YSM Issue 93.1

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FEATUREBiotechnologyISTHE HIDDEN FUTURE OF IN DATA PLAIN STORAGE SIGHTof using DNA as a mediumfor information storage withininanimate objects.The rapidly expanding field ofDNA data storage, dubbed “DNA-ofthings”(DoT), has important implicationsfor industry, specifically digital storage. Associal reliance on digital systems mountsrapidly, current storage architectures suchas hard drives are becoming constrained bythe physical limitations of their shapes andsizes. DNA offers transformative advantagesas a storage medium with its capacity tostore data at unparalleled densities withoutdegrading, as well as its ability to adopt anyconceivable shape through DoT engineering.If properly protected, DNA can withstandboth environmental and artificial stresses,allowing information to potentially be“cold-stored” for thousands of years. Thatlevel of structural integrity combined with asuperior storage density of up to 455 exabytesper gram, where one exabyte equals onethousand petabytes. This value outstrips thecurrently most advanced hard drive storagemethod by 215 orders of magnitude, andrenders DoT an innovation that could definethe next decade of information technology.Sequencing the genetic code of an objectBY NICHOLAS ARCHAMBAULTART BY ZIHAO LINA petabyte is the equivalent of 10 15bytes of digital information, one billiontimes larger than the standard megabytethat composes common digital fileslike an audio clip or high-resolutionpicture. Approximately ten billion users’photos that comprise Facebook’s storagewarehouses amount to 1.8 petabytes ofdata. The entire Netflix library of rawvideo content totals around 3.1 petabytes.Imagine being able to carry petabytesworth of information on a device that fitsin your pocket. Though it may sound farfetched,compact portability of massiveamounts of data is closer to becoming areality than ever before, thanks to recentwork from the bioengineering lab of RobertGrass at ETH Zurich. The researchers’breakthrough paper, published lastDecember, demonstrates the first examplesInterest in DoT’s largely untapped potentialled Grass and his collaborator Yaniv Erlich,Professor of Computer Science at ColumbiaUniversity and Chief Science Officer of theonline genealogy platform MyHeritage,to test DNA’s stability as a vehicle forinformation. “Erlich’s idea was to put not justa trackable barcode but ‘real information’ intomaterials—ideally something connected tothe object itself,” Grass said. They settled on3D printing a Stanford bunny—a commongraphical quality test object—embeddedwith its own blueprint.First, the 45-kilobyte file detailing thebunny’s creation was converted frombinary digital format to a DNA sequence.28 Yale Scientific Magazine March 2020www.yalescientific.org
BiotechnologyFEATURETo protect it against the mechanical andthermal stresses of being incorporatedinto the polymer material that serves asthe “ink” of the 3D printer, the DNA wasencapsulated into silica nanoparticlesprior to mixing. The encoded polymer wasextruded into a filament compatible withordinary desktop 3D printers. Once thebunny was printed, the researchers snippedoff ten milligrams of its ear—an amountequal to 0.3 percent of total bodily mass—in order to recover DNA and synthesizeanother bunny. With the polymer dissolvedand silica beads cleaned, the encapsulateddataset could be processed and the completedigital file recovered. Using DNA from thesame ten milligrams of material, the teamgenerated and recovered perfect digitalfiles from five subsequent generations ofbunnies, including one that was stored fornine months prior to re-synthesis.The final generation of offspring wassubject to sequencing errors and the dropoutof over twenty percent of the original data,but Grass explains that these types of errorsare already overcome by inserting backupdata in the initial phase of the DNA storageprocess. Higher levels of redundancy allowfor more generations of error-free replicas.“If you know that every generation loses twopercent of data then you add ten percentredundancy at the beginning to allow forfive generations. That’s much easier thantrying to solve the problem down the road,”Grass said. The key outcomes of the file’sperfect recovery stand undiminished by theerrors, he added. The bunnies’ generationalsynthesis provided support for the theoreticalpossibility that lost portions of data can berecovered with redundant DNA—a processlikened to solving a sudoku puzzle givenonly limited information. The experimentalso required a miniscule amount of samplematerial to recover the data necessary toengineer subsequent generations. A sampleof such a small scale, essential to recreatingoffspring products without impairing theirappearance or functionality, is only possibledue to DNA’s enormous storage capacity.Inspired by their successful pilot, Erlichurged the group to attempt a more ambitiousfollow-up, embedding more data in a newtype of polymer. For the next experiment,the group repeated the sequencing andmaterial infusion processes, this timefor a 1.4-megabyte YouTube video in atransparent plexiglass polymer that would be3D-printed into a lens. When mounted ontoa frame, the lens exhibited normal opticalproperties, allowing an ordinary-looking,functional pair of glasses to secretly containa DNA-encoded video message. Once again,a mere ten milligrams taken from the framesallowed for full recovery of the video file.A revolutionary industrial forceOnce it is polished, Grass and Erlichenvision DoT technology to broadlyimpact the future of manufacturing onboth personalized and industrial scales.This shared perspective arises from eachscientist’s industrial background—Erlich’sas CSO of MyHeritage and Grass’ as CEOof Turbobeads, a nanotechnology companyhe founded ten years ago.Their group devoted a significant portionof its research to examining factors thatwill influence DoT’s ability to becomea widespread and flexible solution tothe challenges of digital storage. Thisincluded testing new types of polymers thatcould serve as viable materials for DNAstorage, as well as discussing potentialDoT applications and their economicchallenges. Personalized items will likelybe the first industrial application. Dentalimplants, for example, could be encodedthrough DoT with information pertainingto an individual’s unique implant design.The problem, Grass said, would be thehigh upfront cost of encoding an entireblueprint. For every implant, a new setof DNA would have to be synthesized ataround one thousand dollars per megabyte.A more feasible general application couldarise in products with long lifetimes, suchas construction materials or other itemswhich would retain their own instructionsfor replication when traditional data storagemethods may have been lost. Accordingto Grass, however, the most notableimpact will be in the mass-manufacturingindustry, in which the enormous initial costNew ‘DNA-of-Things’ technology has thepower to transform our digitized worldIMAGE COURTESY OF ETH ZURICH/ROBERT GRASSOne lens of these glasses modeled by an assistantresearcher contains DNA encoding a video file.of synthesizing the DNA for the first itemwould be offset by the ability to regenerateidentical replicas with little material and noadded expense. The ten milligrams snippedfrom each of the group’s test bunniestheoretically yielded enough data to createeighty quintillion (10 18 ) offspring withinfive generations—without resynthesizingthe initial DNA even once.Though the researchers’ work suggestsDNA could potentially store files of muchgreater size, their focus is to think in terms ofan everyday budget rather than speculatingabout the dizzying cost of encoding a vastlibrary of information. “At the moment,one hundred kilobytes costs perhaps ten ortwenty dollars,” Grass said. “What can I dowith that? Right now, our products containzero or very little information. What if Icould put just ten kilobytes of informationinto that item instead? That’s the first step.”These preliminary steps havealready turned heads in industrial andgovernmental sectors. Some companiescurrently offer megabyte-scale personalDNA sequencers, and the United StatesIntelligence Advanced Research ProjectsActivity recently committed fifty milliondollars toward DNA data storage research.“We dream of a world where everyonecan do DNA sequencing,” Grass said. “Isee it as our job to give examples, even ifthey’re still academic, which demonstratewhere we can get value out of thistechnology. We have a proof of conceptthat shows that it’s doable. Now the nextstep is to show that we can build a casewhere we can generate value.” The future,it seems, is hidden in plain sight after all. ■www.yalescientific.orgMarch 2020Yale Scientific Magazine29
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