In this work, axially [3,5-bis(3-pyridin-4-ylpropoxy)phenyl]methoxy groups substituted silicon (IV) phthalocyanine 2, napthalocyanine 3 and their water soluble derivatives 2a, 3a were synthesized and DNA interaction, topoisomerases inhibitory properties, cytotoxicity against five carcinoma cell lines of water soluble derivatives were examined. The calf thymus DNA (CT-DNA) binding properties of 2a and 3a were monitored using UV-Vis spectroscopy and agarose gel electrophoresis. The results showed that the compounds interacted to CT-DNA via intercalation with K-b values of 3.94 +/- (0.15) x 10(6) and 1.08 +/- (0.10) x 10(5)M(-1). In DNA cleavage studies, the compounds cleaved to supercoiled pBR322 plasmid DNA significantly with irradiation as compared to without irradiation. The results of topoisomerases studies claimed that both compounds had inhibitory effects against topoisomerases. In the cytotoxicity studies, the CC50 values of the compounds were found in range of 2.15-52.97 mu M against to five carcinoma cell lines. The SI values of 3a were found as 4.51, 1.43 and 3.66 against A549, BT20 and SK-MEL 128 cell lines. The cell cycle arrest was investigated against A549 cells by flow cytometry and obtained results indicated that both compounds induce cell cycle arrest at G(0)/G(1) phase. All of obtained results demonstrated that 3a had lead anticancer agent toward lung, breast and melanoma due to its high selectivity to cancer cell lines.