Enzymatic Synthesis: Our DNA Is Becoming the World’s Tiniest Hard Drive

 

DNA Hard Drive Data Storage Concept

Researchers propose faster method for recording data to DNA, showing promise in fields of digital data storage, neuron recording.

Our genetic code is millions of times more efficient at storing data than existing solutions, which are costly 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 within a couple hundred pounds of DNA.

Using DNA as a high-density data storage medium holds the potential to forge breakthroughs in biosensing and biorecording technology and next-generation digital storage, but researchers haven’t been able to overcome inefficiencies that would allow the technology to scale.

“Nature is good at copying DNA, but we really wanted to be able to write DNA from scratch.” — Keith Tyo, Associate Professor of Chemical and Biological Engineering

Now, researchers at Northwestern University propose a new method for recording information to DNA that takes minutes, rather than hours or days, to complete. The team used a novel enzymatic system to synthesize DNA that records rapidly changing environmental signals directly into DNA sequences, a method the paper’s senior author said could change the way scientists study and record neurons inside the brain.

The research, “Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis,” was published on September 30, 2021, in the Journal of the American Chemical Society. The paper’s senior author, Northwestern Engineering’s Keith E.J. Tyo, said his lab was interested in leveraging DNA’s natural abilities to create a new solution for storing data.

The paper’s senior author, Northwestern engineering professor Keith E.J. Tyo, said his lab was interested in leveraging DNA’s natural abilities to create a new solution for storing data.

“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 to do this involves a slow, chemical synthesis. Our method is much cheaper to write information because the enzyme that synthesizes the 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 ahead of time and can continuously store information.”

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

Bypassing protein expression

Existing methods to record intracellular molecular and digital data to DNA rely on multipart processes that add new data to existing sequences of DNA. To produce an accurate recording, researchers must stimulate and repress expression of specific proteins, which can take over 10 hours to complete.

The Tyo lab hypothesized they could use a new method that they called Time-sensitive Untemplated Recording using Tdt for Local Environmental Signals, or TURTLES, to synthesize completely new DNA instead of copying a template of it, making a faster and higher resolution recording.

As the DNA polymerase continues to add bases, data is recorded into the genetic code on a scale of minutes as changes in the environment impact the composition of the DNA it synthesizes. The environmental changes, such as changes in the concentration of metals, are recorded by the polymerase, acting as a “molecular ticker tape” and indicating to scientists the time of an environmental change. Using biosensors to record changes into DNA represents a major step in proving TURTLES’ viability for use inside cells, and could give researchers the ability to use recorded DNA to learn about how neurons communicate with each other.

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

From brain cells to polluted water

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

“If you look at how current technology scales over time, it could be decades before we can even record an entire cockroach brain simultaneously with existing technologies – let alone the tens of billions of neurons in human brains,” Callisto said. “So that’s something we’d really like to accelerate.”

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

It’s particularly good for long term archival data applications such as storing closed-circuit security footage, which the team refers to as data that you “write once and read never,” but need to have accessible in the event an incident occurs. With technology developed by engineers, hard drives and disk drives that hold years of beloved camera memories also could be replaced by bits of DNA.

Outside of storage, the “ticker tape” function could be used as a biosensor to monitor environmental contaminants, like the heavy metal concentration in drinking water.

While the lab focuses on moving beyond a proof of concept in both digital and cellular recording, the team expressed hope that more engineers would take interest in the concept and be able to use it to record signals important to their research.

“We’re still building out the genomic infrastructure and cellular techniques we need for robust intracellular recording,” Tyo said. “This is a step along the way to getting to 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 E. J. Tyo, 30 September 2021, Journal of the American Chemical Society.
DOI: 10.1021/jacs.1c07331

This work was funded by two National Institutes of Health grants (R01MH103910; and UF1NS107697) and an NIH Training Grant (T32GM008449) through Northwestern University’s Biotechnology Training Program. The research was supported in part through the computational 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 for Research and Northwestern University Information Technology. All next-generation sequencing was done with the help of the Next Generation Sequencing Core facility at the University of Illinois at Chicago. Sanger sequencing was supported by the Northwestern University NUSeq Core Facility. Gel imaging was supported by the Northwestern University Keck Biophysics Facility and a Cancer Center Support Grant (NCI CA060553). The Keck Biophysics Facility’s Azure Sapphire Imager was funded by an NIH grant (1S10OD026963-01). Protein purification was supported by the Northwestern University Recombinant Protein Production Core.

5 Comments on "Enzymatic Synthesis: Our DNA Is Becoming the World’s Tiniest Hard Drive"

  1. Deborah Wheeler Morales | October 6, 2021 at 5:16 pm | Reply

    Just so all the info shuttle-ers won’t feel so small and redundant………..don’t worry, it didn’t self organize.

  2. I’m not sure how the dna is encased, and if it’s in e. coli, how to manage concurrency and get rid of old poles.

  3. These so called scientists are brainless idiots. That giggling bitch wants to reprogram DNA? Why won’t she start with herself, her parents and her children? Stupid people with their godlike ambitions. They plan to turn all humans into slave robots, the ones that remain after deadly “vaccinations”. They already run global genocide by injecting into people death serum they called a “vaccine”. And people are so dumb so brainwashed by lies and propaganda that they go by themselves to these procedures like lambs for the slaughter. They plan to reduce the population of the earth to about 500 millions. So they have to kill the rest. These 500 mil that remain will become slaves of the godlike elites. The ones that run this madness now. Wake up people, there was never any COVID, everything was staged, all the people that died, died from their vaccines, but they say it was COVID. When they said that hospitals are full of infected people, the hospitals were lately empty. They lied to all of us all the time non stop from all media. They scared to take away licenses and bribed all medical personnel so that they lied to people into convincing them to take an injection of death serum. People you need to wake the fk up… Already it’s to late. You not trust a single word from the mouth of politicians and those traitors that they presents as “experts” to you. Wake up. Wake up, it is a global genocide. There is no pandemic, none, zero. You only heart about it from a TV, internet or radio. That is how they brainwashed you. Turn this sh*t off, open your eyes and look around? Do you see any deadly pandemic? Nothing. All this crap is coming from a TV, a radio and the internet. Wake up.

  4. Richard l Dayton | October 8, 2021 at 1:12 am | Reply

    Replying to gm. When you research things to support your views you will find them while ignoring anything else.it seems to me you are well on your way to having no opinions based in reality

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