DNA Hard Drive

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DNA Hard Drive

DNA Hard Drive

If you want to get reductionist about it, a cell is just a really complex, squishy, water-logged robot. That’s the basic idea behind synthetic biology, that by understanding the parts and manufacturing of a biological organism we can use it as a tool for our own selfish purposes. Of course, the first stabs at actually applying this idea were purely practical: put biological workers in a car’s gas tank to make ethanol, or in a landfill to eat harmful garbage, or in the ocean to combat acidification. However, a huge proportion of modern robots are probes or observers that collect information and report it back to us, and that’s one area in which biology has always lagged behind — but that might be about to change.

A team from MIT has published a remarkable study in which they give their e.coli bacteria memory, a hard drive of sorts for a biological machine. Since single celled organisms can’t remember and repeat information, though, that memory comes in the form of DNA, as the cells physically restructure their own genomes to record outside events. This occurs thanks to their core innovative technique called SCRIBE, or Synthetic Cellular Recorders Integrating Biological Events, which inserts a genetic marker into the cell’s genome whenever a prescribed signal is received — and that signal can be almost anything. The team says they haven’t just invented a binary, yes-no bacterial switch, but a modular recorder that can show the strength and distribution of a signal as well.

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.

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.

The technology to read and write DNA is already available today but it’s not necessarily accessible. DNA data storage and access is already possible from a technological standpoint, but not necessarily from an economical one. For example the cost of reading genetic data, or identifying the components of genetic material, is getting dramatically cheaper. For example, you can have the 3 billion bases in your own DNA sequenced for as little as $1000.

However, the cost of writing that data – or chemically synthesizing the sequence of nucleotides that represent your data – is a different story. Specifically, researchers in the UK estimated recently that it would cost more than $12,000 per MB to encode DNA data, but only around $200 per MB to read that data back. The hope is that the techniques for writing DNA will catch up with the amazing progress that is happening in technology to sequence or read DNA. Until there is greater demand, it will be many years until we see greater technological adoption due to cost factors.”

Though the cost factor is a hurdle, Dr. Narayan believes we are well on our way to achieving the goal of large-scale DNA storage. In fact, he believes we are already par way there thanks to DNA barcodes to tag and read genetic data. But in terms of long term storage, he believes DNA offers the perfect choice. “What’s really interesting now is that researchers are using DNA as a medium for digital archival storage because the stability of the DNA structure in principle lets one access the data after centuries under reasonable storage conditions. After all, scientists have been able to “read” the DNA from mammoths and Neanderthals.

This stability can provide far more than just a hard drive to last the ages. Because DNA is always present in a variety of biological environments, the idea of a personal DNA hard drive within the body may also be possible. According to Dr. Narayan, it’s already happening at the microbial level. ”Several years ago researchers built the first self-replicating bacterial cell and they inserted DNA representing text such as the scientists’ names and literary quotations within the functioning DNA of the cell.

This in itself is a perfect biological version of what we currently do today with computers. But while this may be possible, Dr. Narayan wonders if this might be the best approach. For him, it may be better to use more traditional means of data storage: the brain.

Since the average human has about 100 trillon bacteria in or on them it seems there certainly would be room to put your social security number in the genome of some bacteria or virus. However, you would have to hope it stays dormant forever and not become viable and perhaps mutate or erase the information. And then you would have to extract and sequence the DNA. Seems better to just remember the number.

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