Copyright This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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).