In this study, axially 1-acetylpiperazine substituted silicon (IV) phthalocyanine, naphthalocyanine 2, 3 and their water soluble derivatives 2a, 3a were synthesized for the first time and their DNA binding modes (absorption spectral, thermal denaturation and electrophoresis studies), DNA cleavage activities, topoisomerases inhibitory and cytotoxicity effects were investigated. Compounds 2a and 3a showed good binding propensity to CT-DNA with K-b values of 1.25 +/- (0.01) x 10(4) and 1.13 +/- (0.03) x 10(4) M-1. In DNA cleavage studies revealed that the compounds cleaved to supercoiled pBR322 plasmid DNA via the oxidative pathway at irradiation. The compounds inhibited topoisomerase I enzyme in a concentration-dependent manner whilst they had low inhibitory effects against topoisomerase II compared to doxorubicin as a positive control. In vitro studies of the cytotoxicity of the compounds on five carcinoma cell lines indicated that compound 3a had the potential to act as an anticancer drug with CC50 values of 7.83, 3.36, 3.18 and 3.36 mu M toward BT-20, SNU-398, DU-145 and SKMEL 128 compared to cis-platin as a positive control.