|For instance, let's say your have cultured cells or a vibratome
section of tissue and you want to look at DNA, f-actin, your favorite protein and
microtubules (tubulin) by fluorescent light microscopy. We might suggest you use
respectively DAPI (binds to DNA), fluorescein
(bound to phalloidin which binds to f-actin filaments), Cy3
(antibody method for your favorite protein) and Cy5 (antibody
method to alpha or beta tubulin).
In general, you may use any one dye from each of the groupings below for multi-labeling -- this list is not exhaustive. Please consult with us for other special combinations, for instance dyes that excite at 490 nm but have a long Stokes shift to emit inthe red or far-red. Also, there are a lot of options for quantum dots and a few other ways of generating contrast in muti-photon.
Today (20150901) a student pointed out that this table may need an overhaul.
According to http://www.biolegend.com/spectraanalyzer there are new classes of fluorphores that have varying Stokes shifts. One wavelength, such as a 405 nm line on the confocal, can excite multiple emitting dyes that have easily separable emissions such as blue (Brilliant Violet 421), red (Brilliant Violet 570) and near infra-red (Brilliant Violet 711).
Dyes with the same emission ranges, but different excitations (see table above) could also be used as distict probes. The colors could be separated based on multiple passes of excitation.
If you have experience with these, please let us know!
As of June 2015: According to http://www.ebioscience.com/knowledge-center/product-line/efluor/efluor-organic-dyes/efluor-660-comparison-data.htm “eFluor 660 is replacing Alexa Fluor 647 in the eBioscience product offering.” We put it in the "WE RECOMMEND" category above even though we haven't tried it yet because we really have no other choice...
We occasionally get questions about Alexa 700 and similar near-IR dyes. We do not have the filter blocks for any of the widefield epifluorescent scopes. The confocals (depending which one) only detect below 700 to 740 nm. And even if they did, users would have to change focus due to chromatic aberration. Also, we do not have the correct excitation lasers.
This is how the author of this web page perceives the colors.