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I recently read an article about Harvard scientists encoding 700Tb of data in DNA strands. But they encoded the information in base 2, so T and G was a 1 and C and A was a 0. But why binary? Why didn't they just use base 4? It would be much more efficient!

EDIT: here the link

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    $\begingroup$ Simply because silicon-based computers fundamentally work with and store information in binary. So even if we wanted to think of the data in base-4, the computer would still have to convert to binary $\endgroup$ – Maljam Mar 28 '16 at 18:07
  • $\begingroup$ But DNA, as a storage device is base4, so the binary computer should encode the information to base4 to use the whole potential of the storage device. $\endgroup$ – TimurEke Mar 28 '16 at 19:38
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In the research article on the effort, they give the following explanation for doubling up nucleotides, rather than have each nucleotide stand for two bits:

This allows us to encode messages many ways in order to avoid sequences that are difficult to read or write such as extreme GC

In practice, they chose which base of the pair it was randomly (so a 50% GC content), while disallowing homopolymer runs greater than three.

Their scheme also uses barcodes and addresses as the "table of contents"/"index"/"page numbers". (The data wasn't stored on a single long piece of DNA, but on a large number of shorter fragments.) By having a slightly flexible coding scheme, this allows them to potentially avoid inserting those annotation elements within the contents.

Furthermore, a slightly flexible coding scheme would allow them to avoid accidentally encoding a text with part of a select agent's genome. (That is, you wouldn't want to synthesize part of the smallpox genome when you're storing your novel. If you can change the nucleotides used, you can avoid that.)

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    $\begingroup$ Interesting. When I first read the question I wrongly assumed that they had just used two bases in the synthetic DNA, and I wondered if they had avoided C because of its spontaneous deamination to U. This might seem better for long term storage. Wonder why they didn't do that. Presumably something structural. $\endgroup$ – David Mar 29 '16 at 12:12

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