Bone Niche Protects Ancient DNA

Ancient dna can be a treasure trove of information for evolutionary biologists, anthropologists, and archaeologists. Unfortunately, getting reliable data from DNA in fossils can be difficult, because the DNA is damaged and can easily be contaminated with contemporary DNA.

Now, Israeli and U.S. researchers describe a way to mitigate these problems. The team-structural biologist Steve Weiner at Weizmann Institute in Rehovot, Israel; anthropologist Baruch Arensburg from Tel Aviv University; graduate student Michal Salamon at Weizmann Institute and Tel Aviv University; and biogeochemist Noreen Tuross at Harvard University's Peabody Museum-has found that crystal aggregates in bones help preserve ancient DNA and that recovering DNA only from those sites yields material that is more easily analyzed than DNA obtained from whole bone (Proc. Natl. Acad. Sci. USA 2005, 102, 13783).

When DNA is extracted from whole-bone powder, contaminating DNA, damaged DNA, and coextracted inhibitors of the polymerase chain reaction (PCR) can compromise its analysis, Salamon says. Instead of extracting whole-bone powder, Salamon and coworkers retrieve DNA from crystal aggregates. The aggregates are a special, relatively protected niche within the bone, and their use as the extraction substrate is a major advantage, she says.

Crystal aggregates are mineral portions of the bone that can't be separated when the collagen matrix is removed by oxidation with sodium hypochlorite (NaOCl), the main component of household bleach, even if the bone is finely ground. Sodium hypochlorite easily oxidizes exposed organic materials in the powdered bone samples, including contaminating DNA, but not those bound inside the crystal aggregates.

Once the material outside the aggregates has been removed, the aggregates themselves are dissolved in EDTA to remove the mineral component, and the collagen inside the aggregates is converted into gelatin. The DNA is then extracted and available for analysis by PCR and DNA sequencing.

The researchers analyzed DNA from six fossil bones, five of which had been unearthed at archaeological sites in the Levant, the area of the Middle East along the Mediterranean Sea. They recovered larger, better preserved DNA fragments from the crystal aggregates than from untreated powder from the same bones. The method doesn't always work, however. Some bones are so badly preserved that even the aggregates don't contain DNA that can be sequenced, Salamon says.

Hendrik Poinar, assistant professor of anthropology and of pathology and molecular medicine at McMaster University, Hamilton, Ontario, thinks the approach is good, but he's not completely convinced that the DNA they're looking at is from inside the crystal aggregates. It remains unclear whether the DNA they amplify is actually within the crystal aggregate or is DNA that has adhered to the outside of the crystal, he says. If the DNA strongly adheres to the crystal surface, it could survive a bleach attack. In such a case, contaminating DNA could remain.

Matthew Collins, a reader at BioArch, a joint venture of the archaeology, biology, and chemistry departments at the University of York, in England, says questions concerning the effects of different burial environments remain, but he believes that the method is exciting. If the technique can really overcome the problems of damage and contamination, it is arguably second in importance for the study of ancient human DNA only to PCR itself, Collins says.

Unlike studies of other species, including Neanderthals, in the study of ancient human DNA there is no simple way of knowing which of the multiple amplified human sequences is the original one and which are contamination, Collins explains. If the DNA is from a species other than humans, the contamination can be easily recognized from the base sequence itself. If the contamination is human, modern or ancient, scientists can't tell which is the sequence they want. Salamon's approach simply and neatly short-circuits this problem by removing all the contamination during the preparation, Collins says.