Researchers Use DNA to Store and Retrieve Digital Movie

By John Russell

July 18, 2017

From abacus to pencil and paper to semiconductor chips, the technology of computing has always been an ever-changing target. The human brain is probably the computer we use most (hopefully) and understand least. This month in Nature, a group of distinguished DNA researchers report storing and then retrieving a digital movie, a rather famous one at that, in DNA.

Using a DNA editing technique borrowed from nature (CRISPR-Cas), the researchers developed a code for pixels depicting shades of gray using the DNA’s four letters, converted the images, frame by frame, into that code, and coaxed the CRISPR editing machinery to insert the coded DNA into bacteria who did what bacteria do – replicate. The researchers then extracted DNA from the growing population of bacteria, sequenced the newly-generated DNA, decoded it, and reproduced the film clip.

Their paper – “CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria” – is fascinating on many levels. Not only did the researchers succeed in storing the images in reproducing bacteria, they also uncovered more details of the CRISPR process including ferreting out efficiency factors, and pointed, however distantly, to prospects for a bacteria-DNA-based recording system that mighty be used as a “black box flight recorder” for cells.

There are several good accounts of the work including one in The New York Times (Who Needs Hard Drives? Scientists Store Film Clip in DNA written by Gina Kolata) and another from the National Institutes of Health (Scientists replay movie encoded in DNA). The researchers started working with an image of the hand and progressed to capturing the 1878 film by British photographer Eadweard Muybridge showing horses do indeed take flight, briefly, when running and all the hooves are aloft.

 

The researchers – Seth L. ShipmanJeff NivalaJeffrey D. Macklis, and George M. Church – are all from Harvard and very familiar to the genomics research community. In the paper they understandably concentrate on the CRISPR technology, which is widely being researched, rather than on applications. That said the NYT article notes:

“When something goes wrong, when a person gets ill, doctors might extract the bacteria and play back the record. It would be, said Dr. Church, analogous to the black boxes carried by airplanes whose data is used in the event of a crash.

At the moment, all that is “the other side of science fiction,” said Ewan Birney, director of the European Bioinformatics Institute and a member of the group that put Shakespeare’s sonnets in DNA. “Storing information in DNA is this side of science fiction.” Also in the NYT Article, Birney said, “People’s intuition is tremendously poor about just how small DNA molecules are and how much information can be packed into them.”

Storing information in DNA isn’t new. (That’s sort of what it does without regard to traditional computing technology.) It has been used to store computer data (zeros and ones) and even used for certain massively parallel computations before now. Indeed, researchers had already used the CRISPR system to store sequences in bacteria.

The new work yet another step forward. A good encapsulation of the work is provided in the paper’s abstract, excerpted below.

“DNA is an excellent medium for archiving data. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1–Cas2 integrase, the CRISPR–Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity. When harnessed, this system has the potential to write arbitrary information into the genome. Here we use the CRISPR–Cas system to encode the pixel values of black and white images and a short movie into the genomes of a population of living bacteria. In doing so, we push the technical limits of this information storage system and optimize strategies to minimize those limitations.”

Link to New York Times article: https://www.nytimes.com/2017/07/12/science/film-clip-stored-in-dna.html?_r=0

Link to NIH account: https://www.nih.gov/news-events/news-releases/scientists-replay-movie-encoded-dna

Link to video: https://www.youtube.com/watch?v=gK3dcjBaJyo

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