This thesis outlines two projects that examine interactions between DNA and cyanine dyes: 1) Investigation of monomethine cyanine dye through the synthesis and optical characteristics with a goal to synthetically manipulate these systems to develop a fluorescent biological probe. Several asymmetric and one symmetrical monomethine cyanine dyes were synthetically prepared and their optical properties versus structural changes were explored. Representative dyes were selected for spectroscopically investigating DNA binding to enhance existing probe designs. 2) Early stage development of a non-metalated photosensitizer for photodynamic therapy (PDT) by screening experimentally derived cleavage activities of a number of polymethine cyanine dyes with various adjoining heterocycles. Structural characteristics of these dyes which promoted cleavage in the dark were identified and eliminated to allow for more selective photo-induced cleavage to enhance the candidacy of these compounds as photosensitizing agents. All compounds were purified through recrystallization or column chromatography and were characterized via 1H and 13C nuclear magnetic resonance (NMR). Compounds from the first chapter were further characterized using mass spectrometry.