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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DNA Fountain is available at https://github.com/TeamErlich/dna-fountain.
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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.
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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Integrated supplementary information
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.
(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.
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.
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.
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.
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.
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).
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).
Mean values and error bars (s.e.m) of n=3 independent experiments.
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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
Nature Biotechnology (2020)