New Research Could Enable Direct Data Transfer From Computers to Living Cells

News Highlights: New Research Could Enable Direct Data Transfer From Computers to Living Cells.

As the modern world produces more and more data, researchers are trying to find new ways to store everything. DNA holds great promise as an extremely dense and stable storage medium, and now, with a new approach, we could write digital data directly into the genome of living cells.

Attempts to repurpose nature’s built-in memory technology are not new, but over the past decade the approach has received renewed interest and made significant progress. That’s powered by an explosion of data that shows no signs of slowing down. B.year 2025It is estimated that 463 exabytes will be created worldwide every day.

Storing all this data could quickly become impractical with conventional silicon technology, but DNA could hold the answer. For starters, the information density is millions of times better than conventional hard drives, with one gram of DNA you can do store up to 215 million gigabytes.

It is also very stable when stored properly. In 2017, researchers were able to extract the entire genome of an extinct horse species 700,000 years ago. Learning to store and manipulate data in the same language as nature could also open the door to many new opportunities in biotechnology.

The main complication is finding a way to link the digital world of computers and data with the biochemical world of genetics. Currently this relies on synthesizing DNA in the laboratory and although costs are falling rapidly, it is still a complicated and expensive affair. Once synthesized, the sequences must be carefully stored in vitro until ready to be used again, or they can be cleaved into living cells using CRISPR gene editing technology.

Now researchers at Columbia University have demonstrated a new approach that can convert digital electronic signals directly into genetic data stored in the genome of living cells. That could lead to a myriad of uses for both data storage and beyond, says Harris Wang, who led the study published in Nature Chemical Biology.

“Imagine having mobile hard drives that can do real-time computation and physical reconfiguration,” he wrote in an email to Singularity Hub. “We think the first step is to be able to code binary data directly into cells, without having to do in vitro DNA synthesis.

“This is arguably the most difficult part of all approaches to DNA storage. If you can get the cells to talk directly to a computer and connect the DNA-based memory system to a silicon-based memory system, then there are many possibilities in the future. “

The work builds on a CRISPR-based cellular recorder that Wang had previously designed for E. coli bacteria, which detects the presence of certain DNA sequences in the cell and records this signal in the genome of the organism.

The system includes a DNA-based “detection module” that produces increased levels of a “trigger sequence” in response to specific biological signals. These sequences are included in the recorder’s “DNA ticker tape” to document the signal.

In this new work, Wang and colleagues modified the detection module to work with a biosensor developed by another team that responds to electrical signals. Large populations of the bacteria were then placed in a device made up of a series of chambers, allowing the team to expose them to electrical signals.

When they applied a voltage, the levels of the trigger sequence were increased and included in the DNA ticker tape. Racks with a high percentage of trigger sequences were used to represent a binary “1” and their absence a “0”, allowing the researchers to encode digital information directly into the genome of the bacterium.

The amount of data that a single cell can hold is quite small, only three bits. So the researchers came up with a way to encode 24 separate populations of bacteria with different 3-bit chunks of data at the same time for a total of 72 bits. They used this to send the message “hello world!” in the bacteria, and showed that by sequencing the combined population and using a specially designed classifier, they were able to find the message with 98 percent accuracy.

Clearly, 72 bits is far from the storage capacity of modern hard drives, and even cell-free DNA storage techniques now deal in gigabytes. But Wang says this is just a proof of concept, and there are plenty of options to measure the efficiency of the CRISPR machine that powers the recorder, the length of the ticker tape that can be reliably read, and even the electronics that are used. used to encode data.

“All of these things will improve in the years to come and I absolutely think it is possible to scale up the system’s capacity tremendously by several orders of magnitude, even in the short term,” he said.

And storing data in cells instead of in vitro has some significant advantages, he added. For one thing, it is much cheaper to amplify or duplicate the data because you can simply grow more cells than you have to perform complex artificial DNA synthesis. In the paper, the team showed that the recorded information remained stable for 60 to 80 generations of cells.

Cells also already have an inherent ability to protect DNA against environmental influences. They demonstrated this by adding the E. coli cells to non-sterilized potting soil and then reliably retrieving a 52-bit message by sequencing the combined soil microbial community.

Perhaps most exciting of all is the possibility to link this data record to emerging biocomputing research. Researchers have already begun to design the DNA of cells to carry it out logical and memory operations, but creating a direct interface between silicon and genomes could greatly speed up our ability to reprogram cells for our own devices.

Image credit: Ricarda Mölck from Pixabay

Via: singularityhub.com

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