I currently use herring sperm DNA and BSA, plus all the "standard" FISH ingredients (formamide, dextran sulfate, SSC) but am worried that there is still a bit too much background and/or nonspecific probe binding. I was thinking of adding in something like Roche's blocking reagent or ReadyProbes In Situ Hybridization Blocking Solution from Thermo, but wanted to see others experiences with these in FISH/ISH.
Hopefully that was clear - thanks in advance!
Maybe you should specifiy your protocol, I think it depends on your fluorescence system, if you use tyramide kits or directly labelled antibodies, etc. For standard ISH, Boehringer/Roche Blocking reagent, 1%, is recommended. At least using species specific blocking agent (serum) should be considered. If you use a enzyme dependend signal amplification make sure to inactivate all intrinsic enzyme activity (e.g. HRP). Additionally, I strongly recommend acetylation to prevent non-specific binding (which should be included in your protocol anyways).
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