In molecular biology, the term restriction fragment length polymorphism (or RFLP) is used in two related contexts: as a characteristic of DNA molecules (arising from their differing nucleotide sequences) by which they may be distinguished, and as the laboratory technique which uses this characteristic to compare DNA molecules. The technique is utilized in genetic fingerprinting and paternity testing.
Usually, DNA from an individual specimen is first extracted and purified. Purified DNA may be amplified by Polymerase Chain Reaction (PCR). The DNA is then chopped into restriction fragments by endonucleases, which only cut where there are specific DNA sequences recognized by the enzymes. The restriction fragments are then separated according to length by agarose gel electrophoresis. The resulting gel may be enhanced by Southern blotting.
The distance between the locations cut by restriction enzymes (the restriction sites) varies between individuals: so the length of the fragments varies, and the position of certain gel bands differs between individuals (thus polymorphism). This can be used to genetically tell individuals apart. It can also show the genetic relationship between individuals, because children inherit genetic elements from their parents. It is also used to determine the relationships among species.