With DNA Data Storage, 3D-Printed Bunnies Carry Their Own Blueprints

The work “is incredibly interesting from a cultural perspective,” says Drew Endy, who was not involved in the research, and is an associate professor of bioengineering at Stanford. “Imagine a societal norm in which every object must encode the instructions for making the object,” he says. “Given the incredible information density of DNA data storage, such information could, in some commonplace objects such as refrigerators, also include a fully unabridged guide to rebuilding all of civilization.”

The authors of the report say they envision embedding this type of code in important, difficult-to-replace objects such as medical implants, building materials, car parts, and electronic components. Imagine damaging a car bumper and needing to replace it, says Yaniv Erlich, chief science officer at DNA-based genealogy service MyHeritage, and an author of the paper. “If I have DNA embedded in it, I could recover the information about what kind of replacement I need and maybe even print the part myself.” 

The work is part of a recent wave of research exploring the use of DNA as a storage medium. The exponentially increasing amount of data produced globally will need a place to land—some of it long term. DNA, if the costs of sequencing it continue to drop, offers a potential solution

What is DNA data storage? 

DNA’s four letters (A,T, G, and C), which represent life’s chemical building blocks, are, like binary, simply a code. Data can be converted from binary to base 4 and assigned a DNA letter. Data can be stored in DNA far more densely than in hard drives or magnetic tape. DNA lasts longer, too—hundreds to thousands of years. And it can take any shape, as the new paper shows. 

“If you think about any other storage technology, whether it’s tapes or discs or hard drives, they require a certain type of geometry. A tape is a tape. A disc is a disc. A hard drive is quite hard,” which is critical to its functionality, says Erlich, whose work on this project was independent from his work at MyHeritage. “DNA is the only storage technology that doesn’t have a defined geometry on the macroscopic level.”

In making the bunny trinket, Erlich, in collaboration with Robert Grass, a professor at ETH Zürich, converted 3D-printing instructions contained in a 45-kB binary stereolithography (.stl) file into a four-digit code, and synthesized the corresponding DNA. They divided the DNA into short strands of code, called oligonucleotides, and encapsulated them in silica nanoparticles. Then they blended the nanoparticles with biodegradable thermoplastic polyester, and generated a 3D printing filament laced with DNA.

After printing the bunny, the researchers physically clipped off a piece of its ear. “Only a tiny amount is needed,” says Erlich. “The DNA is sparse, but it’s everywhere.” They extracted the DNA and sequenced it using a portable DNA sequencer. Next they decoded the DNA and converted it back to a binary .stl file, yielding the digital instructions for printing the bunny. 

Preserving digital information

In all, the researchers spawned five generations of bunnies, each time clipping a chunk from the previous generation, and decoding the DNA to get the instructions for printing the next clone. The integrity of the data degraded a little each generation, with nearly 6 percent of the original oligonucleotides missing from the first-generation bunny, and more than 20 percent missing from the fifth generation. 

Erlich says his team’s decoding program, called DNA Fountain, allows them to lose up to 80 percent of the DNA data and still retrieve the .stl file. The program’s algorithm fills in the blanks based on the information available, like solving a Sudoku puzzle. Erlich first described DNA Fountain two years ago in the journal Science.

He and his colleagues note that nearly any kind of digital information could be stored in DNA. To test the scalability of that concept, the team stored a 1.4 MB video in DNA in plexiglass spectacle lenses. Using a process similar to that of the bunny, the team successfully retrieved the video file.

That opens up a lot of possible applications. Erlich says he envisions people being able to conceal secret information in objects, or even within other types of digital files. The technology could also be used to make self-replicating robots, he says. 

Maybe it will make the jobs of archaeologists in the future much easier. Imagine the delight of present-day archaeologists if a shard of ancient pottery yielded the information for fabricating a replica of the whole vessel.  

And maybe one day, archaeologists will recover Erlich’s bunny. The tchotchke, by the way, is the Stanford Bunny: one of the most commonly used test models in 3D computer graphics. It has been rendered on screens and 3D printed countless times since its creation in 1994. Now, thanks to DNA storage, the digital instructions for generating this bunny might survive the next couple of millennia.  

This story was updated on 9 December 2019. 

Source: IEEE-Spectrum – Fulltext

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