a The comparison of protein–DNA interacting patterns in hAPE1 AP site-containing dsDNA complex (PDB entry: 5DFI), hAPE1-mismatched dsDNA substrate complex (PDB entry: 5WN5), and mAPE1-recessed dsDNA product complex. The interactions between APE1 and DNA are marked by purple balls. b Superposition of the dsDNAs in the aforementioned APE1–dsDNA complexes. The consistent interaction region emerges in the overlay of these structures, yellow boxes. c–f EMSA measurements of full-length mAPE1 binding with a match or mismatched blunt-ended dsDNA, recessed dsDNA, AP site-containing dsDNA, and 1-nt gapped dsDNA. The band of protein–DNA complex with a lower molecular weight is specifically observed in the binding with AP site-containing dsDNA and matched 1-nt gapped dsDNA. c–f Source data are provided as a Source Data file.