What are the properties of carbocyanine dyes?

Carbocyanine dyes belong to a large family of fluorescent dyes. 

The structure of these fluorochromes is made up of a linked pair of conjugated rings that vary only in one position, which may consist of an oxygen, isopropyl or sulfur group, leading to the DiI, DiO, and DiS families of dyes.

The absorption and emission properties of the dyes are determined by the combination of the Y constituent and the length of the linkage between the pair of rings. Different Y groups and linkage lengths result in variations in the absorption and emission spectra of the dyes.

DiI is maximally excited in the green and fluoresces bright red-orange when viewed through rhodamine filters.

DiO is excited in the blue and fluoresces green when viewed through fluorescein filters. 

Two long alkyl chains that are attached to the fluorochrome, determine the affinity of the probes for the membrane.

Both dyes, DiI and DiO, exhibit intense fluorescence, and their fluorescence fades more slowly than fluorescein or rhodamine fluorescence. This property is advantageous for long-term imaging studies.