Flow cytometry is most frequently used to detect apoptotic DNA fragmentation. Analysis of DNA content by flow cytometry can identify apoptotic cells with fragmented DNA as the cells with fractional DNA content, often called the sub-G cells. The flow-cytometric assay utilizing the fluorochrome acridine orange shows that DNA fragmentation within individual cells is discontinuous likely reflecting different levels of restriction in accessibility of DNA to DNase, by the supranucleosomal and nucleosomal levels of chromatin structure. The presence of apoptotic "sub-Gcells" can also be detected in cells pre-fixed in ethanol but not after fixation in the crosslinking fixatives such as formaldehyde. The late-S and G apoptotic cells  may not be detected with this approach because their fractional DNA content may overlap with that of the non-apoptotic G cells.
Treatment of cells with detergent, prior or concurrently with DNA fluorochrome, also reveals DNA fragmentation by virtue of the presence of the sub-G cells or cell fragments, as defined by Nicoletti et al.
Apoptotic DNA fragmentation can also be detected by the TUNEL assay. The fluorochrome-based TUNEL assay applicable for flow cytometry, correlates the detection of DNA strand breaks with the cellular DNA content and thus with cell cycle-phase position. The avidin-peroxidase labeling TUNEL assay is applicable for light absorption microscopy. Many TUNEL-related kits are commercially available. 
Apoptotic DNA fragmentation is also analyzed using agarose gel electrophoresis to demonstrate a "ladder" pattern at ~180-BP intervals. Necrosis, on the other hand, is usually characterized by random DNA fragmentation which forms a "smear" on agarose gels.