Regardless of which dye you use - tetramethylrhodamine, methyl ester (TMRM), JC-1 or MitoTracker - untreated cells will fluoresce. It's just that cells with reduced mitochondrial membrane potential will fluoresce less. It is the degree of change which is important. JC-1 dye not only changes intensity, but has a ratiometric spectral change in excitation and emission. It is very important to have an untreated control as well as a positive control treated with a mitochondrial membrane potential destabilizer, such as CCCP or FCCP. Most mitochondrial stains are only for use with live cells, as the signal will not be retained to the same degree with fixation.
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