Researchers at Johns Hopkins and North Carolina State universities have developed DNA storage and computing technology that “could put a thousand laptops’ worth of data into DNA-based storage that’s the same size as a pencil eraser,” according to project leader Albert Keung.
The technology uses so-called dendricolloids – soft polymer structures. A paywalled Nature research paper describes it, and the (kind of technical) abstract reads: “Any modern information system is expected to feature a set of primordial features and functions: a substrate stably carrying data; the ability to repeatedly write, read, erase, reload and compute on specific data from that substrate; and the overall ability to execute such functions in a seamless and programmable manner.
“Here we present a DNA-based store and compute engine that captures these primordial capabilities. This system comprises multiple image files encoded into DNA and adsorbed onto ~50-μm-diameter, highly porous, hierarchically branched, colloidal substrate particles comprised of naturally abundant cellulose acetate.
“Their surface areas are over 200 cm2 mg−1 with binding capacities of over 1012 DNA oligos mg−1, 10 TB mg−1 or 104 TB cm−3. This ‘dendricolloid’ stably holds DNA files better than bare DNA with an extrapolated ability to be repeatedly lyophilized and rehydrated over 170 times compared with 60 times, respectively.
“Accelerated ageing studies project half-lives of ~6,000 and 2 million years at 4 °C and −18 °C, respectively. The data can also be erased and replaced, and non-destructive file access is achieved through transcribing from distinct synthetic promoters. The resultant RNA molecules can be directly read via nanopore sequencing and can also be enzymatically computed to solve simplified 3 × 3 chess and sudoku problems. Our study establishes a feasible route for utilizing the high information density and parallel computational advantages of nucleic acids.”
In case that isn’t entirely clear, an NC State University news article has more information.
Keung said: “DNA computing has been grappling with the challenge of how to store, retrieve and compute when the data is being stored in the form of nucleic acids. For electronic computing, the fact that all of a device’s components are compatible is one reason those technologies are attractive. But, to date, it’s been thought that while DNA data storage may be useful for long-term data storage, it would be difficult or impossible to develop a DNA technology that encompassed the full range of operations found in traditional electronic devices: storing and moving data; the ability to read, erase, rewrite, reload or compute specific data files; and doing all of these things in programmable and repeatable ways. We’ve demonstrated that these DNA-based technologies are viable, because we’ve made one.”
Co-researcher Orlin Velev added: “We have created polymer structures that we call dendricolloids – they start at the microscale, but branch off from each other in a hierarchical way to create a network of nanoscale fibers. This morphology creates a structure with a high surface area, which allows us to deposit DNA among the nanofibrils without sacrificing the data density that makes DNA attractive for data storage in the first place.”
Research team member Kevin Lin said: “The ability to distinguish DNA information from the nanofibers it’s stored on allows us to perform many of the same functions you can do with electronic devices. We can copy DNA information directly from the material’s surface without harming the DNA. We can also erase targeted pieces of DNA and then rewrite to the same surface, like deleting and rewriting information stored on the hard drive. It essentially allows us to conduct the full range of DNA data storage and computing functions. In addition, we found that when we deposit DNA on the dendricolloid material, the material helps to preserve the DNA.”
This non-destructive read capability is novel in DNA storage, which usually involves destroying some of the DNA when you read it.
Velev noted: “Our NC State collaborator Adriana San Miguel helped us incorporate the materials into microfluidic channels that direct the flow of nucleic acids and reagents, allowing us to move data and initiate computing commands. Winston Timp’s lab at Johns Hopkins contributed their expertise on nanopore sequencing, which helps us directly read the data in RNA after copying it from DNA on the material’s surface. And James Tuck’s lab – also here at NC State – has developed algorithms that allow us to convert data into nucleic acid sequences and vice versa while controlling for potential errors.”
This research is a highly interesting take on DNA storage, but it does not solve the lengthy data read and write times so far inherent in the technology, which renders its exceedingly long lifetime moot. The idea of enzymatic computation based on microfluidic flows being any kind of feasible alternative to electronic computation is simply bizarre.
The published research paper details are: “A primordial DNA store and compute engine” by Kevin N Lin, Kevin Volkel, Cyrus Cao, Paul W Hook, Rachel E Polak, Andrew S Clark, Adriana San Miguel, Winston Timp, James M Tuck, Orlin D Velev, and Albert J Keung, 22 August 2024, Nature Nanotechnology. DOI: 10.1038/s41565-024-01771-6.
Bootnote
Kevin Volkel and Andrew Clark are former PhD students at NC State. Cyrus Cao and Rachel Polak, PhD, are NC State students. Adriana San Miguel is associate professor of chemical and biomolecular engineering at NC State. James Tuck is professor of electrical and computer engineering at NC State. Winston Timp is associate professor of biomedical engineering at Johns Hopkins University. Paul Hook is a postdoctoral researcher at Johns Hopkins. Orlin Velev is S. Frank and Doris Culberson Distinguished Professor of Chemical and Biomolecular Engineering at NC State. Albert Keung is Goodnight Distinguished Scholar in Innovation in Biotechnology and Biomolecular Engineering at NC State.
Keung and Tuck are co-founders of DNAli Data Technologies, so have potential interest in translating and commercializing DNA-based information systems. Keung, Volkel, Tuck, and Lin are inventors on patent application WO 2020/096679, which has been licensed to DNAli Data Technologies and from which some of this work is derived.
