Our DNA becomes the world’s smallest hard drive

Researchers propose a faster method of recording data to DNA, promising in the fields of digital data storage, neural recording.

Our genetic code is millions of times more efficient at storing data than existing solutions, which are expensive and use immense amounts of energy and space. In fact, we could get rid of hard drives and store all the digital data on the planet in a few hundred pounds of DNA.

The use of DNA as a high-density data storage medium offers the potential for breakthroughs in bio-sensing and bio-recording technology and in next-generation digital storage, but researchers have been unable to overcome inefficiencies that would allow technology to evolve.

Now, researchers from Northwestern University propose a new method of recording information in DNA that takes minutes rather than hours or days. The team used a new enzyme system to synthesize DNA that records rapidly changing environmental signals directly into DNA sequences, a method that the paper’s lead author says could change the way scientists study and record the neurons inside the brain.

The research, “Recording Time Signals with Minute Resolution Using Enzymatic DNA Synthesis,” was published on September 30, 2021 in the Journal of the American Chemical Society. Lead author of the article, Keith EJ Tyo of Northwestern Engineering, said his lab wanted to take advantage of DNA’s natural capabilities to create a new data storage solution.

Lead author of the article, Northwestern Engineering Professor Keith EJ Tyo, said his lab wanted to take advantage of DNA’s natural capabilities to create a new data storage solution.

“Nature is good at copying DNA, but we really wanted to be able to write DNA from scratch,” Tyo said. “The ex vivo (outside the body) way of doing it involves slow chemical synthesis. Our method is much cheaper to write information because the enzyme that synthesizes DNA can be directly manipulated. State-of-the-art intracellular recordings are even slower because they require the mechanical steps of protein expression in response to signals, as opposed to our enzymes which are all expressed in advance and can store information continuously.

Tyo, a professor of chemical and biological engineering at the McCormick School of Engineering, is a member of the Center for Synthetic Biology and studies microbes and their mechanisms to detect and respond to environmental changes quickly.

Bypass protein expression

Existing methods for recording intracellular molecular and numerical data on DNA rely on multipart processes that add new data to existing DNA sequences. To produce an accurate recording, researchers must stimulate and suppress the expression of specific proteins, which can take more than 10 hours.

Tyo’s lab speculated that they could use a new method they called time-sensitive untimed recording using Tdt for local environmental signals, or TURTLES, to synthesize completely new DNA instead of copying one. model thereof, which allows faster and higher resolution recording.

As DNA polymerase continues to add bases, data is recorded in the genetic code on a scale of a few minutes, as changes in the environment impact the composition of the DNA that ‘she synthesizes. Environmental changes, such as changes in the concentration of metals, are recorded by the polymerase, acting like a “molecular magnetic strip” and telling scientists when an environmental change occurs. Using biosensors to record changes in DNA represents a major step in proving the viability of TURTLES for use inside cells, and could give researchers the opportunity to use recorded DNA to find out. more on how neurons communicate with each other.

“This is a really exciting proof of concept for methods that could one day allow us to study the interactions between millions of cells simultaneously,” said Namita Bhan, co-lead author and postdoctoral researcher at the Tyo lab. “I don’t think there is a previously reported direct enzyme modulation recording system.”

Brain cells in polluted water

With more potential for scalability and precision, TURTLES could provide the foundation for tools that catapult brain research. According to Alec Callisto, also co-first author and graduate student of the Tyo Lab, researchers can only study a tiny fraction of the neurons in the brain with today’s technology, and even then there are limits to that. that they know how to do. By placing recorders inside all brain cells, scientists could map responses to stimuli with single-cell resolution across many (millions) neurons.

“If you look at how current technology evolves over time, it could be decades before we can even register an entire cockroach brain simultaneously with existing technologies – not to mention the tens of billions of neurons in the human brain. “said Callisto. “So this is something that we would really like to speed up.”

Outside of the body, the TURTLES system could also be used for a variety of solutions to meet the explosive growth in data storage needs (up to 175 zettabytes by 2025).

This is especially useful for long-term archival data applications such as closed-circuit safety footage storage, which the team calls data that you “write once and never read” but which you don’t read. must have access in the event of an incident. Thanks to technology developed by engineers, hard drives and disk drives that hold years of beloved camera memories could also be replaced with pieces of DNA.

Apart from storage, the ticker tape function could be used as a biosensor to monitor environmental contaminants, such as the concentration of heavy metals in drinking water.

As the lab focuses on moving beyond proof of concept in digital and cellular recording, the team expressed hope that more engineers would be interested in the concept and could use it to record signals. important for their research.

“We are still building the genomic infrastructure and cellular techniques that we need for robust intracellular recording,” Tyo said. “This is a step on the road to reaching our long-term goal. “

Reference: “Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis” by Namita Bhan, Alec Callisto, Jonathan Strutz, Joshua Glaser, Reza Kalhor, Edward S. Boyden, George Church, Konrad Kording and Keith EJ Tyo, September 30, 2021, Journal of the American Chemical Society.
DOI: 10.1021 / jacs.1c07331

This work was supported by two grants from the National Institutes of Health (R01MH103910 and UF1NS107697) and an NIH training grant (T32GM008449) under the biotechnology training program at Northwestern University. The research was funded in part by the computing resources and staff contributions provided for the Quest high-performance computing facility at Northwestern University, which is jointly supported by the Office of the Provost, the Office of Research and Technology of information from Northwestern University. All next generation sequencing was performed with the assistance of the Next Generation Sequencing Center at the University of Illinois at Chicago. Sanger sequencing was supported by Northwestern University NUSeq Core Facility. Gel imaging was supported by Northwestern University Keck Biophysics Facility and a Cancer Center Support Grant (NCI CA060553). Azure Sapphire Imager at the Keck Biophysics Facility was funded by an NIH grant (1S10OD026963-01). Protein purification was supported by the Northwestern University Recombinant Protein Production Core.