Tuesday, November 18, 2014

MIT can now use E. coli DNA tape recorders for living and replicating data storage

Could cloning be on the way?

DNA microchips can now encode arbitrary digital information at a density of over at 700 terabytes per gram. That number could be pushed much higher, theoretically even as high as 455 exabytes per gram. Cold hard storage capacity like that is great, but what if that kind of power could be integrated with something more alive — something like a single cell, or for that matter, integrated into every cell.

Researchers at MIT’s Synthetic Biology Center have just succeeded in writing multiple analog streams of real-time environmental data into the genetically transformed hardware of a distributed population of bacterial cells. Corresponding author Timothy Lu is calling their new technology a “DNA tape recorder” because the data can be written, erased, and rewritten into virtually any location within the genomes of the cell population. These memories are not only stored for the collective lifetime of the population, but can be passed on from generation to generation.

This diagram shows single-stranded DNA recombining with a double-stranded DNA genome. Recombinases are the enzymes that make all this magic possible.

The researchers have another name for these tape recorders — SCRIBEs, for Synthetic Cellular Recorders Integrating Biological Events. The key to making them work was found in a thirty-year-old paper that described a curious genetic structure found in a humble soil bacterium. This structure, known as a retron, is basically an auxiliary single-stranded DNA cache that exists separate from the cell’s main instruction set of double stranded DNA. The researchers discovered that retrons inside of E. coli bacteria will respond proportionally to the presence of certain chemicals. In particular, the rate at which the single stranded DNAs recombine with the main double stranded DNA of the cell could be increased. [Research paper: DOI: 10.1126/science.1256272]

What this all means for analog information storage is that these largely superfluous single DNA strands, now integrated into the heritable genetic base of the cell, preserve an accurate record of the chemical environment of the cell. By inserting photosensitive proteins into the genetic circuit, the researchers were able to turn on the recorder at a precise point in time with a light trigger. The really heady stuff — actually retrieving this stored information — was done in a number of different ways. Sequencing the genomes of the cells determined which bacteria recorded memories of particular events. For example, how long and how much of a particular chemical they were exposed to.

In other cells, the newly recombined DNA could act not just as a data storage, but additionally as a switch for the cell to make a particular antibiotic. Those cells (containing the antibiotic resistance gene) could then be selected from the others by giving all the cells a toxic challenge which killed only those that did not integrate the new informational DNA sequences. Now we have a way to not only encode data, but to actually control the propagation of the data through the population.

The researchers have already compared their bacteria to complex Turing machines, universal computers if you will. Having these little genetic embassies available for private storage and computation, yet largely exempt from much of the day-to-day housekeeping of the cell, may be a powerful tool for turning both bacterial cells, or our own cells, into what we might call “supercells” — cells that do weird and wonderful things, or perhaps act as massively dense data stores for our own human-made analog molecular computers or digital nanotech computers.

Source: ExtremeTech

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