Scientists “program” living bacteria to store data | Science

By Robert F. ServiceJan. 11, 2021 at 13:35

Hard drives and optical drives store gigabits of digital data with the push of a button. But these technologies – like magnetic tapes and floppy disk drives before them – are likely to become obsolete and unreadable when they are outdated by new technologies. Now, researchers have developed a way to electronically write data into the DNA of living bacteria, a storage option unlikely to become obsolete anytime soon.

“This is a very nice step” that could one day stimulate business development, says Seth Shipman, a bioengineer at the Gladstone Institutes and the University of California at San Francisco, who was not involved in the new work. He notes, however, that real-world applications are still a long way off.

DNA is attractive for data storage for several reasons. First, it’s over 1,000 times denser than even the most compact hard drives, allowing it to store the equivalent of 10 full-length digital movies in the volume of a grain of salt. And since DNA is at the heart of biology, the technologies to read and write it are expected to become cheaper and more powerful over time.

Storing data in DNA is not a new idea. To do this, researchers typically convert the numeric string of ones and zeros in a data file to combinations of the four bases of the molecule: adenine, guanine, cytosine, and thymine. They then use a DNA synthesizer to write this code into DNA. But the precision of DNA synthesis decreases the longer the code, so researchers usually break their file into chunks and write them down as DNA snippets between 200 and 300 bases in length. Each code snippet is given an index to identify its location in the file, and DNA sequencers then read the snippets to reassemble the file. But the technology is expensive, costing up to $ 3,500 to synthesize 1 megabit of information. And the DNA vials in which information is stored can degrade over time.

To create a durable, easier-to-code medium, researchers are now working to write data into the DNA of living organisms, which copy and pass their genes on to the next generation. In 2017, a team led by Harris Wang, a systems biologist at Columbia University, used the CRISPR gene editing system to recognize a biological signal, such as the presence of sugar fructose. When researchers added fructose to Escherichia coli cells, gene expression increased in ring-shaped pieces of DNA called plasmids.

Then, the CRISPR components – which evolved to defend bacteria against viral invaders – cut the overexpressing plasmid into pieces and lodged part of it in a specific section of the bacteria’s DNA that “remembers” the viral invaders. previous ones. The genetic bit inserted represented a digital bit. If the fructose signal was absent, the bacteria instead stored a random bit of DNA, representing a numeric zero. Sequence the E. coli DNA then revealed whether the bacteria were exposed to fructose, via one or zero.

But since this setup could only store a few bits of data, Wang and his colleagues replaced the fructose recognition system with one that could encode longer strings of information: an electronic input. They inserted a series of genes into E. coli which allowed cells to increase plasmid expression in response to an electrical voltage. As with the fructose configuration, an increase in expression caused the digital to be stored in the DNA of the bacteria. To read ones and zeros, the researchers simply sequenced the bacteria.

Using this approach, Wang and his colleagues electrically encoded up to 72 bits of data, to write the message “Hello world!” they report today in Nature Chemical Biology. They also showed that they can add E. coli with their message to a mixture of normal soil microbes – then sequence the mixture to retrieve their stored message.

Wang says that data storage in living organisms is still in its infancy. “We’re not going to compete with current memory storage systems,” he says. Researchers will also need to find ways to prevent degradation of their messages as bacteria mutate during replication. But at least for now, it could give James Bond a new tool for hiding posts in plain sight.