Restriction endonucleases -- enzymes that cleave DNA molecules at specific nucleotide sequences depending on the particular enzyme used. Enzyme recognition sites are usually 4 to 6 base pairs in length. Generally, the shorter the recognition sequence, the greater the number of fragments generated. If molecules differ in nucleotide sequence, fragments of different sizes may be generated. The fragments can be separated by gel electrophoresis. Restriction enzymes are isolated from a variety of bacterial genera and are thought to be part of the cell's defenses against invading bacterial viruses. These enzymes are named by using the first letter of the genus, the first two letters of the species, and the order of discovery.