Functionalized fluorescent dyes have attracted great interest for the specifi c staining of subcellular organelles in multicellular organi**s. A novel nanometer-sized water-soluble multi-functional squarylium indocyanine dye ( D1 ) that contains four primary amines is synthesized. The dye exhibits good photostability, non-toxicity and biocompatibility. Isothermal titration calorimetry demonstrates that an affi nity between D1 and DNA is higher than that between D1 and ****ogue of phospholipids. Analysis of circular dichroi** spectra indicates that D1 targets to the DNA minor groove and aggregates to a helix. Because of the distinct affi nity between the dye and subcellular organelles, the dye exhibits difunctional abilities to label the cell nuclei in fi xed cells/tissue and the cell membranes in live cells/tissue. By combination of the two staining capabilities, the dye is further explored as a specifi c marker to distinguish apoptotic cells in live cells/tissue. The research opens a new way to design novel multifunctional dyes for life science applications.