I'm trying to set up a simple MNase assay where I am compare global chromatin compaction of two melanoma cell lines. I want to make sure that I have the same amounts of DNA before I add the MNase. One protocol I have suggests counting nuclei. One suggests adding 2M NaCl to the nuclei and OD another suggests adding 1M NaOH to the nuclei and OD.
I did a pilot where I took ODs with either NaCl or NaOH and then took the nuclei sonicated them and did phenol chloroform and then OD.
The reading after phenol chlor was 500x more than the reading before.
Can anyone recommend an accurate way of measuring the DNA? Or even point me to some simple MNase protocols.