checking sonication using chelex and agarose gel - (Nov/16/2010 )
side by side is always the way to go and it sounds like you don't have to much of a discrepancy in size so I wouldn't worry too much........unless you have to have small fragments. I am surprised that you get frags below 200bp.......I can never seem to get mine below 300 unless I really blast my chromatin during the shearing step. From what KPDE says it seems like Chelex may be more sensitive to certain cell types. MEFs, which I work with, have high DNA density, so maybe the DNA is associated to a greater degree with protein that makes it resistant to traditional ProK/Chelex treatment..........maybe if I ProK treated or chelexed my DNA for an hour as opposed to 30 min for the ProK and 20 min for the Chelex I would see the same results as I see using Szaks.