Nile red is a stain for lipids, so you wouldn't
expect it to work on paraffin sections. The
fluorescence develops when the nile red molecules
are in a hydrophobic environment (lipid droplets,
some bacterial cell walls etc), and the dye has also been
used as a hydrophobic probe to stain protein bands on
SDS-PAGE gels (Daban et al 1991 Anal. Biochem. 199:169-174).

Nile red is present as an impurity in nile blue sulphate
(CI 51180), a dye that can also be used to stain
hydrophobic lipids red (ordinary light) or orange 
(fluorescence). The nile blue/red stain method dates back 
to 1947 (AJ Cain in Q. J. Micr. Sci. 88:383-392) or (probably)
even earlier. In 1987 Bonilla & Prelle introduced it for 
fluorescent staining of lipid droplets in cryosections
of human muscle biopsies, for diagnosing myopathies
(J. Histochem. Cytochem. 35:619-621).

Hope this helps.
-- 
-------------------------
John A. Kiernan
Department of Anatomy and Cell Biology
The University of Western Ontario
London,   Canada   N6A 5C1
   kiernan@uwo.ca
   http://publish.uwo.ca/~jkiernan/
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"Wilhelms, Margaret B" wrote:
> Lin,
> Please let me know if you got any responses to your question about a
> procedure for Nile Red on formalin fixed paraffin embedded tissues.  I too
> am trying to do this and having no results.
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