From Arizona State University, Harnessing Nature Code for Storage

By Richard Harth, science writer, Biodesign Institute, Arizona State University

As the digital world expands, scientists are exploring DNA’s remarkable capacity to store data, converting this ancient molecule into a next-gen information archive.

Researchers at Arizona State University, along with their international partners, have developed a breakthrough method that greatly enhances the capacity and efficiency of DNA storage. This method introduces ‘epi-bits,’ which are akin to movable type in a printing press, capable of being rearranged on a universal DNA template.
(Graphic by Jason Drees)

Since the 1980s, DNA has been considered an ideal medium for storage due to its extraordinary density and stability. DNA can store up to a billion times more information in the same volume compared with traditional silicon-based storage, and encoded sequences can last for centuries under the right conditions.

Researchers from Arizona State University and international collaborators have unveiled a method that significantly increases DNA storage capacity and efficiency using ‘epi-bits,’ which function like movable type in a printing press and can be arranged on a universal DNA template.

The new approach sidesteps the lengthy and expensive process of synthesizing new DNA, making it a quicker, more cost-effective solution. With DNA’s durability and compact nature, this method has the potential to store vast amounts of data in a minuscule space for long durations, offering a major shift from conventional storage technologies.

“It’s encouraging to see that epigenetic principles from biochemistry textbooks and taught in my classroom can be applied seamlessly to DNA storage applications to solve some of the unmet challenges in this field,” says Hao Yan, corresponding author.

Hao Yan, director of Biodesign Center for Molecular Design and Biomimetics, a Milton D. Glick Distinguished Professor in the School of Molecular Sciences at ASU and, as an Alexander von Humboldt Research Award winner, is currently a guest at the University of Stuttgart.

The research appears in the current issue of the journal Nature (see below).

Biological flash drive
Early efforts involved synthesizing new strands from scratch, encoding data one nucleotide at a time – making the process slow, costly and impractical for large-scale use. The method described in the new study bypasses these limitations. 

Instead of building DNA from scratch, the team uses existing strands, modifying them post synthesis with a process inspired by nature’s own method of regulating gene activity: epigenetic modification.

The technique draws on epigenetics, a natural process where chemical groups are added or removed from DNA to regulate gene expression, thereby determining whether a gene is turned on or off. This regulation affects protein production, which drives essential cellular functions. The researchers adapted this natural mechanism, using it to encode digital information instead of biological instructions.

By adding or removing chemical markers known as methyl groups on specific DNA bases, the researchers create epi-bits – tiny molecular data points that function like binary switches. A methylated base (epi-bit 1) and an unmethylated base (epi-bit 0) serve as the equivalent of the binary code used in computers.

The research team used a method called parallel molecular printing, where a universal DNA strand serves as a base and 700 different DNA segments act as building blocks. Each segment contains a unique pattern of epi-bits that represent digital information. By arranging these segments on the base strand, the researchers encoded around 270,000 bits of data, achieving a rate of 350 bits/reaction. The stored data was then read quickly and accurately using advanced sequencing technology.

“This new approach demonstrates how one can harness molecular mechanisms for innovative data solutions, bridging the fields of biology and digital information,” says Laura Na Liu, co-author of the new study.

Laura Na Liu is the director, 2nd Physics Institute, University of Stuttgart, Germany and fellow at Max Planck Institute for Solid State Research.

Advantages over traditional methods
DNA’s stability and compact nature make it an ideal medium for long-term data storage, capable of addressing the exponential growth of global data demands. The inherent stability of DNA means it can store information for hundreds, if not thousands, of years without degradation, making it a promising candidate for future data centers.

The approach works with existing DNA, using a fixed library of segments that can be dynamically modified, eliminating the need for chemical synthesis. This advancement significantly reduces costs and opens the door to practical, large-scale applications.

The researchers describe this method of storing complex data, including images, as having high fidelity and minimal error rates. Compared with existing DNA data storage approaches, the new technique is faster and more economical.

The epi-bit technology could offer a more sustainable and resource-efficient option compared with traditional electronic storage. As global data demands continue to surge, researchers believe that DNA’s compactness and durability could help mitigate the growing environmental impact of large-scale data storage.

Challenges and future directions
Despite the promise of this method, challenges remain. The complexity of methylation-based encoding and the need for precise control over chemical modifications require sophisticated technologies and methods. Achieving high-fidelity writing and reading is critical, as errors in the methylation process or misalignments could lead to data loss or corruption.

However, the potential benefits of this storage medium, including its compact size, environmental resistance and longevity, could outweigh these challenges. With further development, the technique could pave the way for highly efficient, adaptable data storage solutions.

The researchers envision future applications where DNA storage could be combined with molecular computing systems, enabling data to be stored, processed and even computed within the same medium. This would transform DNA from a mere storage molecule into an active participant in data processing.

Such innovations could open possibilities in synthetic biology, bioinformatics and beyond, integrating storage seamlessly with biological functions.

Article: Parallel molecular storage by printing epigenetic bits on DNA

Nature has published an article written by Cheng Zhang, Ranfeng Wu, School of Computer Science, Key Laboratory of High Confidence Software Technologies, Peking University, Beijing, China, Fajia Sun, Center for Quantitative Biology, Peking University, Beijing, China, Yisheng Lin, School of Computer Science, Key Laboratory of High Confidence Software Technologies, Peking University, Beijing, China, Yuan Liang, Jiongjiong Teng, School of Control and Computer Engineering, North China Electric Power University, Beijing, China, Na Liu, 2nd Physics Institute, University of Stuttgart, Stuttgart, Germany, and Max Planck Institute for Solid State Research, Stuttgart, Germany, Qi Ouyang, Long Qian, Center for Quantitative Biology, Peking University, Beijing, China, and Hao Yan, Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ, USA, and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.

Abstract: “DNA storage has shown potential to transcend current silicon-based data storage technologies in storage density, longevity and energy consumption^1,2,3. However, writing large-scale data directly into DNA sequences by de novo synthesis remains uneconomical in time and cost⁴. We present an alternative, parallel strategy that enables the writing of arbitrary data on DNA using premade nucleic acids. Through self-assembly guided enzymatic methylation, epigenetic modifications, as information bits, can be introduced precisely onto universal DNA templates to enact molecular movable-type printing. By programming with a finite set of 700 DNA movable types and five templates, we achieved the synthesis-free writing of approximately 275,000 bits on an automated platform with 350 bits written per reaction. The data encoded in complex epigenetic patterns were retrieved high-throughput by nanopore sequencing, and algorithms were developed to finely resolve 240 modification patterns per sequencing reaction. With the epigenetic information bits framework, distributed and bespoke DNA storage was implemented by 60 volunteers lacking professional biolab experience. Our framework presents a new modality of DNA data storage that is parallel, programmable, stable and scalable. Such an unconventional modality opens up avenues towards practical data storage and dual-mode data functions in biomolecular systems.“