Restriction sites

Restriction sites, or restriction recognition sites, are specific sequences of nucleotides that are recognized by restricting enzymes. The sites are generally palindromic, (because restriction enzymes usually bind as homodimers) and a particular enzyme may cut between two nucleotides within its recognition site, or somewhere nearby. For example, the common restriction enzyme EcoRI recognizes the sequence GAATTC and cuts between the G and the A on both the top and bottom strands, leaving an overhang (an end-portion of a DNA strand with no attached complement) on each end, of AATT. This overhang can then be used to ligate in (see DNA ligase) a piece of DNA with a complementary overhang (another EcoRI-cut piece, for example).