Restriction Enzymes search for exact sequences of a defined length. One of the common features of most enzyme recognition sites is that they are palindromes. Once the backbone is broken, the hydrogen bonds are not sufficient to hold the strands together, and they separate. This type of cut is called staggered , because it results in fragments with single-stranded ends. The single-stranded overhang from one fragment can be paired with any other fragment of DNA, including one from a different organism, that has a complementary sequence, by joining the two fragments together with another enzyme called DNA Ligase .
Restriction Enzymes can also produce fragments without single-stranded ends.
This is called a blunt cut. This example of a blunt cut is from Eco RV, another Restriction Enzyme isolated from E. coli. As opposed to sticky cutters, no complementarity is required, so any two blunt ended fragments can be joined by DNA Ligase. The first three letters identify the organism the enzyme was isolated from. The first letter is from the genus, the next two are from the species name.