Cohesive ends are short single-stranded sequences of DNA, usually 1 to 3 bases long, that are produced at the end of a double-stranded DNA molecule by the action of a type II restriction enzyme that makes staggered cuts in a symmetrical, palindromic sequence (1). For example, Pst1 cuts the sequence 5′ ..CTGCAG.. to give the ends ..C and TGCAG.. . The two ends 3′ ..GACGTC.. ..GACGT.. C.. produced in this way are complementary, so they bind together by base pairing and allow DNA Ligase to repair the break. Furthermore, any fragment cut by an enzyme of this type binds to any other DNA fragment cut by the same enzyme or to one that creates the same cohesive ends. When the cohesive ends ligated together are cut by enzymes that have different recognition sequences, the new sequence is not cut by either enzyme. In the case of BamHI, 5′ ..GGATCC.. and Sau3a, ..GATC.., which produce the same sticky ends ..CCTAGG.. ..CTAG..but have different length recognition sites, the sequence created can always be cut by Sau3a but can be cut only by BamHI if the sequence cut by Sau3a is a BamHI site. Some restriction enzymes recognize degenerate sequences, so that only when both DNA fragments cut with this type of enzyme have the same sequence do they pair and allow ligation. Depending on the position of the cuts in the two strands, either a 5′-strand or the 3′-strand, creating a 5′-overhang or a 3′-overhang is possible, but each enzyme produces only one type.
Cohesive ends are also present on some bacteriophages. For example, on lambda phage they are 12 bases long and are produced by staggered cutting of a symmetrical sequence site (cos site) by a phage enzyme during DNA packaging (2).
