Tandem conjugates are useful for getting extra colors off of one excitation
source. To do this requires some dyes that have a long stokes shift - i.e the
idfference between the excitation and emission peaks is great. Most of the
energy transfer conjugates use either PE or APC, molecules that have been
crafted by nature for energy transfer. As far as I know (which, for being a
software guy, is not great) there isn't an equivalent situation for violet or
UV.
There also are advantages or going further to the red end of the spectrum. Light
sources are MUCH cheaper, and background autofluorescence is decreased. This is
offset somewhat by a drop in detection efficiency of PMTs.
-Marty Bigos
Stanford Shared FACS Facility