I do not think to synchnoise your samples. Otherwise how can you differentiate the early- and late- apoptosis and necrosis  from the same sample?

Piyush, keep in mind that 293 cells express adenoviral E1B, which prevents apoptosis induced through the mitochondrial pathway. I would use a different cell line for your assay. One possibility are HL60 cells, which easily undergo apoptosis in response to a variety of agents along with easily detectable DNA fragmentation. If HL60 are not available, try to treat several cell lines that you have to choose one that dies. If you have to use 293, try to induce apoptosis with staurosporin.

Hope this is helpful.

I would side with Yuri. Leukemic cells (Molt4, Jurkat, HL60) would be better suited to kill and induce DNA fragmentation easily--say, by simple drugs like etoposide. Two problems that you should consder: (1) the extent of apoptosis--is it adequate yet to cause detectable fragmentation? In my experience, PARP-cleavage (widely considered as an apoptosis marker) is not necessarily an indicator of adequate DNA fragmentation. (2) Make sure that your DNA extraction is not shearing your DNA! That happens quite often. As a positive control for both fragmentation and extraction, you can use half a million cells (in 50-100ul, inTBS plus 0.2% Igepal or Triton to permeabilize, plus 2mM CaCl2) and treat 2U of MNase for 5-10min (you may want to do a time course)

Dear Joseph Molnar,

you do not need to synchronise your cell population. Instead you need a cytotxic compound that induce fast and relatively synchronised cell death to get "positive control".

Regards,

Petr Mlejnek

Thank you all for your valuable suggestions..Finally i have observed DNA fragments. Once again for sharing your knowledge to me. Thanks researchgate for providing such a good platform for wide discussion. 

DNA fragmentation whether in megabase, kilobase or 100 base pairs occur in apoptosis, necrosis and necroptosis.