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. 2005 Sep 27;102(39):13783-8.
doi: 10.1073/pnas.0503718102. Epub 2005 Sep 14.

Relatively well preserved DNA is present in the crystal aggregates of fossil bones

Michal Salamon  1 , Noreen Tuross, Baruch Arensburg, Steve Weiner
Affiliations

Relatively well preserved DNA is present in the crystal aggregates of fossil bones

Michal Salamon et al. Proc Natl Acad Sci U S A. .

Abstract

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.

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Figures

Fig. 1.
Fig. 1.
SEM of aggregate fraction from ancient human bone (a) and single crystals (b) from the same bone. Note that the aggregates are in the μm scale range, whereas the crystals are in the nanometer scale range.
Fig. 2.
Fig. 2.
DNA sequences from crystal aggregates (A) and whole bone powder (W) of modern bone samples (1) B. taurus HV-1 sequence, positions 15943–16302. (2) S. scrofa CYTB sequence, positions 14285–14505. Published sequence of B. taurus (24, 25) and S. scrofa (26, 27) are shown in the top line. Bases identical to the reference sequence are indicated by dots.
Fig. 3.
Fig. 3.
qPCR for 239 bp within the 12S rRNA of the fossil P. adeliae bone. DNA template [0.1 μl (dark color) or 2.5 μl (light color)] from aggregates (blue) and whole bone powder (green) were amplified in parallel with blanks of both DNA extraction procedures (yellow) and blanks composed of water for controlling the amplification procedure (pink). (a) Melting curve showing a real product with a melting temperature of 87°C using both extracts and standard (red) but not in the blanks. (b) Comparison between copy numbers of DNA template in each extract (□) with respect to standards (○). The amounts of available DNA template in 0.1 and 2.5 μl of aggregates extract are marked blue whereas those from whole bone powder are marked green.
Fig. 4.
Fig. 4.
The λ inhibition test using the fossil P. adeliae bone. Amplification plot displays the relative fluorescence for each sample at every cycle; red, λDNA (control); blue, λDNA spiked with 0.1 or 2.5 μl of DNA extract from aggregates; green, λDNA spiked with 0.1 or 2.5 μl of DNA extract from whole bone powder; orange, λDNA spiked with 2.5 μl of DNA extraction blanks. No inhibition is seen in reactions with DNA extract from aggregates, whereas a strong inhibition is seen in the reactions with the whole bone powder extract.
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