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Lots of thoughts on this. It's a really interesting area, and the paper doesn't gloss over the challenges. Important caveat right at the top though: "Progress
by entee 10y ago
Lots of thoughts on this. It's a really interesting area, and the paper doesn't gloss over the challenges. Important caveat right at the top though:
"Progress in DNA storage has been rapid: in 1999, the state- of-the-art in DNA-based storage was encoding and recovering a 23 character message [7]; in 2013, researchers successfully recovered a 739 kB message"
That's not a terribly large message. The difficulty of synthesizing large tracts of DNA reliably is a major bottleneck. It was a huge accomplishment when a full, relatively small genome (1x10^6 bases, humans are ~3x10^9) was synthesized in 2010 [1]. Granted for storage purposes, fully synthetic DNA may not be required, but it's still hard to assemble pre-existing DNA into very large constructs.
Sequencing the message itself is on its surface not too hard, I think a current-gen high throughput sequencer can read up to 2 trillion bases in a single run. It's not super fast (1-2d turnaround), or random access though, and the random access nature is one of the innovations in the paper. Still some sequencing approaches are a little quicker it should be possible to leverage modern sequencing tech to make this suitable for archive-level purposes.
Other thoughts on the paper: they have a cool take on how to avoid errors (Huffman code), and take advantage of highly parallel DNA synthesis approaches by properly segmenting the data they want to store into useful chunks. You still have to avoid errors in synthesis and replication for DNA storage, and they take steps to mitigate risk there.
Anyway, cool paper, if anyone knows more about the state of the art of long-DNA strand synthesis I'd love to hear about it!
[1]: http://science.sciencemag.org/content/329/5987/52 http://science.sciencemag.org/content/329/5987/52
- ChuckMcM 10y agoMicrosoft was reporting storing a movie and operating system and some other stuff : http://thehackernews.com/2017/03/dna-data-storage.html http://thehackernews.com/2017/03/dna-data-storage.html
- entee 10y agovery cool, didn't know about this, thanks!
- patall 10y agoI would not be so sure whether it is really necessary or advantagious to have very long DNA strands as information medium. Long DNA strands are very hard to handle under many conditions (we only got into the range of 1 million bp reads last week, it probably wont be in the near future that we get some at a reasonable fraction) and provide limitations like increased replication timing (Polymerase work in the order of 1kbp per minute, else you would need many origins of replication). Shorter fragments (~1kbp) are much easier to handle and sequence and can be reached by almost random access through primers attached to fishing beads.
- entee 10y agoVery much agreed, but then you're stuck with ensuring all the pieces of DNA are faithfully transmitted through the next replication. Essentially you're proposing having tons of 1kbp chromosomes, so you're shifting the problem from having a hard to handle piece of DNA (the longer the harder it is to have it not sheer/break/otherwise get damaged) to faithfully moving around lots of tiny pieces of DNA, and maybe depending on the system needing to guarantee not losing one of them entirely, or ensuring that the copy number of each one doesn't deviate too much from all the others, or both. I think yours is probably the right way, though.