I am trying to do DNA fragmentation assay, procedure is based on internucleaosomal DNA cleavage which is hallmark of apoptosis. I am using etoposide for standardization. I treated U937 cells with 25 µM of etoposide for 1, 3, 6, 9 & 12 hours. DNA was extracted from treated cells by suspending the cell pellet in 20 µl of lysis buffer (10mM EDTA, 50mM Tris at pH 8.0 and 0.5% w/v, SDS) containing proteinase K. The whole lysate was incubated at 50 degree C fro 1 h in water bath. After completion of incubation to the condensate 10 µ l of RNase was added and further incubate for 1 h at 50 degree bath. Tgis was centrifuged for 15 s and ran on 2% agarose gel. But the ladder was not proper plus the lysate was very viscous to load. Any suggestion or advice highly appreciated.