Raman Spectroscopy Offers Non-Destructive Screening for Ancient DNA Preservation in Teeth

A recent study published in Microchemical Journal reported that micro-Raman spectroscopy can accurately and non-destructively predict the likelihood that ancient human teeth contain usable endogenous DNA.¹ This study, which was led by Aggelos Philippidis and Demetrios Anglos at the Institute of Electronic Structure and Laser (IESL) in Greece, demonstrated that Raman measurements of protein-to-mineral ratios in tooth cementum correlate with ancient DNA preservation. The findings suggest archaeologists and paleogeneticists could pre-screen valuable skeletal remains in situ, selecting only the most promising specimens for destructive and costly genetic analysis.¹

Paleogenomics studies ancient DNA from archaeological artifacts and ancient DNA.² This trend represents an expansion of the field, as research has now shifted from primarily focusing on modern man to studying ancient specimens.² Significant growth in the study of ancient specimens is expected as tools and methods improve.²

However, with this growth comes a major question: how should archaeologists determine which samples to prioritize in their research? One of the main challenges in paleogenomics is figuring out what samples are likely to yield sufficient endogenous DNA before sampling.¹ Current ancient DNA extraction requires drilling or fragmenting skeletal material, a process that irreversibly damages rare or culturally significant remains.^1,3 Because DNA preservation varies widely depending on burial conditions and diagenesis, laboratories often invest time and resources processing samples that ultimately yield little usable genetic material.^1,3 The new Raman-based approach proposed in this study aims to reduce such losses by providing a rapid, portable screening tool that can be applied directly to intact specimens.

Why DNA Preservation Matters—and Why It’s Hard to Predict

Ancient DNA and protein analyses have transformed archaeological science, enabling reconstructions of population history, kinship, diet, health, and social structure across millennia.^1,4 Teeth are among the most important substrates for these studies because their mineralized tissues can protect biomolecules long after burial.¹ However, DNA survival is highly variable because of environmental factors, such as soil chemistry, moisture, temperature, and microbial activity.¹ These factors can drive diagenetic degradation of both DNA and proteins, leaving some specimens nearly devoid of endogenous genetic material.

Traditionally, researchers have relied on destructive sampling followed by molecular assays to quantify endogenous DNA content.^1,3 These workflows are expensive and time-consuming and require exceptional preservation. Because these processes involve clean-room processing, library preparation, and sequencing, there is a lot that could go wrong and negatively impact the analysis. Therefore, efficient pre-screening has become a priority in the field, particularly as ethical guidelines increasingly emphasize conservation of archaeological human remains.¹

In this new study, the authors suggest that collagen preservation in teeth can help indicate whether the ancient DNA is still intact enough to be studied. Because both proteins and DNA degrade under similar diagenetic processes, a higher proportion of organic matrix relative to mineral content should correlate with greater likelihood of preserved genetic material.¹ Raman spectroscopy, which can detect vibrational signatures of molecular bonds, offers a way to measure this ratio non-destructively.

Using near-infrared (NIR) (1064 nm) excitation to minimize fluorescence interference, the research team collected spectra from the cementum, which is the protein-rich outer layer of tooth roots known to retain biomolecules.^1,5 The key metric derived from the spectra was the amide-to-phosphate ratio, or [AmI/P] index. This index compares the intensity of the amide I band (~1666 cm⁻¹), associated with collagen proteins, to the phosphate band (~957 cm⁻¹), characteristic of the mineral hydroxyapatite matrix.¹ A higher ratio indicates relatively greater protein content and, by inference, better preservation conditions for DNA.¹

The researchers analyzed 49 archaeological teeth for which endogenous DNA content had already been determined by standard ancient DNA methods at the ancient DNA laboratory of IMBB-FORTH in Crete. These samples were from 8800 BCE to 1941 CE and varied widely in DNA preservation, from near zero to 65 percent endogenous content.¹

The Raman measurements revealed a clear, though modest, positive correlation between the [AmI/P] index and endogenous DNA levels. When the authors set a 5 percent endogenous DNA threshold to distinguish DNA-rich from DNA-poor specimens, the Raman method correctly identified 23 of 25 DNA-rich teeth (92 percent acceptance).¹ Among 20 DNA-poor teeth, 13 were correctly rejected (65 percent rejection).¹

To test predictive performance, the team analyzed 10 additional teeth as unknowns using Raman spectroscopy before genetic testing.¹ The spectroscopic classification accurately predicted their DNA preservation status, achieving high overall accuracy and no false negatives among DNA-rich samples.¹

“The study presented herein demonstrates that Raman spectroscopy can serve as an effective pre-screening method for assessing endogenous DNA preservation in archaeological dental remains,” the authors wrote in their study.¹ “Raman analysis can contribute to the development of a non-invasive approach, enabling field scientists to only select samples having high probability for human DNA preservation while, in parallel, avoiding unnecessary sample destruction.”

In Part 2 of our exploration of this study, we examine the benefits of using Raman spectroscopy to analyze ancient dental samples, and what this means for future archaeological studies.

References

1. Philippidis, A.; Mamali, A.; Pinon, V. et al. In situ microRaman Spectroscopy as a Screening Tool for Assessing Human DNA Preservation in Ancient Dental Remains. Microchem. J. 2026, 117446. DOI: 10.1016/j.microc.2026.117446
2. Fletcher, L. Paleogenomics and Ancient DNA: How Can the Past Inform the Future? Front Line Genomics. Available at: https://frontlinegenomics.com/paleogenomics-and-ancient-dna-how-can-the-past-inform-the-future/#:~:text=Paleogenomics%20is%20the%20study%20of%20ancient%20genetic,and%20psychiatric%20health%20conditions%20such%20as%20schizophrenia (accessed 2026-02-27).
3. Harney, E.; Cheronet, O.; Fernandes, D. M. et al. A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth. Genome Res. 2021, 31 (3), 472–483. DOI: 10.1101/gr.267534.120
4. Slatkin, M.; Racimo, F. 2016. Ancient DNA and Human History. Proc. Natl. Acad. Sci. 2016, 113, 6380–6387. DOI: 10.1073/pnas.152430611
5. Yamamoto, T.; Hasegawa, T.; Yamamoto, Y. et al. Histology of Human Cementum: Its Structure, Function, and Development. Jpn. Dent. Sci. Rev. 2016, 52 (3), 63–74. DOI: 10.1016/j.jdsr.2016.04.002