Type II restriction enzymes, most commonly used for DNA analysis and genetic engineering, each have a unique nucleotide sequence at which it cuts a DNA molecule. A particular restriction enzyme will cleave DNA at that recognition sequence and nowhere else.
Restriction enzymes can also differ in the way they cut the DNA molecule.
Some enzymes cut in the middle of the recognition sequence, resulting in a flush or blunt end . Because of the sequence specificity of restriction enzymes, these enzymes can cut DNA into discrete fragments which can be resolved by gel electrophoresis. Other restriction enzymes can be used to further characterize a particular DNA molecule. The location of these restriction enzyme cleavage sites on the DNA molecule can be compiled to create a restriction enzyme map . These maps are very useful for identifying and characterizing a particular DNA plasmid or region.