I am trying to digestion the genome DNA of my strain,but find that it doesn't work with the enzyme Sau3A I for many hours.My guess is there are stuff along with the genome DNA which prevents Sau3A I from working.And my question is how and what exactly makes it fail to work.Any suggestions?Thank you!
You don't say what your strain is, but there are many bacteria that
have methylases which add methyl groups selectively to A or C residues
in genomic DNA. My organism, for example, methylates the C in the
sequence GATC, and is completely resistant to Sau3AI digestion, as
well as resistant to BamHI digestion, due to the internal GATC site in
the GGATCC recognition sequence for BamHI. So although your DNA may
be inhibiting the reaction, it may also be that the GATC sites are
5-methyl C methylated.