We have a DNA fragmentation ELISA kit from Roche. The protocol suggested NaOH treatment for 30 min as a positive control for DNA fragmentation. We did not get significant result, so I become curious to know what is the underlying mechanism for that?
I always though that NaOH was for cell lysis and change the pH of medium to precipitate DNA genomic and isolate plasmid DNA...maybe the other reactives of the kit make the fragmentation :S or if is a DNA like apoptotic or necrotic not so stable... :S:S:S
In general NaOH denatures DNA to single strands by disrupting hydrogen bonds. Regarding fragmentation below is the link, you can get mechanism underlying the DNA fragmentation under high pH by NaOH.