Restriction endonucleases are used by bacteria to recognize foreign DNA and destroy (restrict) it by introducing double-stranded cuts at characteristic recognition sites. They are named after the bacterial species from which they were first isolated. For example, EcoRI was the (I)st  (R)estriction endonuclease isolated from E. coli: Eco + R + I. Most endonucleases used in molecular biology recognize four or six base sites (tetraschizomers or hexaschizomers, "four-cutters" or "six-cutters"). Some have 10 bp sites, and are called "long cutters" because the interval between sites is much greater.

    Restriction sites are molecular palindromes. A palindrome is a word or phrase that reads the same forward or backward: "Able was I ere I saw Elba", "Madame I'm Adam", "Doc: note, I dissent. A fast never prevents a fatness. I diet on cod". (The one-word record holder is the Finnish word for a soap seller, "Saippuakauppias"). DNA palindromes read the same forward and backward in the double-stranded molecule. In the first example above, the recognition site of EcoRI is 5'-GAATTC-3', so the paired strand is 3'-CTTAAG-5': the double-stranded 6 bp sequence therefore reads the same in either 5'-3' direction. The cut occurs at 5'-G/A on either strand, leaving both with a single-stranded 5'-AATT tail.