How does the cell protect its own DNA from disassembly?

The cell protects its own DNA from disassembly by masking the restriction sites with methyl (CH3) groups so they are unrecognizable to restriction enzymes. 

DNA disassembly is usually caused by restriction enzymes. These enzymes recognize and cut DNA only at specific short nucleotide sequences known as restriction sites or recognition sequences. Attaching methyl groups to the restriction sites in the nucleotides masks them and protects them from disassembly as restriction enzymes cannot recognize methylated sequences.