Peptide nucleic acid is a synthetic DNA mimic in which the sugar-phosphate backbone has been replaced by a peptide backbone. A remarkable feature of PNA is its ability to recognize some sequences within duplex DNA by strand invasion. In order to improve binding properties of PNA, we tested the effect of cooperativity on strand invasion. A PNA targeting six bases within duplex DNA cooperatively binds to 12 base-pair homopurine site by strand invasion. The stability of invasion complexes is dependent on the distance between the target sites.