DNA digital data storage
DNA digital data storage is defined as the process of encoding and decoding binary data to and from synthesized DNA strands. DNA molecules are genetic blueprints for living cells and organisms. Although DNA data storage became a popular topic in the 21st century, it is not a modern-day idea. Its origins date back to 1964-65 when Mikhail Neiman, a Soviet physicist, published his works in the journal Radiotehnika. Neiman wrote about general considerations regarding the possibility of recording, storage, and retrieval of information on DNA molecules. The physicist explained he had the idea from an interview with Norbert Wiener, an American cybernetic, mathematician, and philosopher, published in 1964.
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Among early examples of DNA data storage, in 2007 a device was created at the University of Arizona using addressing molecules to encode mismatch sites within a DNA strand. These mismatches were then able to be read out by performing a restriction digest, thereby recovering the data.
An improved system was reported in the journal Nature in January 2013, in an article led by researchers from the European Bioinformatics Institute (EBI) and submitted at around the same time as the paper of Church and colleagues. Over five million bits of data, were stored, retrieved, and reproduced. All the DNA files reproduced the information between 99.99% and 100% accuracy. The main innovations in this research were the use of an error-correcting encoding scheme to ensure the extremely low data-loss rate, as well as the idea of encoding the data in a series of overlapping short oligonucleotides identifiable through a sequence-based indexing scheme. Also, the sequences of the individual strands of DNA overlapped in such a way that each region of data was repeated four times to avoid errors. Two of these four strands were constructed backwards, also with the goal of eliminating errors. The costs per megabyte were estimated at $12,400 to encode data and $220 for retrieval. However, it was noted that the exponential decrease in DNA synthesis and sequencing costs, if it continues into the future, should make the technology cost-effective for long-term data storage within about ten years. A software called DNACloud was also developed was developed by Gupta and co-workers to encode computer files to their DNA representation. It implements a memory efficiency version of the algorithm proposed by Goldman et al. to encode (and decode) data to DNA (.dnac files).
The long-term stability of data encoded in DNA was reported in February 2015, in an article by researchers from ETH Zurich. The team added redundancy via Reed–Solomon error correction coding and by encapsulating the DNA within silica glass spheres via Sol-gel chemistry.
In March 2017, Yaniv Erlich and Dina Zielinski of Columbia University and the New York Genome Center published a method known as DNA Fountain that stored data at a density of 215 petabytes per gram of DNA. The technique approaches the Shannon capacity of DNA storage, achieving 85% of the theoretical limit. The method was not ready for large-scale use, as it costs $7000 to synthesize 2 megabytes of data and another $2000 to read it.
In March 2018, University of Washington and Microsoft published results demonstrating storage and retrieval of approximately 200MB of data. The research also proposed and evaluated a method for random access of data items stored in DNA. In March 2019, the same team announced they have demonstrated a fully automated system to encode and decode data in DNA.
Research published by Eurecom and Imperial College in January 2019, demonstrated the ability to store structured data in synthetic DNA. The research showed how to encode structured or, more specifically, relational data in synthetic DNA and also demonstrated how to perform data processing operations (similar to SQL) directly on the DNA as chemical processes.
Davos Bitcoin Challenge
On January 21, 2015, Nick Goldman from the European Bioinformatics Institute (EBI), one of the original authors of the 2013 Nature paper, announced the Davos Bitcoin Challenge at the World Economic Forum annual meeting in Davos. During his presentation, DNA-tubes were handed out to the audience with the message that each tube contained the private key of exactly one bitcoin, all coded in DNA. The first one to sequence and decode the DNA could claim the bitcoin and win the challenge. The challenge was set for three years and would close if nobody claimed the prize before January 21, 2018.
Almost three years later on January 19, 2018, the EBI announced that a Belgian PhD student, Sander Wuyts of the University of Antwerp and Vrije Universiteit Brussel, was the first one to complete the challenge. Next to the instructions on how to claim the bitcoin (stored as a plain text and pdf file), the logo of the EBI, the logo of the company that printed the DNA (CustomArray) and a sketch of James Joyce were retrieved from the DNA.
- DNA computing
- DNA nanotechnology
- Natural computing
- Plant-based digital data storage
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