Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

Abstract

The shift to digital systems for the creation, transmission and storage of information has led to increasing complexity in archiving, requiring active, ongoing maintenance of the digital media. DNA is an attractive target for information storage 1 because of its capacity for high density information encoding, longevity under easily-achieved conditions 2-4 and proven track record as an information bearer. Previous DNA-based information storage approaches have encoded only trivial amounts of information 5-7 or were not amenable to scaling-up 8 , and used no robust errorcorrection and lacked examination of their cost-efficiency for large-scale information archival 9 . Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kB of hard disk storage and with an estimated Shannon information 10 of 5.2 × 10 6 bits into a DNA code, synthesised this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-storage scheme scales far beyond current global information volumes. These results demonstrate DNA-storage to be a realistic technology for large-scale digital archiving that may already be cost-effective for low access, multi-century-long archiving tasks. Within a decade, as costs fall rapidly under realistic scenarios for technological advances, it may be cost-effective for sub-50-year archival.Although techniques for manipulating, storing and copying large amounts of DNA have been established for many years [11][12][13] , these rely on the availability of initial copies of the DNA molecule to be processed, and one of the main challenges for practical information storage in DNA is the difficulty of synthesising long sequences of DNA de novo to an exactly-specified design. Instead, we developed an in vitro approach that represents the information being stored as a hypothetical long DNA molecule and encodes this using shorter DNA fragments. A similar approach was proposed by Church et al. 9 in a report * To whom correspondence should be addressed; goldman@ebi.ac.uk. SupplementaryInformation is provided as a number of separate files accompanying this document.Author Contributions N.G. and E.B. conceived and planned the project and devised the information encoding methods. P.B. advised on NGS protocols, prepared the DNA library and managed the sequencing process. S.C. and E.M.L. provided custom oligonucleotides. N.G. wrote the software for encoding and decoding information into/from DNA and analysed the data. N.G., E.B., C.D. and B.S. modelled the scaling properties of DNA-storage. N.G. wrote the paper with discussions and contributions from all other authors. N.G. and C.D. produced the figures.Author Information Data are available online at http://www.ebi.ac.uk/goldman-srv/DNA-storage and in the Sequence Read Archive (SRA) with accession number ERP002040 (to be confirmed). Correspondence and requests for materials should be addressed to N.G. (goldman@ebi.ac.uk). Co...

Effects of prolonged media usage and long-term planning on archival systems

“…However, these represent the case where upfront costs are extremely high while preservation costs are low [30].…”

“…Though these devices do not yet exist, there are multiple efforts in progress to bring a specialized archival device to the market [8,17,30,42,43]. For all these media, initial investment is high (expensive media and readers/writers), but they have high reliability, an extremely long life, and low operational costs in comparison with traditional archiving media (hard disk, tape, and Blu-ray).…”

From Hard Drives to Flash Drives to DNA Drives

“…Because storing information in DNA is easier than reading it, they suggest that DNA may be the ideal method for keeping information that does not need to be frequently accessed and thus ideal for libraries and government records. Please see the article in Nature by Goldman et al 9 *In this situation, PCR is easy to use because the makeup of the DNA strand that needs to be amplified is known. Primers that start the reaction can be easily chosen, and specific zones may be amplified and then read.…”

A vision for ubiquitous sequencing

“…Moving forward, artificial DNA labels can create an edible data structure that includes the type of food, producer, lot number, nutrient information, and presence of known allergens or simply encode a URL to a webpage that contains this information. The length of the DNA label can be relatively short, as recent DNA-specific encoding schemes have proposed methods to robustly code 1.6 bits of information in each DNA base pair (Goldman et al 2013). DNA-labeled products can establish an inexpensive method to identify ingredients and sources of processed food, tracking authenticity, and revealing hidden traces of allergens.…”