Scientists Write ‘Hello World’ in Bacterial DNA With Electricity and CRISPR

The new system shows that it’s possible to encode information directly into bacteria

E. coli bacteria shown under a microscope at 6836X magnification
By storing data in bacteria like E. coli, the data is protected by the same machinery that the cell uses to protect its own DNA. Janice Haney Carr/CDC

One of the first things a budding software engineer learns is how to teach the computer to return the phrase, “Hello world!” So when experimenting with a new way to encode information into bacteria, that was the first message that scientists studying DNA data storage tried out.

A study published on January 11 in the journal Nature Chemical Biology details how the researchers led by Columbia University systems biologist Harris Wang used electricity and the DNA editing tool CRISPR to write “hello world!” into living bacteria’s DNA.

Genetic material like DNA is a potentially useful way to store data because it can store a lot of information in a small space. (For instance, ten full-length digital movies in the space of a grain of salt, Robert F. Service reports for Science magazine.) Because DNA is integral to biology and bioengineering, the storage technology is unlikely to become outdated, John Timmer reports for Ars Technica.

“They are a very long way from having a working system that replaces our digital devices,” says EMBL-European Bioinformatics Institute senior scientist Nick Goldman to New Scientist’s Layla Liverpool. “But it’s a little step along the way to something that might do that.”

Computer code comes down to long strings of ones and zeros, and each digit is called a “bit” of information. A strand of DNA is a chain of four basic chemicals—abbreviated as A, C, G and T—that can be edited using bioengineering tools like CRISPR. In the new study, a change to a genetic sequence translated to a “one,” while no change translated to a “zero.” Any combination of six bacterial bits referred to a letter, number, space or punctuation mark, so the researchers called it a “byte.” (In a computer, a byte is made of eight bits.)

Using bacterial bytes, the scientists created the 12-character message “hello world!”

The electrical editing technique used in the new study builds on previous work led by Wang. In a 2017 study, researchers showed that they could make bacteria that use CRISPR to create a note in their DNA when they encounter the sugar fructose, per Science. The sugar sparked a series of events in each bacterium. First, the cell created a bunch of small rings of DNA, and that prompted CRISPR to snip the rings and save them in the bacterium’s own DNA.

In the new study, the researchers swapped sugar for electricity. Electricity changes one of the chemicals floating in the solution around the bacteria. The bacteria can sense the chemical change and set off a similar chain of events, resulting in a new chunk of code inserted into their DNA. By flipping the electricity on and off, the scientists could change the bacterial DNA code in precise locations.

The entire “hello world!” message didn’t fit in a single bacterium’s genome. Instead, the researchers created eight varieties of bacteria with three bits of information each. Pairs of bacteria strains provided the six bits necessary to create one letter or character. With 12 pairs of bacteria strains, each labeled with the order they should be read in, the scientists created the well-known message.

The system is still in its early days, Wang tells Science magazine. “We’re not going to compete with the current memory storage systems,” he adds.

But with more research, DNA data storage could have several benefits, Wang says. For one thing, genetic code is unlikely to become an outdated storage technology—and research is underway to make it ever-easier to edit and read DNA. Plus, writing data directly into living bacteria means the DNA is protected by organism and that the data will be copied into each new bacterium as the cells divide.

Wang says DNA inside of living bacteria could be a stable way to store data for medium to long-term storage.

“What you’re offering by putting it inside the cell is that the DNA is protected by the cell and the machinery that the cell has to protect its DNA,” says Wang to New Scientist.

The researchers even mixed their batches of data-carrying bacteria with potting soil and then recovered the message after a week. They estimate that the bacteria could hold onto their data for about 80 generations, per Ars Technica. However, the longer the bacteria spend copying their DNA, the more chance they have to introduce a mistake into the bits of information. That could confuse the message.

Harvard University biological engineer George Church tells New Scientist, “This field is progressing exponentially and this paper is a great example.”

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