Extracting DNA from ancient bones currently consists of turning a piece of bone, usually a tooth, into powder, and carrying out an amplification process that multiplies the number of DNA fragments that may be preserved.
Unfortunately, this procedure has two problems: first, DNA is often damaged post mortem and thus may not reflect the genetic structure of the organism under study; second, contamination from anyone in contact with the specimen is a risk. In particular, any modern sequences extracted from it are automatically suspect.
Now, a new method has been devised to address these problems. Scientists have observed that within certain crystal-like regions of partially fossilized bones there may exist DNA in well-preserved state. It is not as good as living-tissue DNA, and in some cases no DNA is preserved in those regions, but it is a lot better than DNA from the entire specimen.
The way this works is counterintuitive: the crystal structures preserve about 2 orders of magnitude less DNA than the entire sample. So, why throw away so much genetic material? Because the amplification process can start with very small numbers of sequences, it doesn't really matter how much DNA you begin with; it's much more important that this DNA be "pure". So, a few good DNA sequences are preferrable to many times more, but mixed with bad ones.
How does one get to the DNA within those crystal aggregates. The researchers have devised a technique which applies a type of acid to the specimen. This acid eats through most of it, but is unable to penetrate the crystals. So, the crystals are all that remain after oxidization. As an added bonus, this process also eats up any contaminant sequences which may have polluted the sample, but such contaminant sequences are unable to penetrate into the crystals.
More research needs to be done to see whether or not this technique can be widely applied, but it certainly seems that scientists are working hard to maximize the extraction of genetic material from ancient remains.
PNAS (Early edition)
Michal Salamon et al.
Relatively well preserved DNA is present in the crystal aggregates of fossil bones
DNA from fossil human bones could provide invaluable information about population migrations, genetic relations between different groups and the spread of diseases. The use of ancient DNA from bones to study the genetics of past populations is, however, very often compromised by the altered and degraded state of preservation of the extracted material. The universally observed postmortem degradation, together with the real possibility of contamination with modern human DNA, makes the acquisition of reliable data, from humans in particular, very difficult. We demonstrate that relatively well preserved DNA is occluded within clusters of intergrown bone crystals that are resistant to disaggregation by the strong oxidant NaOCl. We obtained reproducible authentic sequences from both modern and ancient animal bones, including humans, from DNA extracts of crystal aggregates. The treatment with NaOCl also minimizes the possibility of modern DNA contamination. We thus demonstrate the presence of a privileged niche within fossil bone, which contains DNA in a better state of preservation than the DNA present in the total bone. This counterintuitive approach to extracting relatively well preserved DNA from bones significantly improves the chances of obtaining authentic ancient DNA sequences, especially from human bones.