This study reports the synthesis of three novel axially disubstituted silicon phthalocyanines (1-3-Si) and their quaternized phthalocyanines (1-3-QSi). The resulting compounds were characterized by applying spectroscopic techniques including H-1 NMR, FT-IR, UV-vis, and mass spectroscopy. The biological properties of compounds 1-3-QSi, including DNA cleavage activities, DNA binding modes, and topoisomerase enzyme inhibition activities, were investigated using agarose gel electrophoresis. pBR322 plasmid DNA, CT-DNA, and AL-DNA (isolated from apricot leaf) were used for DNA studies. All the quaternized compounds exhibited acceptable DNA cleavage activities. Human topoisomerase I and E. coli topoisomerase enzymes were used for the topoisomerase I inhibition studies. All the quaternized complexes inhibited topoisomerase I activity. Moreover, these compounds were screened for cytotoxic and apoptotic effects against a human colon cancer cell line (DLD-1) by performing MTT and Annexin V assays. They exhibited toxicity and apoptotic effect on the DLD-1 cell line. The findings reveal that the compounds can be utilized for cancer therapy after further investigations.