Wendy:
Yes, fixation is a likely problem. GFP is small enough that appears to
"leak out" of cells permeablized by alcohol fixation. We have used a brief (no
more than 10 min) 1% paraformaldehyde pre-fix at 4 C to cross-link proteins (and
keep GFP inside) followed by a wash in PBS and then addition of EtOH (or
actually MtOH in our case) per your usual procedure.
All the caveats apply for possible detrimental effects of
paraformaldehyde on the quality of DNA histograms that have been published for
dual staining of intracellular antigens and DNA. For a good review of these see
the chapter by Clevenger and Shankey (pp157-176) in "Clinical Flow Cytometry:
Principles and Applications" published by Williams and Wilkins, 1993.
Good luck!
--Wayne Green wgreen@genetics.utah.edu
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