I am currently using To-Pro-3 Iodide from Molecular Probes as my DNA counterstain for confocal microscopy on cytospun, paraformaldehyde fixed thymocytes. Even at 0.05 uM (1:20000 dilution from 1mM stock) I still get interference between the To-Pro and a FITC labelled secondary antibody to a nuclear protein. Any suggestions? I can not use DAPI or PI as my counterstain either.
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