A restriction enzyme is a protein that recognizes a specific, short nucleotide sequence and cuts the DNA only at that specific site, which is known as restriction site or target sequence.

More than 400 restriction enzymes have been isolated from the bacteria that manufacture them. In live bacteria, restriction enzymes function to defend the cell against invading viral bacteriophages. Restrictions sites in the viral genome (a "happy accident" of nature, as far as the bacteria are concerned, since they don't appear to have any specific function in the virus) are cleaved by the bacterium's restriction enzymes, fragmenting and destroying the DNA of invading bacteriophages before it can incorporate into the host's genome and take over the cell.

A bacterium is immune to its own restriction enzymes, even if it has the target sequences ordinarily targeted by them. This is because the bacterial restriction sites are highly methylated, making them unrecognizable to the restriction enzyme.

Isn't evolution fantastic?

When a restriction enzyme cleaves a restriction site, the reaction creates highly reactive "sticky ends" on the broken DNA. This is useful to the biotechnologist!

By cutting open vector DNA with the same with restriction enzymes used to cleave the target DNA, complementary "sticky ends" are created. This fosters the insertion of the target DNA into the vector:

The fragment is "glued in" with DNA ligase, which creates the phosphodiester bonds necessary to complete the sugar-phosphate backbone of the newly transgenic DNA.

Identity of Restriction Enzymes

  • Restriction enzymes are named for the organism from which they were first isolated. For example

  • Some restriction enzymes also cut DNA to form "blunt" ends (without single-stranded tails), which also can be inserted into target DNA via the action of DNA ligase.
  • DNA ligase isn't picky: it can't tell the difference between foreign and host DNA (who'd figure it would ever have to?), and this enables the creation of chimeric DNA--DNA from two separate sources.
  • Each enzyme recognizes and cuts specific DNA sequences. For example, BamHI recognizes the double stranded sequence:


    Here's another artist's conception of how this works. (Notice the "sticky ends.")

    To summarize...