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. These cleave double stranded DNA at specific points. The point of cleavage depends on the restriction enzyme. This effectively destroys the foreign DNA, which is then degraded further by other endonucleases. This phenomenon is called restriction.

Restriction enzymes are highly specific. They 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, the host must have a system to protect its own DNA. It achieves this by modifying it. It adds methyl groups to it to block the action of the restriction enzymes. This must be done in a way that does not interfere with the DNA's base-pairing. To achieve this, it is usually modified at specific bases on each strand.

Although this system is effective, it is not completely foolproof. Problems can arise during DNA replication. The newly made strands of DNA are not methylated. Usually however, the modification system fixes this and prevents the DNA from being cleaved.

Some viruses have also evolved ways of overcoming it, by modifying their own DNA. They either methylate or glycosylate it, thus blocking the restriction enzymes. To counteract this, some bacteria have restriction systems which only recognize modified DNA. Clearly these bacteria do not modify their own DNA! Other viruses, such as bacteriophages T3 and T7, encode proteins that inhibit the restriction enzymes. Some prokaryotes are able to overcome this by having multiple restriction modification systems.

There are three kinds of restriction modification systems: type I, type II and type III. all of these have a restriction enzyme activity and a methylase activity. They were named in the order of discovery. type II is the most commmon.