A Document on DNA, documented in DNA…….. DNA as a digital storage device

[Picture Credit- Jyoti Yadav]

We often picture our lives as a movie in the making, and ourselves as the protagonists of the sensational saga. I too, having always had a flair for drama, would often picture my life as an unending take, with the record button on, on some invisible omnipresent recorder. In those moments, the scientist in me, however, would pull me back onto solid ground by making its case with just two very strong arguments against the child like fantasy: the first obviously being, that I wouldn’t find someone to record me at all times. The second being, that even if someone did record my life, I would in no way, be able to store that much data in physical storage devices of the likes of pen drives or hard disks.

Eventually, I would realize that the moments which we so desperately want to hold on to, cannot always be captured and stored in more reliable storage devices other than our own neuronal connections.

DNA-the digital storage device

But, what if I told you, that it would someday be possible to record each and every moment of your entire life?

I know what my response would be: I’ll be going to get flyers titled “The Most Awaited Biopic of the Century” printed.

In all seriousness though, scientists have found a way to stably store an extraordinary amount of data in a very short space. Taking a page from Mother Nature’s most reliable Cookbook, the ingredient these scientists had chosen, was DNA. DNA has always been the true recorded evidence of our lives, storing our genetic constitution, which essentially is the encrypted data of our existence as we know it. Hence, the idea to use DNA to store digital data instead seemed almost poetic. Goldman and his colleagues at EBI (European Bioinformatics Institute), being the believers of poetic justice they are, even encoded the Watson and Crick paper on DNA double helix, amongst other information in DNA. ^[1]

Advantages

What scientists did was, take the digital data in its binary form (0 and 1) and encode that information into a stretch of DNA. ^[3] The nucleotide bases have a theoretical capacity to encode 2 bits per nucleotide. However, another group of scientists, George Church and Sriram Kosuri, ^[7] encoded 1 bit per nucleotide base, coding the bases T, G as 1 and A, C as 0. This binary code helped translate digital information into DNA by synthesizing base after base of any given code. This stretch of synthesized DNA could then be stored anywhere, thanks to the amazingly stable nature of these nucleotide bonds.

Another advantage that the volumetric DNA holds over the planar storage devices, is the immense amount of data it can store. 1 gram of DNA can theoretically store up to around 455 Exabytes of data. ^[3]For contextual purposes, it’s worth mentioning that 1 Exabyte=10⁶ TB. Just so you don’t get dizzy with the sheer magnitude of these numbers, let’s try something simpler.  If we take 1 movie to take up 1 GB space, we may successfully be able to store all the feature films (movies over 40 minutes in length) of the world in just around 1microgram of DNA.(To give you a bit more context, there are approximately 500,000 feature films in the world.^[4])

What would it be like?

Let’s say, you had obsessed over your new born and recorded each and every moment of that little angel’s life, until he entered teenage and thought he had had enough drama in his life and didn’t want it to be recorded anymore. So you finish the recording, and store the video memoirs of your son’s early life encoded in DNA and stow it away in a time capsule entombed in a secret chamber. Then, say, 20 years later, one fine day, you want to take a peep at all the awesome memories you had made back in the day, you go to your storage unit and bring out the DNA. You have it sequenced as you would any normal DNA, with the latest techniques available, within hours (with Ion Torrent you can have your DNA sequenced within just 3-4 hours) or maybe even less in the future. ^{[2, 1, 3]} The sequenced DNA can now be read as the binary code to obtain the initial digital information and lo and behold, you can relive all those wonderful moments.

But the impact of DNA being used as a storage device isn’t simply limited to aid all the TV producers into turning people’s lives into reality shows. It goes much beyond.

Entire genome sequences, genomic data of all organisms, the digital data which today’s world transacts in, everything could be securely stored.

Imagine my surprise when I came to know that the first demonstration of DNA having been used as a storage device was in 1988, wherein the coded information amounted up to 35 bits.

Great! Let’s do it! But …….wait?

If this idea has existed for so long, why have we not yet encoded all the digital data of the world into a layer of DNA sheets?

Of course, the general constraints of economic feasibility apply, but like all technological advancements, it gets better over time.

The other issue, preventing this revolutionary shift in paradigm, is the time taken to synthesise/encode the data into DNA. Extracting isn’t easy either. After Kosuri, many prodigious brains (Goldman, Ewan Birney etc.) had tried to push the limits of DNA storage and collaborators from Microsoft and University of Washington in 2016 had even succeeded in storing 200 MB of data in DNA,^[5] which was a huge jump from the earlier record of 739 KB.^[6] To avoid having to read the complete DNA even if you wanted to extract 1 tiny stretch of information, Olgica Milenkovic and her team made use of PCR and other gene-editing techniques such as the CRISPR-cas 9 to edit in address codes flanking the information.^{[3, 8]} This reduced time for extracting the desired information drastically. However, this theoretical marvel is limited in its practical realization just yet.

What lies ahead?

Up until 2011, there was an estimated 1.8 Zettabytes of digital data in the world ^[2] (1 Zettabyte=1000 Exabytes). This means that this gigantic amount of data is being stored somewhere currently. Imagine, if this data could be stored in DNA, it would simply take around 4 grams worth DNA to accomplish this incredible task. We, though, are still a long way from 1.8 Zettabytes.

However, it never hurt anyone to dream. Just like in the ‘I have a dream’ speech by Martin Luther King, which also happens to be a one of the contents of the 739 KB worth data encoded by Goldman into DNA, “let us not wallow in the valley of despair”. We know today, that DNA as a storage device would be a remarkable achievement for mankind to accomplish. I, for one, am definitely looking forward to be able to document the rest of my life, into the longest running, bestselling Documentary of the century. If not that, at least my grandchildren will have some long hours of television ahead of them.

 

References:

Picture Credit: JYOTI YADAV

Articles/Papers:

1. Nature News: http://www.nature.com/news/how-dna-could-store-all-the-world-s-data-1.20496
2. Quartz: Scientists say all the world’s data can fit on a DNA hard drive the size of a teaspoon –https://qz.com/345640/scientists-say-all-the-worlds-data-can-fit-on-a-dna-hard-drive-the-size-of-a-teaspoon/
3. Science: Next Generation Digital Information Storage in DNA : http://science.sciencemag.org/content/337/6102/1628.full
4. https://storyality.wordpress.com/2012/12/17/storyality-19-how-many-movies-are-there/
5. UWToday :Interview with Luis Ceze – http://www.washington.edu/news/2016/07/07/uw-microsoft-researchers-break-record-for-dna-data-storage/
6. Goldman, N. et al. Nature 494, 77–80 (2013).
7. Church, G. M., Gao, Y. & Kosuri, S. Science 337, 1628 (2012).
8. Hossein Tabatabaei Yazdi, S. M., Yuan, Y., Ma, J., Zhao, H. & Milenkovic, O. Sci. Rep. 5, 14138 (2015).

(The above mentioned papers’ abstracts can also be found in PubMed)