Biological Transistors Created Inside Cells Out of DNA

Monday, April 1, 2013

Biological Transistors Created Inside Cells Out of DNA

 Biological Computers
A team of Stanford University bioengineers has taken computing beyond mechanics and electronics into the living realm of biology. The team has made a biological transistor made from genetic material — DNA and RNA — in place of gears or electrons. The team calls its biological transistor the “transcriptor."
Biotech engineers at Stanford University have created the first biological transistor made from genetic materials: DNA and RNA. Dubbed the “transcriptor,” this biological transistor is the final component required to build biological computers that operate inside living cells.

The team's study was recently published in the journal Science.

With this development we are one step closer to a Singularity-related aim of biological computers that can detect changes in a cell’s environment, store a record of that change in memory made of DNA, and then trigger some kind of response — say, commanding a cell to stop producing insulin, or to self-destruct if cancer is detected.  According to Sebastian Anthony, "All of the building blocks of a biological computer are now in place."

Stanford’s transcriptor is essentially the biological analog of the digital transistor. Where transistors control the flow of electricity, transcriptors control the flow of RNA polymerase as it travels along a strand of DNA.

“Biological computers can be used to study and reprogram living systems, monitor environments and improve cellular therapeutics,” said Drew Endy, PhD, assistant professor of bioengineering and the paper’s senior author.
biological computer
The logic element within a three-terminal Boolean integrase EXCLUSIVE OR (XOR) gate such that gate output is high only if control signals are different  Image Source: Bonnet et al./Science

The transcriptors do this by using special combinations of enzymes (integrases) that control the RNA’s movement along the strand of DNA. “The choice of enzymes is important,” says Jerome Bonnet, who worked on the project. “We have been careful to select enzymes that function in bacteria, fungi, plants and animals, so that bio-computers can be engineered within a variety of organisms.”

Like a transistor, which enables a small current to turn on a larger one, one of the key functions of transcriptors is signal amplification. A tiny change in the enzyme’s activity (the transcriptor’s gate) can cause a very large change in the two connected genes (the channel).

By combining multiple transcriptors, the Stanford researchers have created a full suite of Boolean Integrase Logic (BIL) gates — the biological equivalent of AND, NAND, OR, XOR, NOR, and XNOR logic gates. With these BIL gates (pun possibly intended), a biological computer could perform almost computation inside a living cell.

Along with logic gates, a storage system is also needed, as well as some way to connect all of the transcriptors and memory together (a bus). Fortunately, numerous research groups have successfully stored data in DNA — and Endy's team have already developed an ingenious method of using the M13 virus to transmit strands of DNA between cells.

The potential for real biological computers is immense. Potentially this research could lead to fully-functional computers that can sense their surroundings, and then manipulate their host cells into doing just about anything.

Biological computers might be used as an early-warning system for disease, or simply as a diagnostic tool (has the patient consumed excess amounts of sugar, even after the doctor told them not to?) Biological computers could tell their host cells to stop producing insulin, to pump out more adrenaline, to reproduce some healthy cells to combat disease, or to stop reproducing if cancer is detected. Biological computers will probably obviate the use of many pharmaceutical drugs.

SOURCE  Extreme Tech, Stanford University

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