A class of endonucleases that cleaves DNA after recognizing a specific sequence, e.g., BamH1 (5´GGATCC3´), EcoRI (5´GAATTC3´), and HindIII (5´AAGCTT3´). There are three types of restriction endonuclease enzymes:

Type I: Cuts non-specifically a distance greater than 1000 bp from its recognition sequence and contains both restriction and methylation activities.

Type II: Cuts at or near a short, and often palindromic (q.v.) , recognition sequence. A separate enzyme methylates the same recognition sequence. They may make the cuts in the two DNA strands exactly opposite one another and generate blunt ends, or they may make staggered cuts to generate sticky ends. The type II restriction enzymes are the ones commonly exploited in recombinant DNA technology.

Type III: Cuts 24-26 bp downstream from a short, asymmetrical recognition sequence. Requires ATP and contains both restriction and methylation activities.