Nonyl acridine orange is well retained in the mitochondria making it a useful probe for following mitochondria during isolation and after cell fusion. The mitochondrial uptake is reported to not to depend on membrane potential, unlike many other mitochondrial probes. It is toxic at high concentrations and apparently binds to cardiolipin in all mitochondria, regardless of their energetic state. This derivative has been used to analyze mitochondria by flow cytometry, to characterize multidrug resistance and to measure changes in mitochondrial mass during apoptosis.

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