DNA fingerprinting (also often called "DNA profiling") is a powerful tool that allows the unique pattern of certain common polymorphisms within an individual's genome to generate a unique genetic profile. It is most famously used in law enforcement in cases where criminals leave DNA evidence at the crime scene. More commonly, DNA fingerprinting is also used to determine genetic relationships between individuals; this application is widely used in research and paternity testing.
Recent advances in genomics and molecular biology have allowed for several different DNA profiling techniques to be developed. As with any set of tools, each technique has its own advantages and limitations; the best technique to use most often depends on the application or, especially in criminal cases, the situation.
For all of the established methods, the size of a DNA sample required to generate an accurate profile is quite small. Methods relying on PCR amplification are able to generate an individual's complete profile from the DNA found in a single cell.
The original technique for DNA fingerprinting was invented in 1984, before PCR (which was invented around the same time) was available to amplify DNA samples in-vitro. This technique relies on the unique set of restriction fragment length polymorphisms (RFLPs) in a persons genome to generate a profile. Restriction fragments are the fragments generated when DNA is digested with a restriction enzyme. Because restriction enzymes only cut DNA at specific sequences (restriction sites), digesting a sample of the same individual's DNA with a restriction enzyme will always yield the same set of fragments. The nature of restriction sequences is such that they are highly unlikely to occur within functional genes, thus mutations in restriction sites are almost always neutral mutations. Accordingly, these mutations occur randomly and are randomly transmitted to subsequent generations. Because of this, no two people (with the exception of monozygotic twins) have the same distribution of restriction sites in their DNA. Generating a fingerprint with this method is a simple three step process. First the DNA sample is digested with a restriction enzyme. Second, the digested DNA is run on a denaturing gel. Finally, a southern blot, using a probe for a tandem repeat or a microsatellite sequence, is done to reveal the "fingerprint".
The method described above is very reliable, and is still used today for some applications. However, it can often lack the necessary resolution to precisely determine genetic relationships between individuals. Additionally, southern blotting is resource-intensive and time-consuming. The advent of PCR solved these problems; PCR is cheap, fast, and easy to do.
Modern techniques use PCR to amplify the regions of DNA in between randomly occurring short tandem repeats. Because the repeats are randomly distributed in the genome, the length of DNA in between them is also random. Running the PCR products on an agarose gel will separate the fragments generated by size into a series of bands that is unique to the individual.
Bloom et al. (1996). "Laboratory DNA Science".