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Cutting DNA Molecules into Small Fragments Restriction enzymes are endonucleases produced by bacteria that typically recognize specific 4- to 8-bp sequences, called restriction sites, and then cleave both DNA strands at this site. Restriction sites commonly are short palindromic sequences; that is, the restriction-site sequence is the same on each DNA strand when read in the 5'  3' direction.

Many restriction enzymes make staggered cuts in the two DNA strands at their recognition site, generating fragments that have a single-stranded “tail” at both ends. The tails on the fragments generated at a given restriction site are complementary to those on all other fragments generated by the same restriction enzyme. These single-stranded regions, often called “sticky ends,” can transiently base-pair with those on other DNA fragments generated with the same restriction enzyme.