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Totally RAD: Bioengineers create rewritable digital data storage in DNA

Researchers at Stanford have engineered a pair of enzymes to reliably record digital data within the genome of living cells.

“PhD candidate Pakpoom "Ton” Subsoontorn (left) and post-doctoral fellow Jerome Bonnet (right) show off a petri dish with two arrows formed of e. coli modified using the researchers’ Recombin

“PhD candidate Pakpoom "Ton” Subsoontorn (left) and post-doctoral fellow Jerome Bonnet (right) show off a petri dish with two arrows formed of e. coli modified using the researchers’ Recombinase Addressable Data storage device. The top arrow of cells, pointing left, has been modified to glow green when illuminated under ultraviolet light. The second arrow, pointing right, is made of cells with the same section of DNA only flipped in the opposite direction. It glows red under the UV light.| Photo: Norbert von der Groeben

Sometimes, remembering and forgetting are hard to do.

“It took us three years and 750 tries to make it work, but we finally did it,” said Dr. Jerome Bonnet of his latest research, a method for repeatedly encoding, storing, and erasing digital data within the DNA of living cells.

Bonnet, a postdoctoral fellow at Stanford, worked with PhD Candidate Pakpoom Subsoontorn and assistant professor Drew Endy to reapply natural enzymes adapted from bacteria to flip specific sequences of DNA back and forth at will. All three scientists are bioengineers.

Bonnet, a postdoctoral fellow at Stanford, worked with PhD Candidate Pakpoom Subsoontorn and assistant professor Drew Endy

In practical terms, they have devised the genetic equivalent of a binary digit – a “bit” in data parlance. “Essentially, if the DNA section points in one direction, it’s a zero. If it points the other way, it’s a one,” Subsoontorn explained.

In the computer world, their work would form the basis of what is known as non-volatile memory – data storage that can retain information without consuming power. In biotechnology, it is known by a slightly more technical term, recombinase-mediated DNA inversion, after the enzymatic processes used to cut, flip, and recombine DNA within the cell.

The team calls their device a “recombinase addressable data” module, or RAD for short. They reported their findings in the Proceedings of the National Academy of Science.

Stanford bioengineer Drew Endy discusses why he views biology as a technology that can be engineered to the benefit of humankind. He’s working on open source bioengineering tools and using DNA for cellular level data storage.

Reliable and rewritable

The team’s success arose directly from the interdisciplinary environment at Stanford. “We were fortunate to connect early on with Prof. Michele Calos’s group in the Genetics Department.  Her team helped us to select among many natural enzymes for those that had the best chance of being engineered to help us rewrite data,” Endy said.

To make their system work, the team had to control the precise dynamics of two opposing proteins, integrase and excisionase, within the same cell. “Previous work had shown how to flip the genetic sequence – albeit irreversibly – in one direction through the expression of a single enzyme,” Bonnet said, “but we needed to reliably flip the sequence back and forth, over and over, in order to create a fully reusable binary data register, so we needed something different.” 

“The problem is that the proteins do their own thing. If both are active at the same time, or concentrated in the wrong amounts, you get a mess and the individual cells produce random results,” Subsoontorn continued. 

The researchers found it was fairly easy to flip a section of DNA in either direction. “But we discovered time and again that most of our designs failed when the two proteins were used together within the same cell,” said Endy. “Ergo: Three years and 750 tries to get the balance of protein levels right.”

Bonnet has now tested RAD modules in microbes that have doubled more than 100 times and the switch has held. He has likewise switched the latch and watched a cell double 90 times, and set it back. The latch will even store information when the enzymes are not present. In short, RAD works. It is reliable and it is rewritable.

“The Endy group’s one-bit memory device is a further demonstration that a biological engineering approach incorporating directed evolution can be used to build digital behaviors in biological systems,” said Eric Klavins, associate professor at the University of Washington and an expert in synthetic biology. “Furthermore, the system seems to be remarkably robust, which is quite difficult to achieve in synthetic biology.”

Engineering living memories

For Endy and team, the future of computing then becomes not only how fast or how much can be computed, but when and where computations occur and how those computations might impact our understanding of and interaction with life.

“One of the coolest places for computing,” Endy said, “is within biological systems.”

His goal is to go from the single bit he has now to eight bits – or a “byte” – of programmable genetic data storage.

“A byte of programmable data storage within the DNA of living cells would seem an incredibly powerful tool for studying cancer, aging, organismal development, and even the natural environment,” said Endy, brimming with the enthusiasm of a child who has just received his first microscope.

Researchers could count how many times a cell divides, for instance, and that might someday give scientists the ability to turn off cells before they turn cancerous.

“I’m not even really concerned with the ways genetic data storage might be useful down the road, only in creating scalable and reliable biological bits as soon as possible. Then we'll put them in the hands of other scientists to show the world how they might be used,” he said.

To get there, however, science will need many new tools for engineering biology, Endy added, but it will not be easy. “Such systems will likely be 10-50 times more complicated than current state-of-the-art genetic engineering projects,” he said.

For what it is worth, Endy anticipates their second bit of rewritable DNA data will arrive faster than the first and the third faster still, but it will take time.

“We’re probably looking at a decade from when we started to get to a full byte,” he said. “But, by focusing today on tools that improve the engineering cycle at the heart of biotechnology, we’ll help make all future engineering of biology easier, and that will lead us to much more interesting places.”