 9,16,17 Interestingly, many of these alkylation lesions are repaired through the direct removal of the adduct. Other than the photolyase that catalyzes direct reversal of the thymine dimer created by UV light, 18,19 all known direct DNA repair proteins are engaged in alkylation DNA damage repair. These are the N-terminal domain of the Escherichia coli (E. coli) Ada protein, the O 6 -alkylguanine-DNA alkyltransferase family, and the AlkB family. 9 1.1.1. Alkylation of DNA-Alkylating reagents can be divided into S N 1 and S N 2 types based on the mechanism of the alkylation attack. The alkylation susceptibility of each site on the bases or backbone varies depending on the reagent used (Figure 1); the resulting lesions also have different mutagenic and cytotoxic effects. The N 7 -position of guanine is the most vulnerable site on DNA; unsurprisingly, it also serves as the best ligand on the DNA for metal ions such as platinum(II). 20 Treating double-stranded DNA (dsDNA) with methylating agents such as methylmethane sulfonate (MMS, an S N 2 type methylating agent) or N-methyl-N′nitrosourea (MNU, an S N 1 type methylating agent) typically results in 70-80% of the methylation occurring on the N 7 -position of guanine. Despite being the most abundant product of alkylation damage, N 7 -methylguanine is relatively innocuous and is removed mostly through spontaneous depurination. 21 The resulting abasic site is toxic and repaired enzymatically. 22 The N 3 -methyladenine is the second most abundant alkylation lesion formed in dsDNA. This lesion can block DNA replication and is removed by AlkA in E. coli and 3methyladenine-DNA-glycosylases. [23][24][25] The S N 1 type methylating agents such as MNU and N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) are highly mutagenic because they attack the oxygen atoms on DNA bases to give a significant amount of O 6 -methylguanine (O 6 -meG) and a small amount of O 4 -methylthymine (Figure 1). 13,14 O 6 -meG mispairs with thymine during DNA replication, which gives rise to a transition mutation of G:C to A:T. 26-29 Thus, this lesion must be rapidly located and removed in order to maintain the integrity of the genome. The O 6 -alkylguanine-DNA alkyltransferase family o...