Scientists embedded images in the genomes of bacteria to test the limits of DNA storage.
DNA data storage is a big deal. Partly, it’s because we’re based on DNA, and any research into manipulation of that molecule will pay dividends for medicine and biology in general — but in part, it’s also because the world’s most wealthy and powerful corporations are getting discouraged at cost estimates for data storage in the future. Facebook, Apple, Google, the US government, and more are all making astounding investments in storage (“exabyte” is the buzzword now). But even these mega-projects can only put off the inevitable for so long; we are simply producing too much data for magnetic storage to keep up, without a major unforeseen shift in the technology.
The promise of using DNA as storage means you could conceivably save every photo you’ve ever taken, your entire iTunes library, and all 839 episodes of Doctor Who in a tiny molecule invisible to the naked eye—with plenty of room to spare.
But what if you could keep all that digital information on you at all times, even embedded in your skin? Harvard University geneticist George Church and his team think it might be possible one day.
They’ve used the gene-editing system CRISPR to insert a short animated image, or GIF, into the genomes of living Escherichia coli bacteria. The researchers converted the individual pixels of each image into nucleotides, the building blocks of DNA.
They delivered the GIF into the living bacteria in the form of five frames: images of a galloping horse and rider, taken by English photographer Eadweard Muybridge, who produced the first stop-motion photographs in the 1870s. The researchers were then able to retrieve the data by sequencing the bacterial DNA. They reconstructed the movie with 90 percent accuracy by reading the pixel nucleotide code.
The method, detailed in Nature, is specific to bacteria, but Yaniv Erlich, a computer scientist and biologist at Columbia University who was not involved in the study, says it represents a scalable way to host information in living cells that could eventually be used in human cells.
The modern world is increasingly generating massive amounts of digital data, and scientists see DNA as a compact and enduring way of storing that information. After all, DNA from thousands or even hundreds of thousands of years ago can still be extracted and sequenced in a lab.
DNA’s key special attribute it data storage density: how much information can DNA fit into a given unit volume? The NSA’s largest, most notorious data-center is an enormous, sprawling complex full of networked racks of magnetic storage drives — but according to some estimates, DNA could take the volume of data contained in about a hundred industrial data centers and store it in a space roughly the size of a shoe box.
So far, much of the research into using DNA for storage has involved synthetic DNA made by scientists. And this GIF—only 36 by 26 pixels in size—represents a relatively small amount of information compared to what scientists have so far been able to encode in synthetic DNA. It’s more challenging to upload information into living cells than synthesized DNA, though, because live cells are constantly moving, changing, dividing, and dying off.
Erlich says one benefit of hosting data in living cells like bacteria is better protection. For example, some bacteria still thrive after nuclear explosions, radiation exposure, or extremely high temperatures.
Beyond just storing data, Seth Shipman, a scientist working in Church’s lab at Harvard who led the study, says he wants to use the technique to make “living sensors” that can record what is happening inside a cell or in its environment.
“What we really want to make are cells that encode biological or environmental information about what’s going on within them and around them,” Shipman says.
Though this technique won’t be used anytime soon to load large quantities of data into your body, it could prove to be a valuable research tool. One possible use would be to record the molecular events that drive the evolution of cell types, such as the formation of neurons during brain development.
Shipman says you could deposit these bacterial hard drives in the body or anywhere in the world, record something you might be interested in, collect the bacteria, and sequence the DNA to see what information has been picked up along the way.
However, storing information in DNA differs from computer RAM in some pretty significant ways. Most notable is speed; part of what makes RAM RAM is that its easy-access system is also a quick access system, allowing it to hold data the computer might need at an instant’s notice, and make it available on those timescales.
On the other hand, DNA is significantly harder and slower to read than conventional computer transistors, meaning in terms of access speed it’s actually less RAM-like than your average computer SSD or spinning magnetic hard-drive.
That’s because the incredible abilities of evolution’s data storage solution were tailored to evolution’s unique needs, and those needs don’t necessarily include performing thousands of “reads” per second. Regular, cellular DNA data storage has to untangle the complex chromatin structure of stable DNA, then unwind the DNA double helix itself, make a copy of the sequence of interest, then zip everything right back up the way it was — it takes a while
Source : Nature
Images credit: Images courtesy of Seth Shipman | Harvard University