Restriction modification system

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The restriction modification system is used by bacteria, and perhaps other prokaryotic organisms to protect themselves from foreign DNA, such as bacteriophages.

Bacteria have restriction enzymes, also called restriction endonucleases, which cleave double stranded DNA at specific points, which is then degraded further by other endonucleases. This prevents infection by effectively destroying the foreign DNA belonging to the bacteriophage.

Restriction enzymes are highly specific, and only cleave at specific points. They recognize specific sequences of DNA which are usually 4-6 base pairs long, and often palindromic. Given that the sequences they recognize are very short, the bacterium itself will almost certainly have many of these sequences present in its own DNA. Therefore, in order to prevent destruction of its own DNA by the restriction enzymes, the bacteria marks its own DNA by adding methyl groups to it. This modification must not interfere with the DNA base-pairing, and therefore, usually only a few specific bases are modified on each strand. There are three kinds of restriction modification systems: type I, type II and type III, all with restriction enzyme activity and a methylase activity. They were named in the order of discovery, although the type II system is the most common.

Some viruses have evolved ways of subverting the restriction modification system, usually by modifying their own DNA, by adding methyl or glycosyl groups to it, thus blocking the restriction enzymes. Other viruses, such as bacteriophages T3 and T7, encode proteins that inhibit the restriction enzymes.

To counteract these viruses, some bacteria have evolved restriction systems which only recognize and cleave modified DNA, but do not act upon the host's unmodified DNA. Some prokaryotes have developed multiple types of restriction modification systems.