Photodynamic therapy (PDT) is a promising approach used in the treatment of cancer, age related macular degeneration, psoriasis, and other diseases. Our research is focused on the discovery of new photonucleases for use in PDT. This study evaluates the photo-induced DNA cleaving abilities of a series of acridine and phenazine-based chromophores. The extended, aromatic ring systems of these compounds are expected to intercalate between adjoining base pairs in the DNA double-helix. Once irradiated, strand breakage, or nicking of plasmid DNA is achieved at micromolar concentrations of compound (pH 7.0 and 22 °C). Our scavenger experiments show that this process occurs as a result of direct electron transfer to oxygen and/or by means of energy transfer which results in the production of singlet oxygen. Three of the photonucleases being examined were designed to chelate metal. These exhibited increased levels of DNA photocleavage in the presence of copper(II).