An Empirical Comparison of Preservation Methods for Synthetic DNA Data Storage.
DNA data storage
synthetic DNA
synthetic DNA preservation
Journal
Small methods
ISSN: 2366-9608
Titre abrégé: Small Methods
Pays: Germany
ID NLM: 101724536
Informations de publication
Date de publication:
05 2021
05 2021
Historique:
received:
06
11
2020
entrez:
20
12
2021
pubmed:
21
12
2021
medline:
24
3
2022
Statut:
ppublish
Résumé
Synthetic DNA has recently risen as a viable alternative for long-term digital data storage. To ensure that information is safely recovered after storage, it is essential to appropriately preserve the physical DNA molecules encoding the data. While preservation of biological DNA has been studied previously, synthetic DNA differs in that it is typically much shorter in length, it has different sequence profiles with fewer, if any, repeats (or homopolymers), and it has different contaminants. In this paper, nine different methods used to preserve data files encoded in synthetic DNA are evaluated by accelerated aging of nearly 29 000 DNA sequences. In addition to a molecular count comparison, the DNA is also sequenced and analyzed after aging. These findings show that errors and erasures are stochastic and show no practical distribution difference between preservation methods. Finally, the physical density of these methods is compared and a stability versus density trade-offs discussion provided.
Identifiants
pubmed: 34928102
doi: 10.1002/smtd.202001094
doi:
Substances chimiques
Magnetite Nanoparticles
0
DNA
9007-49-2
Trehalose
B8WCK70T7I
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e2001094Subventions
Organisme : Microsoft
Organisme : DARPA
Informations de copyright
© 2021 The Authors. Small Methods published by Wiley-VCH GmbH.
Références
S. M. H. T. Yazdi, Y. Yuan, J. Ma, H. Zhao, Sci. Rep. 2015, 5, 14138. https://doi.org/10.1038/srep14138.
Y. Erlich, D. Zielinski, Science 2017, 355, 950, https://doi.org/10.1126/science.aaj2038, https://doi.org/10.1126/science.aaj2038.
K. J. Tomek, K. Volkel, A. Simpson, A. G. Hass, E. W. Indermaur, J. Tuck, A. J. Keung, bioRxiv, http://biorxiv.org/lookup/doi/10.1101/591594.
L. Organick, S. D. Ang, Y.-J. Chen, R. Lopez, S. Yekhanin, K. Makarychev, M. Z. Racz, G. Kamath, P. Gopalan, B. Nguyen, C. N. Takahashi, S. Newman, H.-Y. Parker, C. Rashtchian, K. Stewart, G. Gupta, R. Carlson, J. Mulligan, D. Carmean, G. Seelig, L. Ceze, K. Strauss, Nat. Biotechnol. 2018, 36, 242. https://doi.org/10.1038/nbt.4079. ISBN: 1364298980840.
L. Organick, Y.-J. Chen, S. Dumas Ang, R. Lopez, X. Liu, K. Strauss, L. Ceze, Nat. Commun.11, 1. https://doi.org/10.1038/s41467-020-14319-8.
J. Bonnet, M. Colotte, D. Coudy, V. Couallier, J. Portier, B. Morin, S. Tuffet, Nucleic Acids Res. 2009, 38, 1531. https://doi.org/10.1093/nar/gkp1060, ISBN: 1362-4962 (Electronic) 0305-1048 (Linking).
R. N. Grass, R. Heckel, M. Puddu, D. Paunescu, W. J. Stark, Angew. Chem. Int. Ed. 2015, 54, 2552. ISBN: 2012290248.
R. Guthrie, JAMA 1961, 178, 863.
T. C. Boothby, H. Tapia, A. H. Brozena, S. Piszkiewicz, A. E. Smith, I. Giovannini, L. Rebecchi, G. J. Pielak, D. Koshland, B. Goldstein, Mol. Cell 2017, 65, 975.
A.-L. Fabre, A. Luis, M. Colotte, S. Tuffet, J. Bonnet, PLoS One 2017, 12, 11.
M. E. Allentoft, M. Collins, D. Harker, J. Haile, C. L. Oskam, M. L. Hale, P. F. Campos, J. A. Samaniego, M. T. P. Gilbert, E. Willerslev, G. Zhang, R. P. Scofield, R. N. Holdaway, M. Bunce, Proc. R. Soc. B 2012, 279, 4724.
T. Lindahl, B. Nyberg, Biochemistry 1972, 11, 3610.
GenTegra, GenTegra DNA User Guide - Ambient Temperature Storage and Transport of Purified DNA, Version C 2014, https://nbsscientific.co.uk/wp-content/uploads/sites/8/2020/02/GenTegraDNA-User-Guide.pdf.
D. Clermont, S. Santoni, S. Saker, M. Gomard, E. Gardais, C. Bizet, Biopreserv. Biobanking 2014, 12, 176.
S. E. Howlett, H. S. Castillo, L. J. Gioeni, J. M. Robertson, J. Donfack, Forensic Sci. Int.: Genet. 2014, 8, 170.
A. Xavier Kohll, P. L. Antkowiak, W. D. Chen, B. H. Nguyen, W. J. Stark, L. Ceze, K. Strauss, R. N. Grass, Chem. Commun. 2020, 56, 3613. https://doi.org/10.1039/D0CC00222D, https://pubs.rsc.org/en/content/articlelanding/2020/cc/d0cc00222d.
W. D. Chen, A. X. Kohll, B. H. Nguyen, J. Koch, R. Heckel, W. J. Stark, L. Ceze, K. Strauss, R. N. Grass, Adv. Funct. Mater. 2019, 29, 1901672.
M. Colotte, D. Coudy, S. Tuffet, J. Bonnet, Biopreserv. Biobanking 2011, 9, 47.
I. S. Reed, G. Solomon, J. Soc. Ind. Appl. Math. 1960, 8, 300.
S. Newman, A. P. Stephenson, M. Willsey, B. H. Nguyen, C. N. Takahashi, K. Strauss, L. Ceze, Nat. Commun. 2019, 10, 1.
N. V. Ivanova, M. L. Kuzmina, Mol. Ecol. Resour. 2013, 13, 890.
R. C. Dobberstein, J. Huppertz, N. von Wurmb-Schwark, S. Ritz-Timme, Forensic Sci. Int. 2008, 179, 181.
L. Greenspan, J. Res. Natl. Bur. Stand., Sect. A 1977, 81A, 89.