NEW YORK – An international team of researchers has developed a DNA-based storage architecture to produce materials with immutable memory, which could be used to store electronic health records or facilitate the development of self-replicating machines.
This 'DNA-of-things' (DoT) storage framework uses DNA molecules to record data, the researchers wrote in a study published on Monday in Nature Biotechnology. These molecules are then encapsulated in nanometer silica particle-encapsulated DNA (SPED) beads, which are fused into various materials that are used to print or cast objects in any shape.
The researchers used DoT to three-dimensionally print a Stanford Bunny — a computer graphics 3D test model developed by Greg Turk and Marc Levoy in 1994 — that contained a 45-kB digital DNA blueprint for its own synthesis. This configuration is reminiscent of biological organisms, in which the instructions for making an object reside within the organism itself, the researchers noted.
They synthesized five generations of the bunny, each from the memory of the previous generation without additional DNA synthesis or degradation of information, showing that the data can be perfectly and rapidly retrieved from the 3D object by consuming a minute quantity of material using a portable sequencer.
The researchers clipped about 10 mg of printed material from the ear of the bunny, or about 0.3 percent of the total material, and released the SPED beads to extract the DNA. The recovered DNA library was amplified and then sequenced using an Illumina iSeq — the process took 17 hours and yielded more than 1 million reads.
They then conducted multi-round replication experiments using the DoT architecture by creating three offspring 3D structures using material from the parent Stanford Bunny, then extracting and sequencing the DNA. The researchers then repeated the same procedure for a total of five generations, where each generation contained material created by fusing the PCR-amplified DNA molecules of the previous experiment.
Finally, to demonstrate the ability to store the DNA long term, they sequenced a fifth-generation Bunny nine months after its synthesis, sequenced the information and used it to generate a further product generation. The researchers found that they were able to perfectly retrieve the file from all five generations of progeny, including the retrieval of information nine months after synthesis.
They then tested the scalability of DoT by storing a 1.4 MB video in DNA in plexiglass spectacle lenses. "The end result was a pair of ordinary-looking glasses with ordinary-transmittance lenses that secretly stored a video message," the team wrote.
To test whether they could retrieve the video, the researchers excised a 10-mg piece of the plexiglass and dissolved it in acetone, leaving only the SPED beads. They then followed their standard extraction steps, yielding 0.4 ng of DNA, corresponding to about 6,000 copies of the encoded file. Sequencing with iSeq resulted in 5.7 million paired-end reads.
"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," the authors wrote. "It may also facilitate the development of self-replicating machines."
They posited that the DoT architecture could be used in applications where blueprint-level information is required to be accessible, either in a personalized item or a mass-manufactured object. For example, in the field of 3D medical or dental implants, each structure is unique and must be customized for the precise anatomical structure of the patient. Because SPED beads are nontoxic, DoT would allow for the design of the implant and other medical information to be stored in the implant itself, offering a long-range back-up alternative to traditional electronic medical records.
"Our results suggest that one DoT library has sufficient replicating capacity to produce storage material for a virtually unlimited supply of objects," the authors concluded.