EMBL-EBI researchers make DNA storage a reality

28 01 2013

Researchers at the EMBL-European Bioinformatics Institute (EMBL-EBI) have created a way to store data in the form of DNA – a material that lasts for tens of thousands of years. The new method, published in the journal Nature, makes it possible to store at least 100 million hours of high-definition video in about a cup of DNA.

Dr Nick Goldman of EMBL-EBI, looking at synthesized DNA in a phial. Photo credit: EMBL Photolab.

Dr Nick Goldman of EMBL-EBI, looking at synthesized DNA in a phial. Photo credit: EMBL Photolab.

There is a lot of digital information in the world – about three zettabytes’ worth (that’s 3000 billion billion bytes) – and the constant influx of new digital content poses a real challenge for archivists. Hard disks are expensive and require a constant supply of electricity, while even the best ‘no-power’ archiving materials such as magnetic tape degrade within a decade. This is a growing problem in the life sciences, where massive volumes of data – including DNA sequences – make up the fabric of the scientific record.

 

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

 

Reading DNA is fairly straightforward, but writing it has until now been a major hurdle to making DNA storage a reality. There are two challenges: First, using current methods it is only possible to manufacture DNA in short strings. Secondly, both writing and reading DNA are prone to errors, particularly when the same DNA letter is repeated. Nick and co-author Ewan Birney, Associate Director of EMBL-EBI, set out to create a code that overcomes both problems.

 

“We knew we needed to make a code using only short strings of DNA, and to do it in such a way that creating a run of the same letter would be impossible. So we figured, let’s break up the code into lots of overlapping fragments going in both directions, with indexing information showing where each fragment belongs in the overall code, and make a coding scheme that doesn’t allow repeats. That way, you would have to have the same error on four different fragments for it to fail – and that would be very rare.”

 

The new method requires synthesizing DNA from the encoded information: enter Agilent Technologies, Inc, a California-based company that volunteered its services. Ewan and Nick sent them encoded versions of: an .mp3 of Martin Luther King’s speech, “I Have a Dream”; a .jpg photo of EMBL-EBI; a .pdf of Watson and Crick’s seminal paper, “Molecular structure of nucleic acids”; a .txt file of all of Shakespeare’s sonnets; and a file that describes the encoding.

 

“We downloaded the files from the Web and used them to synthesise hundreds of thousands of pieces of DNA – the result looks like a tiny piece of dust,” explains Emily Leproust of Agilent. Agilent mailed the sample to EMBL-EBI, where the researchers were able to sequence the DNA and decode the files without errors.

 

“We’ve created a code that’s error tolerant using a molecular form we know will last in the right conditions for 10 000 years, or possibly longer,” says Nick. “As long as someone knows what the code is, you will be able to read it back if you have a machine that can read DNA.”

 

Although there are many practical aspects to solve, the inherent density and longevity of DNA makes it an attractive storage medium. The next step for the researchers is to perfect the coding scheme and explore practical aspects, paving the way for a commercially viable DNAstorage model.

 

Source Article: Toward practical high-capacity low-maintenance storage of digital information in synthesised DNA. Nature; DOI: 10.1038/nature11875. Published online 23 January 2013.

 

About EMBL-EBI

The EMBL-European Bioinformatics Institute (EBI) is part of the European Molecular Biology Laboratory (EMBL) and is located on the Wellcome Trust Genome Campus in Hinxton near Cambridge, UK. The EBI grew out of EMBL’s pioneering work in providing public biological databases to the research community. It hosts some of the world’s most important collections of biological data, including DNA sequences (ENA),protein sequences (UniProt), the genomes of animals and plants, three-dimensional molecular structures, data from gene expression experimentsprotein-protein interactions and reactions and pathways. EMBl-EBI’s many research groups are continually developing new tools to support the biocomputing community. EMBL-EBI plays an important role in the 1000 Genomes Project and coordinates ELIXIR, the emerging research infrastructure for life science data in Europe. www.ebi.ac.uk

 

About EMBL

The European Molecular Biology Laboratory is a basic research institute funded by public research monies from 20 member states (Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom) and associate member state Australia. Research at EMBL is conducted by approximately 85 independent groups covering the spectrum of molecular biology. The Laboratory has five units: the main Laboratory in Heidelberg, and outstations in Hinxton (EMBL-EBI), Grenoble, Hamburg, and Monterotondo (near Rome). The cornerstones of EMBL’s mission are: to perform basic research in molecular biology; to train scientists, students and visitors at all levels; to offer vital services to scientists in the member states; to develop new instruments and methods in the life sciences and to actively engage in technology transfer activities. Around 190 students are enrolled in EMBL’s International PhD programme. Additionally, the Laboratory offers a platform for dialogue with the general public through various science communication activities such as lecture series, visitor programmes and the dissemination of scientific achievements.

 

ebi.ac.uk [en línea] Hinxton (UK): ebi.ac.uk, 28 de enero de 2013 [ref. 23 de enero de 2013] Disponible en Internet: http://www.ebi.ac.uk/Information/News/press-releases/press-release-01232013-DNA_storage.html

 

 


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