The probes I use are BHQ-FAM labelled, sequence specific probes. I am out of primers and would like to utilize the spare probes.
The fact that it is a BHQ-Fam is actually an excellent labeling for ISH as it provides higher signal to noise. Unfortunately...
directly labelled probes can be used for rna FISH when you have several sets. Please see:
Raj, A., Bogaard, P. Van Den & Rifkin, S. Imaging individual mRNA molecules using multiple singly labeled probes. Nature Methods 5, 877–879 (2008).
The use of individually labeled probes is primarily for the spatial resolution again, as you are not looking at antibody/enzyme amplified signal, and each dot represents a single molecule. Unfortunately, that requires the quantum yield/brightness per RNA molecule to be high.
To solve this, people have used 5 distinct oligo probes to hybridize and see mRNA molecules successfully, but for robustness the paper recommends much higher numbers, around 48, which I assume is far more probes then you should normally have laying around.
Personally, I would not expect to see ISH signal unless you have 4 more probes. If you are setup for some ISH, it wouldn't hurt to try, but with no amplification, it will be difficult to see the signal from a single FAM molecule/mRNA unfortunately.
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