2. Handiest tool

3. Junky genes speak

4. Latest and greatest

Laboratory manager George Gaucys with the toaster-sized PCR machine, able to mulitply DNA on the lab bench. PCR is key to STR. No kidding!

Like the scribblings of ancient scribes, the lines on this gel electrophoresis machine reveal all. The distance traveled from the starting point reveals the weight of each bit of DNA; a clue to its structure.

Junk reading
Over the past 15 years or so, it's become ever-easier to analyze repeats in junk DNA -- to turn trash into treasure, so to speak.

In 1984, the English scientist Alec Jeffries invented RFLP (restriction fragment length polymorphism -- we see that hand in the back of the room). The technique used "restriction enzymes" -- chemicals that cut the DNA molecule at specific locations, leaving smaller fragments where specific repeats could be counted.

Using complicated statistics, scientists could compare the genetics of the crime-scene sample and the suspect.

After its successful use in 1986, RFLP gained popularity for identifying tissue samples at a crime scene -- and for proving that a sample did not come from a suspect. But RFLP required more than 200 lab steps, driving technicians nuts and raising costs and chances for error. And it took weeks to carry out -- valuable time during which the police might be investigating the wrong suspect, allowing the trail to grow cold so the real villian could escape.

By about 1995, a much faster, cheaper and better technique entered the picture. STR -- short tandem repeats -- works, as the name implies, with shorter hunks of DNA, and it has become a favorite of forensic and medical labs alike. "It may only take 50 steps, it's much simpler," says Lars Jorgensen, who's used both techniques for paternity testing at the Madison, Wis., office of the American Red Cross.

PCR 'n STR
Say you have an invisibly small gob of DNA -- taken from blood, sweat or tears at a crime scene. Twenty years ago, even had DNA testing been available, that would have been too little DNA. Today, a toaster-sized polymerase chain reaction (PCR) machine can, in a few hours, produce billions of copies of a specific stretch of DNA.

Although PCR has reduced DNA multiplication to about the level of button-pushing, the technology deservedly won the Nobel prize for chemistry. PCR rests on the biological fact that DNA must accuratley copy itself whenever genes are doubled during cell division, and PCR cleverly exploits this ability.

PCR does, however, speed up this process -- and adds a twist called a "primer." This artificial chemical locates a specific stretch of DNA bases and directs that duplication occur in one direction only from that stretch.

DNA has two matching strands, and by placing the right primer on each strand, you can duplicate whatever stretch is between them. For DNA fingerprinting, you simply choose primers so the repeats just described are between them.

The PCR machine heats this strand, disengaging the double helix and producing two sub-strands, each with a string of bases along it. The machine cools slightly, and, with the help of a natural enzyme, each strand gathers bases to form the opposite, or complementary, strand, recreating the full double-helix of DNA.

The system works because DNA bases are choosy: A will join only to T, and C only to G. Because of that, the first cycle turns the original strand into two identical strands. After 28 cycles, one strand becomes 2²⁸ strands -- plenty of identical DNA for analytical purposes.

Gelly donut
Since the original strand was chosen to contain only the repeated region, the next step in DNA fingerprinting is to weigh each strand to count the repeats. The weighing takes place in a gel electrophoresis machine, which propels bits of DNA through an electric field. Because each bit receives equal electric force, smaller bits move faster than larger ones. The result is the inscrutable array of dark bands seen above.

We don't want to bog down in the details of gel electrophoresis -- just pronouncing it strains our cerebral capacity -- but you read the gel with a template that tells you how many repeats are present, based on the distance each strand has moved on the gel.

Now things get interesting. The number of short tandem repeats in junk DNA, remember, vary from one person to the next. Databases on STR DNA in unrelated people show expected variations in the overall population, at each of the sites where the DNA is analyzed.

Finding the same number of repeats at one site is suggestive but not conclusive, if, say one person in 10 has the same number of repeats. "One by itself is not specific," says Laber.

But if you find the same odds at two sites, suddenly the odds drop to one in a hundred. If you examined 13 sites specified by the FBI, and found that same one-in-ten odds, the odds that a similar DNA fingerprint would exist in any one person would be one in 10 trillion (10¹³). DNA fingerprinting typically produces intimidating odds, says Laber. Translated: The odds are that no living person would have that DNA -- except whoever left the tissue sample at the crime scene.

Testing DNA testing
Powerful technologies like DNA fingerprinting often have unforeseen effects. The federal CODIS database, for example, could become something akin to a national warehouse of biological data. And while it cannot, at present, be used to determine who would be susceptible to what genetic illness, will it never be usable for that?

The national DNA database has raised questions. Whose DNA will be entered into the database so a comparison can be made after a crime? All people? All men, since men commit most rapes and murders? Only arrestees? Only convicts? Only certain convicts? How does the Fourth Amendment restriction on search and seizure affect DNA taken from a swab inside the mouth?

The use to of DNA fingerprinting to evaluate innocence for convicts is gaining approval -- if evidence remains available. Richard Dieter, of the Death Penalty Information Center, says the attitude among prosecutors "seems to be evolving. It was resisted as new evidence that should not be allowed. Now the chances are that DNA testing will be allowed."

Because such testing is standard for new trials, he says, "There are not going to be these kinds of cases 20 years from now, cases that look back, because the DNA testing will be done." Today, he adds, there "is a window of cases with people still in prison, on death row" who can be helped -- if they are innocent, and if DNA samples are available.

Death penalty opponents say the Ochoa case highlights a larger problem: False confessions made to avoid the death penalty. Ochoa, for example, confessed despite being innocent and having no criminal record. "The Ochoa case ... serves to highlight the phenomenon of false confessions caused by fear of the death penalty," says Keith Findley, who co-directs the University of Wisconsin-Madison project that helped exonerate the Texas man (see "DNA Testing Clears..." in the bibliography).

DNA fingerprinting may be the best thing for law enforcement since the cop show, but it's not perfect, since it requires biological evidence from the perpetrator. And even if such evidence is present, Dieter says, no amount of technology can "substitute for having a fair trial, for having open files so both sides know the evidence, for having a good lawyer. There are still problems that need to be addressed that DNA does not deal with."

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