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The bottom line is that toxicity studies have yet to been done on DAPI. I have seen one article questioning its use (Qin, 2011 using it on MSCs).
DAPI is known to be semi-permeant to cells and thus it does get in. As a very high affinity DNA binding dye with a degree of permeance it will almost certainly have toxic effects. This is the nature of DNA-intercalators.
To the contrary, DRAQ7 has already been tested in highly sensitive bioassays for DNA damage (see Akagi et al, Feb 2013 issue of Cytometry Part A) and even after several days at very high concentrations did not have an impact on cell health. They also used DRAQ7 alongside TMRM as a reporter of mitochondrial health and the read-outs are equally supportive of DRAQ7 as a long-term, real-time reporter of cell integrity / permeabilisation.
We have other anecdotal evidence in rapidly proliferating SUD-4-DHL cells over 4 days and a further collaborator has been using it in real-time analysis of nano-particle toxicity in fibroblast cultures, over 2 days.
Answered on Apr 26 2013