When archeologists find a pile of ancient bones or fossils, they sometimes try to extract DNA from the bones to learn more about human predecessors or animals that are now extinct. But most of these artifacts contain degraded DNA, and only intact DNA can provide useful information from DNA sequencing, an expensive process. Now a mass spectrometry-based technique could help archeologists triage old bones quickly and cheaply for DNA analysis (Anal. Chem., DOI: 10.1021/ac301333t).
Julie Wilson, a mathematician at the University of York, in the U.K., developed the technique with York researchers Nienke L. van Doorn and Matthew J. Collins. Their method works by assessing the molecular integrity of the bone protein collagen and uses that measurement as a proxy for DNA integrity.
In particular, researchers compare levels in collagen of the amino acids glutamine and glutamic acid. Over time, glutamine degrades into glutamic acid through a deamidation reaction. Since collagen and DNA both degrade through hydrolytic reactions (deamidation and deamination, respectively), the researchers speculate that a bone or fossil with high amounts of degraded collagen is unlikely to have intact DNA.
“Sometimes bone can look quite intact but be actually quite damaged on the microscopic scale,” comments Tim Wess, at Cardiff University, who was not involved in the work. The degradation’s cause may be groundwater or microbes, he says.
To measure levels of each amino acid, the researchers took 87 samples from bones and fossils found at a variety of sites dating to the Roman era and Neolithic period, and they analyzed them with mass spectrometry. To determine the extent of deamidation, the team compared peaks for glutamine and glutamic acid in the data. The team then modeled the extent of collagen damage.
The new technique complements and costs less than other methods that provide hints about the molecular integrity of a bone or other collagen-based artifacts, Wess says. Those other methods include his technique for studying the bone mineral apatite using small angle X-ray scattering.
What’s really exciting, Wess says, is the possibility, hinted at in the York group’s paper, that researchers could use glutamine deamidation to date collagen-based artifacts, such as bone or parchment.
Carbon dating can measure the age of collagen artifacts as old as about 60,000 years. Measuring the extent of glutamine deamidation could enable researchers to date artifacts back 1,000,000 years, well beyond carbon dating’s horizon, Wess says. It could work because collagen can last for 1,000,000 years, Collins says.
The dating application is still speculative, Wilson adds, but the research team is working to validate it.