Cyanine dyes have been used for labeling biomolecules such as proteins and DNA. The fluorescent properties and possibility of photosensitization by these molecules made them candidate drugs in image-guided surgery and in photodynamic therapy (PDT). In this study, we are exploring the theranostic properties of novel cyanine dyes with a goal to find near infrared photo nucleases in order to achieve an ideal photosensitizer that could be potentially used in PDT. Duplex DNA photo cleavage by pentamethine bridged near infrared cyanine dye was investigated. The detailed chemistry of dyes photo physical and photochemical properties, mechanism of dye-DNA interactions, DNA binding modes, and species involved in photo cleavage reactions were studied. The effects of different types of heterocyclic rings, variation in the length of the polymethine bridge, and the effect of electron withdrawing substitution on the dyes were investigated with a goal to achieve a new generation NIR drugs in photo therapy.