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Stanford's RAD device for switching DNA sequences back and forth  (Source: Science Daily)
RAD could one day be used to help study cancer, aging and organismal development

Stanford University researchers have found a way to switch certain DNA sequences back and forth.

Jerome Bonnet, PhD, study leader and postdoctoral scholar at Stanford University, along with graduate student Pakpoom Subsoontorn and assistant professor Drew Endy, have created a technique for encoding and erasing digital data in living cells' DNA. In other words, they have made a genetic equivalent of a binary digit where a section of DNA points in one direction indicating a zero, and another section points in a different direction indicating a one.

The researchers created a device called a recombinase addressable data module, or RAD. RAD is used to modify sections of DNA with natural enzymes from bacteria. These enzymes, when applied to a section of DNA, glow red or green when RAD is in use. This shows how the one-celled organisms will glow under ultraviolet light depending on the orientation of the section of DNA. This allows the researchers to flip the DNA sequences back and forth.

Previous research allowed sections of DNA to be switched, but only indefinitely. They couldn't be switched back. But the Stanford researchers found a way to switch the sequences back through controlling two key proteins: integrase and excisionase. By controlling the dynamics of these two proteins, they created a fully reusable binary data register. Without control of these proteins, they would become active at the same time or concentrated in the wrong amounts, leading to individual cells creating random results. When the proteins were used together in the same cell, there was no balance or control, but the researchers used them separately and were able to switch the DNA sequences back and forth.

"It took us three years and 750 tries to make it work, but we finally did it," said Bonnet.

Bonnet tested the RAD modules in single microbes, and they were able to switch the DNA sequences over 100 times. The method allowed for repeat encoding, storing and erasing of digital data within the DNA of biological cells.

The next step is to go from a single bit to eight bits, or a full byte, of programmable data storage. This, however, will take about a decade according to Endy.

"I'm not even really concerned with the ways genetic data storage might be useful down the road, only in creating scalable and reliable biological bits as soon as possible," said Endy. "Then we'll put them in the hands of other scientists to show the world how they might be used."

RAD could one day be used to help study cancer, aging and organismal development.

Source: Science Daily

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In the future...
By Motoman on 5/23/2012 12:26:46 PM , Rating: 2 will add memory to your computer by attaching another gerbil to your eSATA port.

Just remember to feed your RAM, or else you'll lose your term paper.


Just had a thought - what if the gerbil actually saw in it's mind what you were doing in RAM? Like playing COD? +1 really freaked out gerbil.

RE: In the future...
By geddarkstorm on 5/23/2012 1:57:44 PM , Rating: 2
There are some really interesting uses for this. Unfortunately, biological stuff just doesn't have much longevity. But the idea of switching the direction of DNA sequences around at will could allow us to better control genes that are on and off in our experiments (by targeting the promoters for instance); leading to far more advanced genetic studies. As the article says, this could be profound for cancer research, and disease research in general.

RE: In the future...
By Church of Dirac on 5/23/2012 5:34:30 PM , Rating: 2
DNA is rather stable when properly stored. It does not undergo autocatalyis like RNA. Also, some proteins are notoriously stable even after refluxing in acid or being exposed to the environment for years. So a biotech based computer is not necessarily out of the question. Just keep those proteases and nucleases away!

RE: In the future...
By geddarkstorm on 5/23/2012 9:22:17 PM , Rating: 2
You mean the proteases and nucleases secreted from your skin, or can be carried on your breath?

DNA doesn't autocatalyse strand breaks like RNA, you're completely right. However, DNA depurinates (loses A's and G's) in water (see ). Consequently, water is mutagenic under physiological conditions. A computer based on DNA that uses proteins to flip the sequences naturally has to be in a water based solution, and naturally will depurinate over time, literally breaking down.

Proteins are also labile in water. While some proteins are conformationally stable at low pH's they don't actually last long, and water autocatalyzes strand breaks of proteins by hydrolyzing the peptide bond. Proteins that do last a long time in the environment are usually in dessicated areas, safely away from water (such as encased in ancient bone in arid soil).

So, unfortunately, biotech computers are out of the question. It's never going to happen. They will break down pretty rapidly, do not function rapidly (we're talking on order of seconds to flip DNA), are not easily synchronized (molecules are in free tumble due to brownian motion and not always at the right place at the right time at the right energy level), are not miniturizeable and thus low density (DNA is the size of DNA, can't shrink it like we can lithography etchings), are not realistically scalable, need to be in liquid, extremely sensitive to temperature, need constant upkeep, and are very difficult to input information to and read information from (adjusting the right levels of those proteins for flipping DNA is not easy, and requires a Rube-Goldberg machine like system). This issues are inherent to the physical properties of the molecules in discussion themselves, so not a simple matter to circumvent.

Silicon based electronics are superior in every way. But, it is an interesting field none the less, as there's a lot we can learn about designing living systems to our liking. Just don't read too much into this (they were using bacteria the whole time over time scales of days) and get too worked up about making actual computers from them; we have better uses for this really awesome types of research.

RE: In the future...
By ZmaxDP on 5/23/2012 6:29:21 PM , Rating: 2
So, what you're saying is that GB will one day stand for Gerbilbytes???

"Nowadays you can buy a CPU cheaper than the CPU fan." -- Unnamed AMD executive

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