The restriction modification system (RM system) is found in bacteria and other prokaryotic organisms, and provides a defense against foreign DNA, such as that borne by bacteriophages.
Bacteria have restriction enzymes, also called restriction endonucleases, which cleave double-stranded DNA at specific points into fragments, which are then degraded further by other endonucleases. This prevents infection by effectively destroying the foreign DNA introduced by an infectious agent (such as a bacteriophage). Approximately one-quarter of known bacteria possess RM systems and of those about one-half have more than one type of system.
As the sequences recognized by the restriction enzymes are very short, the bacterium itself will almost certainly contain some within its genome. In order to prevent destruction of its own DNA by the restriction enzymes, methyl groups are added. These modifications must not interfere with the DNA base-pairing, and therefore, usually only a few specific bases are modified on each strand.
Endonucleases cleave internal/non-terminal phosphodiester bonds. They do so only after recognising specific sequences in DNA which are usually 4–6 base pairs long, and often palindromic.