Ultimate Gene Machine

By J. Madeleine Nash/Chicago

Imagine an amplifier powerful enough to convert the inaudible whir of butterfly wings into a mighty roar. That's what a new tool called PCR routinely does to the most infinitesimal snippets of DNA, the molecule that carries the genetic blueprint for all living things. Within the space of a few hours, an unprepossessing aluminum box stuffed with test tubes can create a billion copies of what started out as a single strip of DNA. A dividing cancer cell would take at least a month to perform the same stupendous feat. "This technique," marvels Dr. Harley Rotbart, a microbiologist at the University of Colorado School of Medicine, "can reproduce genetic material even more efficiently than nature."

PCR stands for polymerase chain reaction, polymerase being the enzyme that triggers the replication of DNA inside dividing cells. All PCR does is reproduce, in a test tube, this basic biological process, turning it into a chain reaction that can be endlessly repeated by having a machine alternately raise and lower the temperature in the test tube. "The beauty of PCR is that it's technically so simple," observes cell biologist Peter Parham of Stanford University.

Since the first working machine was developed six years ago by a team of Cetus Corp. researchers, including biochemist Kary Mullis, PCR has enabled researchers to study even the faintest, most fragmentary traces of DNA found in specks of dried blood, strands of hair, chips of bone. In the journal Nature last week, for example, a team of British researchers recounted how they successfully identified a teenage murder victim from skeletal remains eight years old. First they extracted DNA from bone cells in the dead girl's femur. Then they obtained DNA from blood samples donated by the couple believed to be her parents. Using a PCR machine as their microscope, they went on to magnify and examine the unique genetic markers the dead girl shared with her parents. The evidence helped to convict two men of the crime earlier this year.

To date, PCR has been used to compare the DNA of extinct animals with their closest living relatives. It has assisted the U.S. military in identifying the remains of soldiers who died during Operation Desert Storm. It is beginning to help physicians detect small numbers of cancer cells circulating in the bloodstream and make prenatal diagnoses of genetic diseases such as sickle- cell anemia, as well as ensure better matches between organ donors and transplant recipients.

PCR may also soon aid scientists in solving a number of historical mysteries. Among them: whether the man who drowned in Argentina in 1979 really was Nazi war criminal Dr. Josef Mengele, and whether Abraham Lincoln suffered from Marfan's syndrome, an inherited disease characterized by gangly limbs, poor eyesight and a weak heart. "The applications of this technology are literally as wide as your imagination!" exclaims University of Virginia geneticist Dr. Thaddeus Kelly.

Among the areas where PCR is starting to make important inroads:

MEDICAL DIAGNOSTICS. Already PCR has begun to help physicians determine which babies born to AIDS-infected mothers also harbor the virus. Since all newborns carry their mother's antibodies whether or not they are actually infected, standard antibody tests are inconclusive. PCR, however, can home in on the minute quantities of viral DNA that may be present in only 1 out of 100,000 . cells. A positive diagnosis means the baby can immediately begin therapy with AZT.

PCR-based diagnostic tests are also under development for Lyme disease, tuberculosis and viral meningitis. Present tests for tuberculosis, which involve culturing and growing the bacteria, take up to a month to confirm a diagnosis. PCR can do the job in a few hours. Current tests are unable to distinguish viral meningitis quickly from the far more dangerous bacterial form of the disease, which is most common in infancy. As a result, all babies found to have meningitis are treated as if they had the more lethal form. With a PCR diagnosis, those with viral meningitis could be spared unnecessary hospitalization and medication. "There is a big financial saving, a big emotional saving, and substantial reduction in risk to the baby," says Colorado's Rotbart, who is helping to develop the test.

FORENSIC SCIENCE. Amplified by PCR, the DNA in a single sperm cell can link a suspect to a rape victim. Theoretically, a single epithelial cell found in saliva can be traced back to the person who, say, licked a stamp on a letter bomb. In California's San Mateo County, charges against a man arrested and jailed for a brutal rape were dropped in 1988 after a PCR test showed he could not have been the attacker. A year later another man was arrested in another rape case. Not only did a DNA marker make him a suspect in the unsolved rape, but the victim's jewelry was found in his girlfriend's possession and his fingerprint matched one found on the victim's car. Result: a conviction.

EVOLUTIONARY BIOLOGY. Thanks to PCR, it is now possible to extract badly degraded DNA sequences from ancient sources and enlarge them like photographic prints. Thus far, PCR has been used to examine minuscule fragments of DNA taken from the brain cells of humans buried 8,000 years ago in a Florida bog. Analysis of such DNA can shed light on the emigration patterns of ancient peoples and perhaps some of the diseases that afflicted them. The technique has also been used to examine DNA from animal skins in natural-history museums and from the frozen remains of woolly mammoths. Among the unresolved questions that PCR may eventually shed light on is whether the Neanderthals were an unsuccessful offshoot of the evolutionary tree or the direct ancestors of modern humans. It may also be able to unravel the mystery of what happened to the ancient Celts, who once populated most of Western Europe. "Now," says University of Leicester geneticist Alec Jeffreys, "there is a genetic time machine for looking back into the past."

Sometimes PCR is compared to a computer that speedily executes the most complex calculations. But its significance far exceeds a simple increase in efficiency and productivity. Like the radio telescope and the electron microscope, it represents an advance of a fundamental nature. Before PCR, scientists could not consider analyzing the DNA contained in a single cell, much less the degraded DNA recovered from dried blood or old bones. PCR, says Dr. Barry Eisenstein, chairman of the Department of Microbiology at the University of Michigan Medical School, "is enabling us to answer questions we only dreamed of five years ago."

Ironically, the technology's biggest virtue is also its major drawback: it is so sensitive to tiny bits of DNA that even the most minute contamination of laboratory samples can lead to false results. This sometimes vexing problem, however, has not stopped the flow of creative and occasionally wild ideas about PCR's applications. Researchers at Hoffmann-La Roche Inc., which recently agreed to pay Cetus $300 million for the rights to PCR, are interested in developing a whole series of DNA identification tags. To foil counterfeiting, for instance, everything from paper currency to designer jeans and compact discs might be laced with DNA markers. Oil carried in tankers and toxic chemicals carried in trucks might similarly be "branded" by molecules of synthetic DNA. With PCR, a spill of unknown origin could then be traced back to the responsible party.

Like many, Arthur Caplan, director of the Center for Biomedical Ethics at the University of Minnesota, believes that PCR will revolutionize everything from medicine and biology to anthropology and history. It is a prospect he finds both exhilarating and disturbing. Technically, it would be possible, by examining DNA samples from the descendants of Thomas Jefferson and those of his slave Sally Hemings, to determine once and for all whether Jefferson, as rumored, fathered some of Hemings' children. Would this be an appropriate use of the new technology? "Let me put it this way," says Caplan. "Because of PCR, I'm not worried about going out of the bioethics business anytime soon."

With reporting by Anne Constable/London and Andrew Purvis/New York