The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils
Open accessAbstract
Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate ( k ) of 5.50 × 10 –6 per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model ( R 2 = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.
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Despite DNA's long-term stability in well-controlled environments such as ancient bone, both aqueous solutions and dried DNA only exhibit a half-life on the order of months to a few years under ambient conditions.
“Despite DNA’s long-term stability in well-controlled environments such as ancient bone, with storage durations as long as several hundred thousand years,54,55 both aqueous solutions and dried DNA only exhibit a half-life on the order of months to a few years under ambient conditions.56”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [54]
DNA offers massive parallelization of copy, delete, and read operations; it takes the same amount of time for one or billions of molecules.
“As a molecular storage system, DNA offers massive parallelization of copy, delete, and read operations; it takes the same amount of time for one or billions of molecules.”
From Integrating DNA Encapsulates and Digital Microfluidics for Automated Data Storage in DNA (2022) · cites this paper as [7]
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Chen, W. D., Kohll, A. X., Nguyen, B. H., Koch, J., Heckel, R., Stark, W. J., Ceze, L., Strauss, K., & Grass, R. N. (2019) · Advanced Functional Materials · doi:10.1002/adfm.201901672 · Cited by 104 · see citing works
Robust direct digital-to-biological data storage in living cells.
Yim, S. S., McBee, R. M., Song, A. M., Huang, Y., Sheth, R. U., & Wang, H. H. (2021) · Nature Chemical Biology · doi:10.1038/s41589-020-00711-4 · Cited by 83 · see citing works
Addressable configurations of DNA nanostructures for rewritable memory
Chandrasekaran, A. R., Levchenko, O., Patel, D. S., MacIsaac, M., & Halvorsen, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx777 · Cited by 79 · see citing works
A DNA-Based Archival Storage System
Bornholt, J., Lopez, R., Carmean, D. M., Ceze, L., Seelig, G., & Strauss, K. (2016) · ACM SIGOPS Operating Systems Review · doi:10.1145/2954680.2872397 · Cited by 77 · see citing works
Toward a DNA-Based Archival Storage System
Bornholt, J., Lopez, R., Carmean, D. M., Ceze, L., Seelig, G., & Strauss, K. (2017) · IEEE Micro · doi:10.1109/mm.2017.70 · Cited by 75 · see citing works
An Empirical Comparison of Preservation Methods for Synthetic DNA Data Storage
Organick, L., Nguyen, B. H., McAmis, R., Chen, W. D., Kohll, A. X., Ang, S. D., Grass, R. N., Ceze, L., & Strauss, K. (2021) · Small Methods · doi:10.1002/smtd.202001094 · Cited by 67 · see citing works
Integrating DNA Encapsulates and Digital Microfluidics for Automated Data Storage in DNA
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Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences
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A DNA-Based Archival Storage System
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Mikutis, G., Schmid, L., Stark, W. J., & Grass, R. N. (2019) · AIChE Journal · doi:10.1002/aic.16433 · Cited by 32 · see citing works
Preservation of DNA for Data Storage
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Silica Microcapsules for Long‐Term, Robust, and Reliable Room Temperature RNA Preservation
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Buko, T., Tuczko, N., & Ishikawa, T. (2023) · BioTech · doi:10.3390/biotech12020044 · Cited by 21 · see citing works
“Dehydratation Ancient bone 521 years 13 ◦C x [52] Filter Paper 4 years RT 82.”
BackgroundMolecular paleobiology — Progress and perspectives
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A Characterization of the DNA Data Storage Channel
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Ribonucleotide errors, RNase HII, and ribonucleotide excision repair
Cresti, J. R., & Simmons, L. A. (2026) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2026.2704628
“Although relative stability estimates vary, it is clear that DNA is stable over longer periods of time than RNA (Bada et al. 1994; Hofreiter et al. 2001; Willerslev et al. 2004; Allentoft et al. 2012; Matange et al. 2021).”
- Authors
- Allentoft, M. E., Collins, M., Harker, D., Haile, J., Oskam, C. L., Hale, M. L., Campos, P. F., Samaniego, J. A., Gilbert, M. T. P., Willerslev, E., Zhang, G., Scofield, R. P., Holdaway, R. N., & Bunce, M.
- Affiliations
- University of Copenhagen (DK)
- University of York (GB)
- Murdoch University (AU)
- University of Canterbury (NZ)
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
- BGI Group (China) (CN)
- Canterbury Museum (NZ)
- Corresponding author
- Allentoft, Morten E.
- Bunce, Michael
- ORCID
- Venue
- Proceedings of the Royal Society B: Biological Sciences
- Publisher
- The Royal Society
- Published
- 2012-10-10
- Volume
- 279
- Issue
- 1748
- Pages
- 4724-4733
- ISSN
- 0080-4649 (ISSN-L)
- 0962-8452
- 1471-2954
- PMC
- PMC3497090
- OpenAlex
- W2126557729
- Cited by
- 633
- References
- 70
- Citations by year
- 2026: 39 · 2025: 38 · 2024: 37 · 2023: 48 · 2022: 51 · 2021: 86 · 2020: 44 · 2019: 48 · 2018: 50 · 2017: 44 · 2016: 48 · 2015: 39 · 2014: 34 · 2013: 25 · 2012: 1
- FWCI
- 19.02
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the Royal Society B Biological Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Murdoch University Research Portal (submittedVersion)
- eSpace (Curtin University) (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Funders
- Royal Society
- Royal Society Te Apārangi
- Lundbeckfonden (R109-2012-9995, R70-2010-6286, R38-2008-3048, R24-2008-2527)
- Danmarks Frie Forskningsfond (10‐081390)
- Natural Environment Research Council (NE/G000204/1)
- Australian Research Council (FT0991741)
- Marsden Fund
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Archaeology and ancient environmental studies
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- mitochondrial DNA, nuclear DNA, fossil bones, radiocarbon dating, exponential decay model, burial temperature, taphonomy, bone diagenesis, ancient DNA preservation
- MeSH terms
- Animals, Birds, Bone and Bones, DNA, Mitochondrial, Fossils, Half-Life, Hydrogen-Ion Concentration, Kinetics, Models, Genetic, New Zealand, Temperature, Radiometric Dating, Real-Time Polymerase Chain Reaction
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