By combining triplex-forming bis-peptide nucleic acid (bis-PNA) with Ce(IV)/EDTA, double-stranded DNA was selectively hydrolyzed at a predetermined homopyrimidine/homopurine site, which is difficult to be targeted by the previous strategy using pseudocomplementary PNAs (pcPNAs). These homopyrimidine/homopurine sequences take various important roles in vivo, and thus, the present site-selective DNA cutters should be useful in biology, biotechnology, medicine, and other fields.