DNA is methylated, but when it is amplified why does it lose its methylation? I'm asking this in connection with the use of DPN1 enzyme which is used to distinguish between template DNA and mutated DNA while doing Site Directed Mutagenesis.
In vitro synthesized DNA strands (that have never been inside a cell) remain non-methylated. Template strands coming from E.coli remain methylated.These are the bases for DpnI discrimination.