This article first appeared in the St. Louis Beacon, Feb. 17, 2010 - Last week's newspaper (the old-fashioned printed kind) carried a wonderful story about the genome of someone who lived in the frozen western shore of Greenland more than 4,000 years ago. Much of what was most wonderful about the story, however, is a little subtle for someone not versed in the science - hence today's column. I have always viewed my column ON SCIENCE not as reporting but as teaching, as a vehicle for me to EXPLAIN the science of the day.
So if you will bear with me, that is what I am going to do. First I am going to bring you up to speed on two areas of today's science, DNA fingerprinting and PCR, then we will tackle the new story.
DNA Fingerprinting
DNA fingerprinting is a process used to compare samples of DNA. Just as fingerprinting revolutionized forensic evidence in the early 1900s, so DNA fingerprinting is revolutionizing courtrooms today. A hair, a minute speck of blood, a drop of semen, all can serve as sources of DNA to convict or clear a suspect.
How does DNA fingerprinting work? The process, invented in 1985 by British geneticist Alec Jeffreys, depends critically on two simple facts - his genius was in putting them together in a new and novel way. The two facts are:
#1. Every person on earth has a unique genome, his or her DNA sequence differing from everybody else's at thousands of different places scattered along the chromosomes.
#2. DNA-cutting enzymes cut DNA by each recognizing a specific sequence, almost always a six-nucleotide sequence like GAATTC, and these sequences occur by chance many thousands of time in the 6 billion-nucleotide human genome.
When Jeffreys put these two facts together, he realized that the DNA differences between people must by chance occur within six-nucleotide cutting sites lots of times. This realization has a very important consequence that led Jeffreys directly to his invention.
LOOKING AT HIS OWN DNA: If Jeffreys were to cut up his DNA using a particular cutting enzyme, the collection of fragments he obtained from himself could be visualized in the laboratory by injecting the collection of fragments at the end of a gel slab and applying an electric current. Because DNA molecules carry an electrical charge, the fragments will all start to migrate toward the other side of the gel slab - but the longer the fragment, the slower it migrates (it has to elbow its way past a forest of gelatin fibers). After a while, when Jeffreys turns off the current, the fragments are spread out across the gel, the smaller fragments located further along the gel.
Why should the DNA fragments be of different sizes? Because of fact #1 above. Because the cutting sites are scattered around randomly, sometimes two of them will occur close together (resulting in a small fragment when the DNA is cut that migrates very fast) and sometimes two of them will occur far apart (resulting in a large fragment that migrates much more slowly).
COMPARING TWO PEOPLE'S DNA: Now comes Jeffreys' realization: If you repeat this experiment with another person's DNA, you will not get the same pattern! Because of fact #2 above, some of the cutting sites in his DNA will have had a nucleotide changed in the other person's DNA. Some of his thousands of GAATTC sites, for example, might have undergone a change to GATTTC or TAATTC, or .... Any one of the six nucleotides might have changed at any of the thousand potential cutting sites, and in every instance of change, the enzyme will no longer recognize that site as a place to cut, so you get one long fragment instead of two short ones. In the same way, a site that in his DNA was GATTTC might with a single nucleotide change become GAATTC in the other person's DNA, and what was a long fragment in Jeffreys' DNA would become two short fragments when the other person's DNA was cut by the enzyme.
Because there is so much variation, no two people will ever display the same array of fragment sizes on a gel. The gel pattern of an individual's DNA becomes in effect a DNA "fingerprint," unique to him or her alone.
In practice, it is impractical to look at all the thousands of DNA fragments present on a gel. The process of DNA fingerprinting uses "probes" to fish out particular sequences to be compared from among the thousands on the gel. Probes are bits of radioactive DNA that bind to particular locations that occur randomly many, many times in the genome, "lighting up" all the fragments that contain that sequence. When Jeffreys looks at his DNA, the probes will light up a selection of the bands (those containing the probe sequence) for him to examine. If he were to employ a different probe targeting a different highly repeated sequence, he would "see" a different selection of the DNA fragments on the gel.
In courts, three or more different probes are used. If several different probes are used, the chance of any two individuals having the same gel pattern is less than one in a billion. DNA fragments that bind the probes are then visible on autoradiographic film as dark bands. Just as Jeffreys had suggested, the autoradiograph gel patterns are in essence DNA "fingerprints" that can be used in criminal investigations and other identification applications.
The first time DNA evidence was used in a court of law, it pointed the finger of guilt at a rapist. The rape victim had called the police as soon as she escaped, and a vaginal swab was taken from her within hours of her attack. From the swab semen was collected and the semen DNA analyzed. DNA probes were used to characterize DNA isolated from the rape victim, from the semen left by the rapist, and from the prime suspect Tommie Lee Andrews.
In the photograph, taken from the trial record, you can see that the semen pattern matches that of the suspect Andrews, while it is not at all like that of the victim. Other probes produced similar results. On Nov. 6, 1987, the jury returned a verdict of guilty, the first time a person in the United States was convicted of a crime based on DNA evidence. Since this verdict, DNA fingerprinting has been admitted as evidence in thousands of court cases.
PCR
Forensic analysis such as that used to convict Andrews 23 years ago depends critically on having enough DNA to carry out the analysis. A semen sample has lots of DNA-containing human cells, and both suspect and victim were available to supply blood samples rich in cells. But what do you do when there is no conveniently available sample of the perpetrator's cells from which to extract DNA, no semen or blood?
That would seem to be the great hitch in using Jeffreys' approach in the courtroom. However, as it turns out this is not the deal-breaker it at first seems. Two years before Jeffreys went public with his DNA fingerprinting proposal, a lab technician in California named Kary Mullis had an idea (for which he won the Nobel Prize) that allowed tiny DNA samples, as little as that found in a single human hair, to be magnified to many million of copies.
In Mullis' process, now universally called PCR (for Polymerase Chain Reaction), a double-stranded DNA fragment is heated so it becomes single stranded. Each of the strands is then copied by DNA polymerase to produce two double-stranded fragments. The fragments are heated again and copied again to produce four double-stranded fragments. This cycle is repeated many times, each time doubling the number of copies, until enough copies of the DNA fragment exist for analysis.
Ancient Man Has a Haircut
Now with DNA fingerprinting and PCR under our belt, we can tackle the recent news report of scientists examining the genome of ancient man. Only eight whole genomes of humans have been decoded so far in the 10 years since the human sequence was first completed, all the genomes of living humans. It would be exciting indeed to be able to look back in time, to compare today's living humans to humans long dead. We could hope to see how mankind is evolving, and perhaps grasp at understanding why.
Of course, to do this you have to find yourself an ancient man - a frozen human, say. No easy task. Dr. Eske Willerslev of the University of Copenhagen, Denmark, certainly did not find it so. His speciality is ancient DNA, and he spent two months a year ago searching for and fruitlessly digging in potential gravesites associated with a Greenland prehistoric Saqqag Eskimo settlement called Qeqertasussuk. Any frozen human remains? Nope.
Then serendipity strikes. As reported by Nicholas Wade in the New York Times last Thursday, a discouraged Willerslev complained to a friend about his poor field season digging in the permafrost, only to have his friend tell him that his father had found a weird hair sample at the same site 20 years earlier in 1986. The four swatches of hair, so thick his father had initially thought them to be from a bear, were still in existence, kept in a plastic bag in the National Museum of Denmark.
The hair, when retrieved and examined, seemed to have no follicles - all of the individual hairs simply ended, as if the individual had had a haircut! Now this news might have seemed discouraging a few years ago, as biologists used to think that DNA was present only in the cells at the root of a hair, not in the hair shaft made of the protein keratin. But it turns out follicle cells become incorporated into the growing shaft and their DNA is sealed in by the keratin, protecting it from being degraded by bacteria and fungi. There were traces of DNA in the ancient hair from Greenland -- not a lot of DNA, but well preserved and clearly different from that of modern humans.
Using PCR, it was possible to greatly amplify the Saqqag DNA, and, eventually, fully sequence its genome. The analysis of how living humans differ from this ancient man has only begun, but one surprise has already been encountered. Its closest living relatives are not today's Greenland Eskimos, but rather the Chukchis people living on the easternmost tip of Siberia! Unknown till now, there must have been a migration from Siberia across the northern edge of North America to Greenland about 5,000 years ago. Now, if you are a student of human early history, that's interesting.
What tickles me is how very modern science is being used to learn about very ancient humans. Neat.
'On science'
George B. Johnson's "On Science" column looks at scientific issues and explains them in an accessible manner. There is no dumbing down in Johnson's writing; rather he uses analogy and precise terms to open the world of science to others.
Johnson, Ph.D., professor emeritus of Biology at Washington University, has taught biology and genetics to undergraduates for more than 30 years. Also professor of genetics at Washington University’s School of Medicine, Johnson is a student of population genetics and evolution, renowned for his pioneering studies of genetic variability.
He has authored more than 50 scientific publications and seven texts, including "BIOLOGY" (with botanist Peter Raven), "THE LIVING WORLD" and a widely used high school biology textbook, "HOLT BIOLOGY."
As the founding director of The Living World, the education center at the St Louis Zoo, from 1987 to 1990, he was responsible for developing innovative high-tech exhibits and new educational programs.
Copyright, George Johnson