DNA technology delivers both data storage and computing capabilities for the first time

Researchers from North Carolina State University and Johns Hopkins University have demonstrated a technology that uses DNA rather than traditional electronics to perform a range of data storage and computation functions – repeatedly storing, retrieving, calculating, erasing or rewriting data. Previous DNA data storage and computation techniques have been able to perform some, but not all, of these tasks.

The paper, titled “Primitive DNA Store and Computational Engine,” appears in the journal Nature. Nature Nanotechnology.

“In traditional computing, we take for granted that the way we store data and the way we process it are compatible with each other,” says Albert Keung, project leader and co-corresponding author of the study.

“But the reality is that data storage and data processing happen in separate parts of the computer, and modern computers are complex networks of technologies,” said Keung, an associate professor of chemical and biomolecular engineering and a Goodnight Fellow at North Carolina State University.

“DNA computing has addressed the challenge of how to store, retrieve and compute on data when it’s stored in the form of nucleic acids,” Keung says.

“In the case of electronic computing, the fact that the components of the devices are all interchangeable is one of the things that makes these technologies so attractive. However, so far it has been thought that while DNA data storage might be useful for long-term data storage, it would be difficult or impossible to develop a DNA technology that encompasses all the operations found in traditional electronic devices – storing and moving data; reading, erasing, rewriting and rereading specific data files; performing calculations – all of this programmably and repeatedly.”

“We’ve demonstrated that DNA-based technology is viable, because we actually built it.”

This new technique is made possible by recent technologies that allow for the creation of soft polymeric materials with unique morphologies.

“Specifically, we created polymer structures that we call dendricolloids, which start out at the microscale but branch out into one another in a hierarchical manner to form a network of nanoscale fibers,” said co-corresponding author Orrin Berev, the S. Frank and Doris Culberson Distinguished Professor of Chemical and Biomolecular Engineering at North Carolina State University.

“This morphology creates a high-surface-area structure that allows DNA to be deposited between the nanofibrils without sacrificing the data density that makes DNA attractive for data storage.”

“A piece of DNA-based storage the size of a pencil eraser could hold the equivalent of 1,000 laptops’ worth of data,” Keung says.

“The ability to distinguish between DNA information and the nanofibers in which it is stored could enable them to perform many of the same functions that electronic devices can perform,” says Kevin Lin, lead author of the paper and a former doctoral student at North Carolina State University.

“We can copy DNA information directly from the surface of the material without damaging the DNA. We can also erase a target piece of DNA and rewrite it on the same surface, similar to how you can delete and rewrite information stored on a hard drive. This essentially allows us to perform all of the DNA data storage and computing functions. Furthermore, we have found that by attaching DNA to dendricolloid materials, the materials can help preserve DNA.”

“You could say that Keung’s team is providing the equivalent of a microcircuit, and the dendricolloid material my team created is providing the circuit board,” Velev says.

“Our collaborator, Adriana San Miguel at North Carolina State University, helped us incorporate the material into microfluidic channels that direct the flow of nucleic acids and reagents, allowing data to move and computing commands to be initiated. Winston Timpf’s lab at Johns Hopkins University provided our expertise in nanopore sequencing, which allows us to read the data in the RNA directly after copying it from the DNA on the material’s surface, and James Tuck’s lab at North Carolina State University developed algorithms that can convert data into nucleic acid sequences and vice versa, while controlling for potential errors.”

The researchers have demonstrated that their new data storage and computation technology, which they call a “primitive DNA storage and computation engine,” is capable of solving simple Sudoku and chess problems. Tests have shown that the technology can safely store data for thousands of years in commodity space without degrading the DNA that stores the information.

“What’s more, the dendrocolloid host material itself is relatively cheap and easy to manufacture,” Berev says.

“There’s great promise for molecular data storage and computation, but big questions remain about how practical this field will be,” Keung says. “We looked back at the history of computing and how the birth of ENIAC impacted the field. We wanted to develop something that would inspire the field of molecular computing, and we hope that what we’ve done here is a step in that direction.”

The paper was co-authored by former NC State doctoral students Kevin Forkel and Andrew Clark, NC State doctoral students Cyrus Kao and Rachel Pollack, NC State associate professor of chemical and biomolecular engineering Adriana San Miguel, NC State professor of electrical and computer engineering James Tuck, NC State associate professor of biomedical engineering Winston Timpf, Johns Hopkins associate professor of biomedical engineering, and Johns Hopkins postdoctoral fellow Paul Hook.