Restriction enzymes as molecular scissors

Restriction enzymes are proteins that bacteria make as a defence against viruses, and laboratories have borrowed them. Each enzyme recognises its own short sequence of DNA and cuts at or near it. That short sequence is called the recognition site, or restriction site. Because the enzymes snip DNA at chosen places, they are called molecular scissors.

Restriction enzymes are one type of endonuclease, a broader class of enzyme. An endonuclease cuts within a DNA chain.

A site is often palindromic: the partner strand carries the same sequence when each strand is read in the 5' to 3' direction. Tai I, for example, recognises ACGT, a site whose partner strand also reads ACGT when read 5' to 3'.

The enzyme and its site make direct physical contact. It makes many hydrogen bonds with the bases of the site, and only after this recognition does it change shape and activate its cutting site. It reads the surface of the DNA as a protein, and does not pair with it the way a nucleic acid would.

Cutting at predictable places gives fragments of known length. DNA is negatively charged, and on a gel the small fragments travel faster, so the fragments separate by size into a pattern of bands. A change in a single base can create or destroy a site, so the pattern reveals differences between gene versions (alleles).

For gene cloning, the enzyme cuts both the gene to be inserted and a plasmid (a small circle of DNA found in bacteria), so the two have matching ends. DNA ligase, which joins DNA pieces together, then joins them permanently. A textbook example is putting the human insulin gene into a plasmid of the bacterium Escherichia coli so that the bacteria make human insulin.