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Novel system stores, retrieves digital images in DNA

18 Apr 2016

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The team from the Molecular Information Systems Lab housed in the UW Electrical Engineering Building, in close collaboration with Microsoft Research, is developing a DNA-based storage system that it expects could address the world's needs for archival storage.

First, the researchers developed a novel approach to convert the long strings of ones and zeroes in digital data into the four basic building blocks of DNA sequences: adenine, guanine, cytosine and thymine.

"How you go from ones and zeroes to As, Gs, Cs and Ts really matters because if you use a smart approach, you can make it very dense and you don't get a lot of errors," said Seelig, a UW associate professor of electrical engineering and of computer science and engineering. "If you do it wrong, you get a lot of mistakes."

The digital data is chopped into pieces and stored by synthesising a massive number of tiny DNA molecules, which can be dehydrated or otherwise preserved for long-term storage.

The UW and Microsoft researchers are one of two teams nationwide that have also demonstrated the ability to perform "random access" to identify and retrieve the correct sequences from this large pool of random DNA molecules, which is a task similar to reassembling one chapter of a story from a library of torn books.

Molecular Information Systems Lab research team

Figure 3: The Molecular Information Systems Lab research team: Front (left to right): Bichlien Nguyen, Lee Organick, Hsing-Yeh Parker, Siena Dumas Ang, Chris Takahashi. Back (left to right): James Bornholt, Yuan-Jyue Chen, Georg Seelig, Randolph Lopez, Luis Ceze, Karin Strauss. Not pictured: Doug Carmean, Rob Carlson, Krittika d'Silva. (Tara Brown Photography/University of Washington)

To access the stored data later, the researchers also encode the equivalent of zip codes and street addresses into the DNA sequences. Using polymerase chain reaction (PCR) techniques, commonly used in molecular biology, helps them more easily identify the zip codes they are looking for. Using DNA sequencing techniques, the researchers can then "read" the data and convert them back to a video, image or document file by using the street addresses to reorder the data.

Currently, the largest barrier to viable DNA storage is the cost and efficiency with which DNA can be synthesised (or manufactured) and sequenced (or read) on a large scale. But researchers say there's no technical barrier to achieving those gains if the right incentives are in place.

Advances in DNA storage rely on techniques pioneered by the biotechnology industry, but also incorporate new expertise. The team's encoding approach, for instance, borrows from error correction schemes commonly used in computer memory, which hadn't been applied to DNA.

"This is an example where we're borrowing something from nature, DNA, to store information. But we're using something we know from computers, how to correct memory errors, and applying that back to nature," said Ceze.

"This multidisciplinary approach is what makes this project exciting. We are drawing from a diverse set of disciplines to push the boundaries of what can be done with DNA. And, as a result, creating a storage system with unprecedented density and durability," said Strauss.

The research was funded by Microsoft Research, the National Science Foundation and the David Notkin Endowed Graduate Fellowship.


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