Apoptotic DNA fragmentation, visualised by the DNA laddering assay (left). A 1 kb marker (middle) and control DNA (right) are included for comparison. Apoptotic DNA fragmentation is a key feature of apoptosis, a type of programmed cell death.Apoptosis is characterized by the activation of endogenous endonucleases with subsequent cleavage of chromatin DNA into internucleosomal fragments of roughly 180 base pairs (bp) and multiples thereof (360, 540 etc.).n apoptotic DNA fragmentation, the DNA is cleaved in the internucleosomal linker region, which is the part of the DNA not wrapped around the histones. CAD cleaves DNA at internucleosomal linker sites between nucleosomes, protein-containing structures that occur in chromatin at ~180-bp intervals.