In this study axially 1-morpholinopropan-2-ol disubstituted silicon phthalocyanine 4 and axially 3-morpholinophenol disubstituted silicon phthalocyanine 5 and their quaternised water soluble derivatives (4a and 5a) were synthesised for the first time. The structural characterisations of these novel compounds were performed by a combination of FT-IR, H-1 NMR, UV-vis and mass. The binding propensity of the compounds with CT-DNA was performed using UV-vis absorption titration, competitive ethidium bromide and thermal denaturation experiments. These studies revealed that 4a and 5a intercalate to CT-DNA with 3.94 +/- (0.11) x 10(4) M-1 and 1.71 +/- (0.09) x 10(4) M-1. The DNA cleavage ability of 4a and 5a was investigated using supercoiled pBR322 plasmid DNA on agarose gel electrophoresis. 4a indicated excellent photocleavage activity under light irradiation at 650 nm in a concentration-dependent manner. However, 5a showed low cleavage activities under light irradiation at 12.5 mu M and 25 mu M but it had moderate cleavage activity at 50 mu M. The BSA interaction experiment showed that quenching mechanisms of BSA with 4a and 5a were found as static quenching using UV-vis spectroscopy. All of these results suggest that 4a has a superior photosensitiser agent for photodynamic therapy to that of 5a due to DNA photocleavage properties.