SYTOX Green is nucleic acid stain that is impermeant to live cells, a characteristic that makes the dye a convenient indicator of living and dead cells within a culture. SYTOX Green also performs very well, however, as a nuclear counterstain in combination with other fluorophores for multicolor fluorescence microscopy applications. The dye is especially well suited for use with both gram-positive and gram-negative bacteria, which necessitate an extremely bright signal. When SYTOX Green binds to DNA, the fluorescence quantum yield is enhanced more than 500-fold. In this bound state, the SYTOX Green/DNA complex exhibits an absorption maximum of 504 nanometers and an emission maximum of 523 nanometers with a 0.53 quantum yield.

The culture of Indian Muntjac deer skin fibroblast cells featured in the digital image above was labeled for the cytoskeletal filamentous actin network with Alexa Fluor 350 conjugated to phalloidin, for intracellular mitochondria with MitoTracker Red CMXRos, and for DNA with SYTOX Green. Images were recorded in grayscale with a QImaging Retiga Fast-EXi camera system coupled to an Olympus BX-51 microscope equipped with bandpass emission fluorescence filter optical blocks provided by Omega Optical. During the processing stage, individual image channels were pseudocolored with RGB values corresponding to each of the fluorophore emission spectral profiles.