Box 1 | Mechanisms of DNA repair of N- and O-methylated bases in DNA

From the following article:

Repairing DNA-methylation damage

Barbara Sedgwick

Nature Reviews Molecular Cell Biology 5, 148-157 (February 2004)

doi:10.1038/nrm1312

3-Methyladenine-DNA-glycosylase

Methylated bases with destabilized glycosyl bonds, such as N3-methyladenine (shown as -N-CH3) are excised by 3-methyladenine (3-meA)-DNA-glycosylase (blue). Several additional activities are required to complete repair of the resulting abasic sites. An apurinic endonuclease incises the baseless site, a DNA polymerase inserts a single nucleotide and a DNA ligase seals the single-stranded gap. This pathway, which is initiated by a DNA-glycosylase, is known as base excision repair.

Repairing DNA-methylation damage 

1-Methyladenine-DNA-dioxygenase

N1-methyladenine and N3-methylcytosine in DNA are stable, modified bases that are mostly generated in single-stranded (ss)DNA (shown as -N-CH3 in a region of ssDNA). These lesions are repaired using oxidative demethylation by 1-methyladenine (1-meA)-DNA-dioxygenases (purple). They require dioxygen and alpha-ketoglutarate as co-substrates and Fe2+ as a cofactor.

They oxidize the methyl adduct, which results in its destabilization and release as formaldehyde (HCHO). Other products of the reaction are succinate and CO2. The damaged base directly reverts to the unmodified form.

O6-Methylguanine-DNA-methyltransferase

The significant lesion O6-methylguanine (O6-meG) and the minor lesion O4-methylthymine are methylated on their exocyclic oxygens (shown as CH3-O-), and are directly demethylated by O6-meG-DNA-methyltransferases. These proteins transfer the methyl group to an active-site Cys residue. Repair by the methyltransferases requires no cofactors or additional activities.

The methyl groups and their different fates in the different reactions — as excised methylated base (for example, 3-meA), released HCHO or self-methylated methyltransferase — are shown in red.