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I understand that DNA fragmentation is a molecular indicator of apoptosis. What distinguishes this as a hallmark of programmed cell death, versus one of necrosis?

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Although both involve DNA fragmentation, the pattern produced is very different. During apoptosis, DNA fragmentation is done in a regular, controlled pattern, which if run on a gel produces a characteristic "ladder" pattern. Necrosis, on the other hand, is a more stochastic process, and will produce a smear. This details the difference rather nicely, including different ways to assay for either one in table 18.3.1 such as morphological staining or flow cytometry.

Here's a nifty image from the link. Figure 18.3.2. M is the marker, and in panel A, a conventional gel, lane 1 is apoptotic DNA, lane 2 is unprocessed DNA, and lane 3 is necrotic DNA. In panel B, a pulsed-field gel, lanes 1 2 and 3 are untreated, apoptotic, and necrotic, respectively.

Here's a nifty image from the paper

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I understand that DNA fragmentation appears as a regular pattern on a conventional gel. However, I wonder how can the experimenter distinguish apoptosis from necrosis on a typical FACS experiment using propidium iodine DNA staining? –  skyde Aug 1 '13 at 23:14

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