Scheme for the appearance of DSBs and SMD.
Methylated bases are first removed by Mag1 glycosylase to form AP sites. In apn1/2 mutants AP sites are nicked by AP lyases (Ntg1, Ntg2 and Ogg1). If two nicks are close enough, they would result in a derived DSB and undergo resection and HR mediated repair. When the two nicks are not closely-spaced, a derived-DSB might still be formed during attempted removal of the α,β-unsaturated aldehyde (3′-dRP) possibly by helicases that generate a single-stranded 3′-flap, and nucleases or other proteins that remove the blocked group and restore a ligatable 3′-end. Inefficient removal of multiple flaps, secondary structures from single stranded region or flaps as well as stably bound proteins might result in molecules with retarded mobility (i.e., SMD).
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