Rewritable DNA memory shown off

Rewritable DNA memory shown off

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The technique uses two proteins adapted from viruses to "flip" the DNA bits.

Though it is at an early stage, the advance could help pave the way for computing and memory storage within biological systems.

A team reporting in Proceedings of the National Academy of Sciences say the tiny information storehouses may also be used to study cancer and aging.

The team, from Stanford University's bioengineering department, has been trying for three years to fine-tune the biological recipe they use to change the bits' value.

The bits comprise short sections of DNA that can, under the influence of two different proteins, be made to point in one of two directions within the chromosomes of the bacterium E. coli.

The data are then "read out" as the sections were designed to glow green or red when under illumination, depending on their orientation.

The trick was to balance the effects of two competing proteins - integrase and excisionase

The two proteins, integrase and excisionase, were taken from a bacteriophage - a virus that infects bacteria. They are involved in the DNA modification process by which the DNA from a virus is incorporated into that of its host.

The trick was striking a balance between the two counteracting proteins in order to reliably switch the direction of the DNA section that acted as a bit.

After some 750 trials, the team struck on the right recipe of proteins, and now have their sights set on creating a full "byte" - eight bits - of DNA information that can be similarly manipulated.

The work is at the frontier of biological engineering, and senior author of the research Drew Endy said that applications of the approach are yet to come.

"I'm not even really concerned with the ways genetic data storage might be useful down the road, only in creating scalable and reliable biological bits as soon as possible," Dr Endy said.

"Then we'll put them in the hands of other scientists to show the world how they might be used."

As the DNA sections maintained their logical value even as the bacteria doubled 90 times, one clear application would be in using the DNA bits as "reporter" bits on the proliferation of cells, for example in cancerous tissue.

But longer-term integrations of these computational components to achieve computing within biological systems are also on the researchers' minds.

"One of the coolest places for computing is within biological systems," Dr Endy said.

By Clive Cookson, Science Editor January 23, 2013 6:47 pm Financial Times

Genetics may offer the best option for archiving vast amounts of man-made data, according to scientists who have demonstrated a working DNA storage and retrieval system.

A team at the European Bioinformatics Institute in Cambridge developed the new method to meet the huge challenge of storing the deluge of electronic data produced in the digital age. Current technology such as hard drives is expensive and requires an electricity supply, while alternative storage mechanisms, such as magnetic tape and disks, deteriorate over time. Conceived by scientists Nick Goldman and Ewan Birney over beers in a Hamburg pub, EBI’s DNA alternative is both durable and extremely compact.

The EBI team used the chemical letters of a DNA sample – G, A, T and C – to encode the 1s and 0s of several digital recordings. These amounted to almost a megabyte of data, including sound, pictures and text.

The scientists estimate that a cup of DNA, which has evolved over 3bn years to hold genetic information, could store 100m hours of high-definition video.

“We already know that DNA is a robust way to store information because we can extract it from bones of woolly mammoths, which date back tens of thousands of years, and make sense of it,” said Dr Goldman. “It’s also incredibly small, dense and does not need any power for storage, so shipping and keeping it is easy.”

The DNA code was emailed to Agilent, a biotechnology company in California, which turned it into physical DNA molecules and posted the resulting freeze-dried powder back to Cambridge. “The result looks like a tiny piece of dust,” said Emily Leproust of Agilent.

Using a DNA reading machine, EBI was able to reconstruct the original digital data with 100 per cent accuracy. The data included Martin Luther King’s “I have a dream” speech, a photo of EBI’s lab, the text of all Shakespeare’s sonnets and Watson and Crick’s famous research paper on DNA’s “double helix” structure.

Other researchers have previously used DNA to store digital data, including a Harvard University team that encoded a book last year. But Dr Goldman said EBI’s system was the first to correct translation errors between the digital and DNA codes, and can also be scaled up for real archival storage. The results were published in the journal Nature.

Dr Birney and Dr Goldman plan to work towards a commercially viable repository in which a gram of DNA could safely store as much data as a million CDs for more than 10,000 years. Although the practical details are still to be worked out, an archive might store large amounts of data in vials of DNA dust, each with an indexing system encoded in the DNA to help retrieve individual files.