DNA Profiling

By Dr. Michael Baden

While it's generally accepted that scientists can identify an individual's unique DNA pattern, it's not so widely understood how. To that end the following is a brief explanation of the process that was first used to bring Colin Pitchfork to justice in 1987 and has been a vital criminal investigation tool ever since.

What is DNA profiling?

To understand DNA profiling, you first have to know that large portions of any single person's DNA are the same as every other person's. Because we're all human beings, a large chunk of our DNA is dedicated to our species-specific traits - we have feet instead of hooves, skin instead of scales, etc. But other sections - or fragments - of human DNA are unique to the individual. These fragments are called polymorphic because they vary in shape from person to person. Essentially, DNA profiling is the process of separating an individual's unique, polymorphic, fragments from the common ones. 

How does it work?

Actually, there are two processes of DNA profiling in common use. They are restriction fragment length polymorphism (or RFLP for short) and allele-specific testing. While they're similar in many ways, the two processes have significant differences.

Restriction fragment length polymorphism is the process used to identify Colin Pitchfork. This approach to DNA profiling can pretty much be summed up, "extract it, chop it, sort it, photograph it." RFLP requires a relatively large sample of DNA - twenty-five or more hairs or a nickel-sized blood or semen stain - and the fresher the better. This can be a drawback in criminal cases, where DNA is often taken from tissues that are degraded or contaminated by exposure to the elements.

Once the DNA's been extracted, it's mixed with a chemical called a restriction enzyme. Essentially, the restriction enzyme cuts the DNA into fragments (the so-called restriction fragments) at specific points in the DNA sequence.

The next step is to sort the fragments, using a technique called electrophoresis. The fragments are put at the end of a foot-long block of gel, then the gel is zapped with several hundred volts of electrical current. The current causes the fragments to move towards the other end of the block of gel. The shorter fragments move farther and faster than the longer ones, so once the current's been shut off, the fragments have lined up according to length.

So now you've got the actual DNA pattern - it's strewn along the block of gel. The problem is you can't see it yet. In order to make the DNA fragments visible, an ultra-thin nylon membrane, called a blot, is placed on top of the gel. Via capillary action, the blot soaks up the DNA pattern, intact. Then, synthetic DNA called a genetic probe is applied to the blot. While all of the DNA contained in the sample has been transferred from the gel to the blot, the probe DNA is designed to attach itself to the polymorphic - and only the polymorphic - fragments. All other DNA is washed off, leaving just the unique fragments. The probe material is radioactive, so when a piece of X-ray film is pressed against the blot, a photo called an autoradiograph or autorad (meaning "self-radiating") is created, containing the familiar "bar code" pattern of a DNA "fingerprint."

Allele-specific testing, like RFLP, works by seeking out polymorphic fragments of DNA, a specific type called alleles. Essentially, this process looks for particular alleles in the DNA sample. But because many people may have the tested-for alleles in their DNA, this process results in a much less precise profile. Using allele-specific testing methods, it's possible to determine that a DNA sample is from one out of 10,00 to 100,000 people, as opposed to one out of billions with RFLP.

If allele-specific testing is less precise, why use it?

Allele-specific testing can be done on a much smaller, less pure sample of DNA and takes far less time than RFLP. In a criminal case in which you're trying to extract DNA from a single strand of hair or drop of blood, or you have only skeletal remains of the victim, this is a distinct advantage. And, by using a process called Polymerase Chain Reaction (PCR), it's possible to "amplify" the smaller DNA sample.

How does PCR work?

Fortunately for forensic scientists, with a little help, DNA molecules are able to make copies of themselves. By adding an enzyme called polymerase to the DNA sample, then placing it in a device called a thermocycler, scientists create a chain reaction in which the DNA copies - or amplifies - itself. Basically a very precise heater, the thermocycler repeatedly raises and lowers the temperature of the DNA and, after several cycles, there's enough of it to test.

Are there other types of DNA profiling?

Scientists are continually refining DNA-testing methods, making them faster and more specific. One new development is testing for short tandem repeats (STRs)r, a PCR-based allele-specific test that can get results from samples that were previously too damaged to be usable.