Length‐dependent DNA degradation kinetic model: Decay compensation in DNA tracer concentration measurements
Abstract
DNA is often used as a tracer in both environmental fluid flow characterization and in material tracking to avoid counterfeiting and ensure transparency in product value chains. The main drawback of DNA as a tracer is its limited stability, making quantitative analysis difficult. Here, we study length‐dependent DNA decay at elevated temperatures and under sunlight by quantitative PCR and show that the stability of randomly generated DNA sequences is inversely proportional to the sequence length. By quantifying the remaining DNA length distribution, we present a method to determine the extent of decay and to account for it. We propose a correction factor based on the ratio of measured concentrations of two different length sequences. Multiplying the measured DNA concentration by this length‐dependent correction factor enables precise DNA tracer quantification, even if DNA molecules have undergone more than 100‐fold degradation. © 2018 American Institute of Chemical Engineers AIChE J, 65: 40–48, 2019
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
DNA decay by hydrolysis scales with the number of nucleotides per oligo, so a proportional increase in the expected number of errors is anticipated for longer oligos.
“While both micro- and macroscopic storage systems are independent of sequence length, DNA decay by hydrolysis scales with the number of nucleotides per oligo and, thus, a proportional increase in the expected number of errors is anticipated.73”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [73]
Cites
Instability and decay of the primary structure of DNA
Lindahl, T. (1993) · Nature · doi:10.1038/362709a0 · Cited by 5,679 · see citing works
Predicting DNA duplex stability from the base sequence
Breslauer, K. J., Frank, R., Blöcker, H., & Marky, L. A. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.11.3746 · Cited by 1,837 · see citing works
Rate of depurination of native deoxyribonucleic acid
Lindahl, T. L., & Nyberg, B. (1972) · Biochemistry · doi:10.1021/bi00769a018 · Cited by 1,558 · see citing works
REPAIR OF OXIDATIVE DAMAGE TO DNA: Enzymology and Biology
Demple, B., & Harrison, L. (1994) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.63.070194.004411 · Cited by 1,495 · see citing works
Molecular Mechanisms of Ultraviolet Radiation‐Induced DNA Damage and Repair
Rastogi, R. P., Richa, Kumar, A., Tyagi, M. B., & Sinha, R. P. (2010) · Journal of Nucleic Acids · doi:10.4061/2010/592980 · Cited by 1,329 · see citing works
Kwok, S., Kellogg, D. E., McKinney, N., Spasic, D., Goda, L., Levenson, C., & Sninsky, J. J. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.4.999 · Cited by 1,032 · see citing works
The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils
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., et al. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.1745 · Cited by 633 · see citing works
Ground‐Water Tracers — A Short Review
Davis, S. N., Thompson, G. M., Bentley, H. W., & Stiles, G. (1980) · Ground Water · doi:10.1111/j.1745-6584.1980.tb03366.x · Cited by 269 · see citing works
Bhat, S., Herrmann, J., Armishaw, P., Corbisier, P., & Emslie, K. R. (2009) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-009-2729-5 · Cited by 218 · see citing works
Ptak, T., Piepenbrink, M., & Martac, E. (2004) · Journal of Hydrology · doi:10.1016/j.jhydrol.2004.01.020 · Cited by 218 · see citing works
Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum
Hansen, H. B., Damgaard, P. D. B., Margaryan, A., Stenderup, J. T., Lynnerup, N., Willerslev, E., & Allentoft, M. E. (2017) · PLoS ONE · doi:10.1371/journal.pone.0170940 · Cited by 217 · see citing works
Adsorption of DNA on clay minerals and various colloidal particles from an Alfisol
Cai, P., Huang, Q., Zhang, X., & Chen, H. (2005) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2005.05.019 · Cited by 196 · see citing works
Anti-Counterfeit Technologies: A Pharmaceutical Industry Perspective
Bansal, D. (2013) · Scientia Pharmaceutica · doi:10.3797/scipharm.1202-03 · Cited by 158 · see citing works
An efficient method for long-term room temperature storage of RNA
Fabre, A.-L., Colotte, M., Luis, A., Tuffet, S., & Bonnet, J. (2014) · European Journal of Human Genetics · doi:10.1038/ejhg.2013.145 · Cited by 151 · see citing works
Paunescu, D., Puddu, M., Soellner, J. O. B., Stoessel, P. R., & Grass, R. N. (2013) · Nature Protocols · doi:10.1038/nprot.2013.154 · Cited by 151 · see citing works
Self-citationMechanistic studies on depurination and apurinic site chain breakage in oligodeoxyribonucleotides
Suzuki, T., Ohsumi, S., & Makino, K. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.23.4997 · Cited by 130 · see citing works
Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens
Weiß, C. L., Schuenemann, V. J., Devos, J., Shirsekar, G. S., Reiter, E., Gould, B. A., Stinchcombe, J. R., Krause, J., & Burbano, H. A. (2016) · Royal Society Open Science · doi:10.1098/rsos.160239 · Cited by 129 · see citing works
Puddu, M., Păunescu, D., Stark, W. J., & Grass, R. N. (2014) · ACS Nano · doi:10.1021/nn4063853 · Cited by 127 · see citing works
Self-citationPaunescu, D., Fuhrer, R., & Grass, R. N. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201208135 · Cited by 104 · see citing works
Self-citationSelective Incision of the α‐N5‐Methyl‐Formamidopyrimidine Anomer by Escherichia coli Endonuclease IV
Christov, P. P., Banerjee, S., Stone, M. P., & Rizzo, C. J. (2010) · Journal of Nucleic Acids · doi:10.4061/2010/850234 · Cited by 74 · see citing works
Toward Trash That Thinks: Product Tags for Environmental Management
Saar, S., & Thomas, V. M. (2002) · Journal of Industrial Ecology · doi:10.1162/108819802763471834 · Cited by 71 · see citing works
Hydrological Tracers Using Nanobiotechnology: Proof of Concept
Sharma, A. N., Luo, D., & Walter, M. T. (2012) · Environmental Science & Technology · doi:10.1021/es301561q · Cited by 69 · see citing works
DNA tracers with information capacity and high detection sensitivity tested in groundwater studies
., I. H. S., Torgersen, J. S., Haldorsen, S., & Aleström, P. (1999) · Hydrogeology Journal · doi:10.1007/s100400050200 · Cited by 67 · see citing works
Particles with an identity: Tracking and tracing in commodity products
Păunescu, D., Stark, W. J., & Grass, R. N. (2015) · Powder Technology · doi:10.1016/j.powtec.2015.12.035 · Cited by 67 · see citing works
Self-citationA DNA Tracer System for Hydrological Environment Investigations
Liao, R., Yang, P., Wu, W., Luo, D., & Yang, D. (2018) · Environmental Science & Technology · doi:10.1021/acs.est.7b02928 · Cited by 67 · see citing works
The protective effect of clay minerals against damage to adsorbed DNA induced by cadmium and mercury
Hou, Y., Wu, P., & Zhu, N. (2013) · Chemosphere · doi:10.1016/j.chemosphere.2013.08.069 · Cited by 41 · see citing works
Walsh, S. D. C., & Saar, M. O. (2010) · Water Resources Research · doi:10.1029/2009wr007895 · Cited by 40 · see citing works
Mechanisms of degradation of DNA standards for calibration function during storage
Rossmanith, P., Röder, B., Frühwirth, K., Vogl, C., & Wagner, M. (2010) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-010-2943-2 · Cited by 34 · see citing works
Submicrometer-Sized Thermometer Particles Exploiting Selective Nucleic Acid Stability
Puddu, M., Mikutis, G., Stark, W. J., & Grass, R. N. (2015) · Small · doi:10.1002/smll.201502883 · Cited by 21 · see citing works
Self-citationPăunescu, D., Mora, C. A., Puddu, M., Krumeich, F., & Grass, R. N. (2014) · Journal of materials chemistry. B · doi:10.1039/c4tb01552e · Cited by 18 · see citing works
Self-citationHalter, M. C., & Zahn, J. A. (2016) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/s10295-016-1876-x · Cited by 12 · see citing works
Use of Synthetic DNA as New Tracers for Tracing Groungwater Flow and Multiple Contaminants
., I. H. S., Aleström, P., & Haldorsen, S. (2001) · Journal of Applied Sciences · doi:10.3923/jas.2001.233.238 · Cited by 11 · see citing works
A Characterization of the DNA Data Storage Channel
Heckel, R., Mikutis, G., & Grass, R. N. (2019) · Scientific Reports · doi:10.1038/s41598-019-45832-6 · Cited by 9 · see citing works
Self-citationTaillefer (2000) · doi:10.1002/(sici)1520-6017(200001)89:1
Flagged first, then by citations
Cited by
Sorted by citations
Emerging Approaches to DNA Data Storage: Challenges and Prospects
Doricchi, A., Platnich, C. M., Gimpel, A., Horn, F., Earle, M., Lanzavecchia, G., Cortajarena, A. L., Liz-Marzán, L. M., Liu, N., Heckel, R., et al. (2022) · ACS Nano · doi:10.1021/acsnano.2c06748 · Cited by 235 · see citing works
Self-citationDNA stability: a central design consideration for DNA data storage systems
Matange, K. R., Tuck, J. M., & Keung, A. J. (2021) · Nature Communications · doi:10.1038/s41467-021-21587-5 · Cited by 212 · see citing works
Persistence and degradation dynamics of eDNA affected by environmental factors in aquatic ecosystems
Joseph, C., Faiq, M. E., Li, Z., & Chen, G. (2022) · Hydrobiologia · doi:10.1007/s10750-022-04959-w · Cited by 92 · see citing works
Jo, T., Takao, K., & Minamoto, T. (2021) · Environmental DNA · doi:10.1002/edn3.253 · Cited by 90 · see citing works
A digital twin for DNA data storage based on comprehensive quantification of errors and biases
Gimpel, A. L., Stark, W. J., Heckel, R., & Grass, R. N. (2023) · Nature Communications · doi:10.1038/s41467-023-41729-1 · Cited by 38 · see citing works
Self-citationShin, J., Kim, S. R., Xie, Z., Jin, Y., & Wang, Y. (2024) · Biosensors · doi:10.3390/bios14040194 · Cited by 33 · see citing works
Ahuja, S., Kumar, M., Nandeshwar, R., Kondabagil, K. R., & Tallur, S. G. (2022) · Scientific Reports · doi:10.1038/s41598-022-12818-w · Cited by 27 · see citing works
Biopolymer/plasmid DNA microspheres as tracers for multiplexed hydrological investigation
Liao, R., Zhang, J., Li, T., Luo, D., & Yang, D. (2020) · Chemical Engineering Journal · doi:10.1016/j.cej.2020.126035 · Cited by 24 · see citing works
Liao, R., Zhao, F., Hamada, S., Yang, P., Xu, H., Luo, D., & Yang, D. (2020) · Nano Today · doi:10.1016/j.nantod.2020.100958 · Cited by 24 · see citing works
Tracking Water with Synthetic DNA Tracers Using Droplet Digital PCR
McCluskey, J., Flores, M. E., Hinojosa, J., Jafarzadeh, A., Moghadam, S. V., Phan, D., Green, R. T., & Kapoor, V. J. (2021) · ACS ES&T Water · doi:10.1021/acsestwater.0c00245 · Cited by 20 · see citing works
Simulation of experimental synthetic DNA tracer transport through the vadose zone
Wang, C., Liu, G., McNew, C. P., Volkmann, T. H. M., Pangle, L. A., Troch, P. A., Lyon, S. W., Kim, M., Huo, Z., & Dahlke, H. E. (2022) · Water Research · doi:10.1016/j.watres.2022.119009 · Cited by 18 · see citing works
Foppen, J. W. (2023) · Wiley Interdisciplinary Reviews Water · doi:10.1002/wat2.1681 · Cited by 18 · see citing works
Jo, T. (2022) · Environmental DNA · doi:10.1002/edn3.383 · Cited by 15 · see citing works
Gimpel, A. L., Stark, W. J., Heckel, R., & Grass, R. N. (2024) · Digital Discovery · doi:10.1039/d4dd00220b · Cited by 15 · see citing works
Self-citationChakraborty, S., Foppen, J. W., & Schijven, J. F. (2022) · Colloids and Surfaces A Physicochemical and Engineering Aspects · doi:10.1016/j.colsurfa.2022.129625 · Cited by 15 · see citing works
Information decay and enzymatic information recovery for DNA data storage
Meiser, L. C., Gimpel, A. L., Deshpande, T., Libort, G., Chen, W. D., Heckel, R., Nguyen, B. H., Strauß, K., Stark, W. J., & Grass, R. N. (2022) · Communications Biology · doi:10.1038/s42003-022-04062-9 · Cited by 12 · see citing works
Self-citationThe application of DNA nanotechnology to trace water environmental pollution
Wang, C., Yang, D., Luo, D., & Liao, R. (2023) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/tb-2023-0363 · Cited by 8 · see citing works
The Impact of Flow Velocity on Environmental DNA Detectability for the Application in River Systems
Dercksen, J. A., Foppen, J. W., Blom, A., Trimbos, K. B., Gebert, J., Bogaard, T. A., & Stancanelli, L. M. (2025) · Environmental DNA · doi:10.1002/edn3.70111 · Cited by 6 · see citing works
Doniec, A., Januła, M., Grzmil, P., & Kupiec, T. (2022) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2022.102751 · Cited by 6 · see citing works
Liu, G., Guo, L., Wang, C., Liu, J., Hu, Z., Dahlke, H. E., Xie, E., Zhao, X. L., Huang, G., Niu, J., et al. (2023) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2023.167378 · Cited by 4 · see citing works
Yunxiang, L., Peng, R., Qin, M., Li, H., & Xianfei, C. (2025) · Colloids and Surfaces A Physicochemical and Engineering Aspects · doi:10.1016/j.colsurfa.2025.136872 · Cited by 2 · see citing works
Harikai, N., Takada, Y., Saito, M., Zaima, K., & Shinomiya, K. (2023) · Biopreservation and Biobanking · doi:10.1089/bio.2023.0021 · Cited by 2 · see citing works
Prasetyoningrum, P. A., Junitha, I. K., & Yulihastuti, D. A. (2023) · Metamorfosa Journal of Biological Sciences · doi:10.24843/metamorfosa.2023.v10.i01.p19 · Cited by 2 · see citing works
DNA Barcode Quantification As a Robust Tool for Measuring Mixing Ratios in Two-Component Systems
Kohll, A. X., Koch, J., Chen, W. D., O’Dwyer, C., Mikutis, G., Stark, W. J., & Grass, R. N. (2019) · ACS Applied Bio Materials · doi:10.1021/acsabm.9b00735 · Cited by 1 · see citing works
Self-citationZhang, J., Chen, L., Sun, J., Li, S., Zhou, Y., Wu, Z., Li, C., Zheng, Z., & Luo, R. (2026) · Nature Communications · doi:10.1038/s41467-026-71485-x · Cited by 1 · see citing works
A Superior “Thumb” Drive: Optimizing DNA Stability for DNA Data StoragePreprint
Liu, J.-Y. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.11.540302 · Cited by 1 · see citing works
A novel method for quantitation of AAV genome integrity and residual DNAs using duplex digital PCRPreprint
Tereshko, L., Zhao, X., Gagnon, J., Lin, T.-C., Ewald, T., Feschenko, M. S., & Mason, C. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.19.546797
Švedaitė, D., Kriučkova, A., Morkvėnas, A., Karabanovas, V., Stankūnavičius, G., Klima, V., Urbonavičius, J., & Ivanec-Goranina, R. (2025) · Biomolecules · doi:10.3390/biom15060889
Zhang, J., Chen, L., Sun, J., Li, S., Zhou, Y., Wu, Z., Li, C., Zheng, Z., & Luo, R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.29.673174
Liu, G., Wang, C., Dahlke, H. E., Walter, M. T., Xie, E., Zhao, X., Huang, G., Huang, Q., He, X. S., Wang, X., et al. (2026) · Water Resources Research · doi:10.1029/2025wr042716
Liao, R., Yang, D., Šimůnek, J., & Luo, D. (2026) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/csb-2026-0846
- Authors
- Mikutis, G., Schmid, L., Stark, W. J., & Grass, R. N.
- Affiliations
- ETH Zurich (CH)
- Corresponding author
- Grass, Robert N.
- Venue
- AIChE Journal
- Publisher
- Wiley
- Published
- 2018-10-24
- Volume
- 65
- Issue
- 1
- Pages
- 40-48
- ISSN
- 0001-1541 (ISSN-L)
- 1547-5905
- OpenAlex
- W2895530948
- Cited by
- 32
- References
- 34
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 3 · 2023: 8 · 2022: 8 · 2021: 3 · 2020: 2 · 2019: 1
- FWCI
- 0.53
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- AIChE Journal (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Identification and Quantification in Food
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- DNA degradation, DNA stability, sequence length, correction factors, material tracking, sunlight degradation, elevated temperature degradation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
