A DNA-of-things storage architecture to create materials with embedded memory

Abstract

DNA storage offers substantial information density1,2,3,4,5,6,7 and exceptional half-life3. We devised a ‘DNA-of-things’ (DoT) storage architecture to produce materials with immutable memory. In a DoT framework, DNA molecules record the data, and these molecules are then encapsulated in nanometer silica beads8, which are fused into various materials that are used to print or cast objects in any shape. First, we applied DoT to three-dimensionally print a Stanford Bunny9 that contained a 45 kB digital DNA blueprint for its synthesis. We synthesized five generations of the bunny, each from the memory of the previous generation without additional DNA synthesis or degradation of information. To test the scalability of DoT, we stored a 1.4 MB video in DNA in plexiglass spectacle lenses and retrieved it by excising a tiny piece of the plexiglass and sequencing the embedded DNA. DoT could be applied to store electronic health records in medical implants, to hide data in everyday objects (steganography) and to manufacture objects containing their own blueprint. It may also facilitate the development of self-replicating machines.

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Fig. 1: DoT workflow and proof-of-principle 3D printing of a Stanford Bunny.
Fig. 2: DoT objects can be replicated for multiple generations.
Fig. 3: A video is concealed in reading glasses.

Data availability

The input files are available at https://figshare.com/s/283543df2b734b7988c6.

The sequencing files are available on the European Nucleotide Archive website, under accession code PRJEB35217.

Code availability

DNA Fountain is available at https://github.com/TeamErlich/dna-fountain.

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Acknowledgements

The authors thank the Christen group at ETH for giving access to the iSeq 100 sequencing device. Y.E thank B. Zaks for helpful discussions. Financial support by the ETH Zurich is kindly acknowledged.

Author information

The idea for the study was by conceived by Y.E. and R.N.G. The study was conceptualized by R.N.G., Y.E., W.J.S. and K.M. Coding was done by Y.E. Experimental work was performed by J.K. 3D printing was carried out by S.G. Visualization was performed by J.K. and R.N.G. The first draft was written by Y.E. All authors contributed to reviewing, editing and providing additional text for the manuscript. The order of the first two authors, who contributed equally, was determined lexigraphically.

Correspondence to Yaniv Erlich or Robert N. Grass.

Ethics declarations

Competing interests

Y.E. is an employee of MyHeritage, owner of Erlich Lab LLC, and holds patents in the area of DNA storage. ETH Zurich holds patents on DNA encapsulation. Y.E. and R.N.G are listed as inventors on a patent application in the field of DNA of things.

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Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Integrated supplementary information

Supplementary Fig. 1 The robustness of encapsulated DNA versus free DNA in the DoT architecture.

Chemical and thermal stability of the encapsulated DNA compared to non-encapsulated DNA. For the thermal stability assessment, solid state DNA and SPED encapsulated DNA were stored at 60 °C for one week at 50% relative humidity. For stability against aggressive chemical species, DNA and encapsulated DNA were treated with bleach and reactive oxygen species (ROS) in aqueous solution. *denotes values <10-5. Mean values and error bars of n=3 independent experimental experiments.

Supplementary Fig. 2 The sequence design for the DoT experiments.

(a) primer design of sequencing adapters as used in DoT (b) list of primer and index sequences used in DoT (c) oligo architecture for each of 12,000 features Oligonucleotide sequences.

Supplementary Fig. 3 SPED beads.

Scanning- (left) and scanning transmission (right) electron microscopy images of the SPEDs, which are about 160nm large particles comprising each ca. 60 DNA strands (DNA not visible). Scale bar = 200nm.

Supplementary Fig. 4 Time estimates for each stage in the replicating experiments.

Handling and overall process timing for the individual steps in the formation and, reading of the DoT objects. Time estimation resulting from 6 independent experiments.

Supplementary Fig. 5 The error rates as a function of generation.

M: master DNA library before any incorporation to an actual filament or silica beads. P: Parent (generation number 1), F1-F5: all subsequent generations. Each plot shows the average (green triangle), median (orange), interquartile range (beige), and the 5%-95% percentile range (bars) (A) The frequency of deletions per synthesized nucleotide (B) The frequency of insertions per synthesized nucleotide (C) The frequency of substantiations per synthesized nucleotide.

Supplementary Fig. 6 The length distribution of oligos as a function of generation.

Each curves is a density plot of the oligo lengths. M: master DNA library before any incorporation to an actual filament or silica beads. P: Parent (generation number 1), F1-F5: all subsequent generations (A) logarithmic scale (B) regular scale.

Supplementary Fig. 7 The distribution of sequence reads as a function of the original number of “G”s in the oligo in each generation.

Design is the actual file sent to sequencing. Master is the master DNA library before any incorporation to an actual filament or silica beads. P-F5 are product generations as described in the main text.

Supplementary Fig. 8 Cost of DoT.

Under the current scenario, the current laboratory scale costs were taken. For the future scenario, a 100 fold reduction in library cost was assumed, together with yield and cost optimization in product manufacturing (see discussion in Supplementary Note 6).

Supplementary Fig. 9

Thermal stability of an encapsulated DNA file in PCL filament for different 3D printing (green) and filament extrusion (black) process temperatures. Error bars represent standard errors of experimental triplicates. The black and green lines represent a nonlinear regression for each dataset according to Arrhenius law for a first order decay reaction (see Supporting Information).

Supplementary Fig. 10 qPCR cycle threshold as a function of logarithm of the SPED concentration.

Mean values and error bars (s.e.m) of n=3 independent experiments.

Supplementary Information

Supplementary Information

Supplementary Figs. 1–10 and Notes 1–10.

Reporting Summary

Supplementary Video 1

The DNA of things (DoT). Step-by-step workflow of DoT.

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Koch, J., Gantenbein, S., Masania, K. et al. A DNA-of-things storage architecture to create materials with embedded memory. Nat Biotechnol 38, 39–43 (2020) doi:10.1038/s41587-019-0356-z

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