In this study, new BODIPY dyes (2, 3) and their water soluble derivatives (2a, 3a) were synthesized for the first time. The identity of BODIPY dyes 2-3a were confirmed by H-1 NMR, C-13 NMR, FT-IR, UV-Vis and mass spectrometry. The binding properties of 2a and 3a with CT-DNA have been investigated absorption titration, competitive ethidium bromide, viscosity and electrophoresis experiments. These binding studies claimed that 2a and 3a intercalate with CT-DNA. The Kb values of 2a and 3a calculated as 3.58 +/- (0.08) x 10(5) M-1 and 1.27 +/- (0.10) x 10(5) M-1, indicating that the compounds have strong binding affinities to CT-DNA. The DNA-photocleavage activities of 2a and 3a were investigated using supercoiled pBR322 plasmid DNA on agarose gel electrophoresis. 2a and 3a have remarkable photocleavage activities in the presence of irradiation at 650 +/- 20 nm via hydroxyl radical and singlet oxygen pathways. To determine to quenching mechanism of BSA with compounds were performed using UV-Vis absorption spectroscopy. The results demonstrated that the compounds might bind to BSA via static quenching mechanism. The results suggested that synthesized new water soluble BODIPY compounds have strong affinity to CT-DNA and BSA and can effectively cleavage activities by irradiation. (C) 2017 Elsevier Ltd. All rights reserved.