Question

How does the restriction enzyme prevent the cutting of the endogenous DNA?

Answer 1

These enzymes are found in bacteria and archaea and provide a defence mechanism against invading viruses.[4][5] Inside a prokaryote, the restriction enzymes selectively cut up foreign DNA in a process called restriction digestion; meanwhile, host DNA is protected by a modification enzyme (a methyltransferase) that modifies the prokaryotic DNA and blocks cleavage. Together, these two processes form the restriction modification system.[6]
Over 3000 restriction enzymes have been studied in detail, and more than 600 of these are available commercially.[7] These enzymes are routinely used for DNA modification in laboratories, and they are a vital tool in molecular cloning.