Stanford University scientists working in the new discipline of synthetic biology have devised a “genetic transistor” that mimics the classic three terminal transistor found in many electronic devices and computers.
The new device is intended to have broad applications for a variety of “cellular circuits” that will allow programming of individual cells to perform tasks such as monitoring the cell for pollutants (like Poly-Aromatic Hydrocarbons, PAHs, and Radical Oxygen Species, ROSs) and disease progression. They may even be used to switch on a cell’s molecular medicine or biofuel production machinery.
Over the past ten years or so, there have been several impressive advances in electronic circuit mimicry using DNA, RNA and various proteins. These earlier molecular devices tended to have very specific functionality; they tended to work only in the precise cellular niches for which they were designed such as triggering the expression (“up-regulating”) of a particular gene in response to a specific cell signal.
But Drew Endy and colleagues at Stanford University in Palo Alto, California, sought a more multi-purpose/multi-functional device — like the electronic version used in myriad household/personal devices — that could be utilized for a greater variety of cell-programming and monitoring functions. To do this, they decided to model their device — which they call a “transcriptor” — on the most common type of transistor: the three terminal (electrode) transistor. This classic transistor — a tiny electronic switching device — has three component electrodes: the main control “gate”, and two additional electrodes referred to as “source” and “drain” electrodes.
When a relatively small or weak current of electrons makes contact with the gate, the gate “opens”, allowing for a larger/stronger current to flow between the source and drain electrodes. The device works as a signal amplifier — a function that turns out to be critical for intracellular applications that depend on gene-based circuitry; internal cell signals tend to be quite weak and transient and are commonly drowned out by cell “noise” (noise is present in all circuits and noise reduction is an issue in nearly every system involving signal detection, whether electro or bio ).
Building a Genetic Circuit – Controlling the Flow of Transcripts
Like the electronic version, the Stanford team’s version has three components: an engineered DNA strand, an RNA polymerase (RNA-P, and enzyme that reads DNA sequences and copies these into messenger RNA molecules), and proteins (enzymes) called integrases — derived from bacterial viruses — which have the ability to excise, invert and/or delete small segments of DNA.
In the synthetic transcriptor, the DNA strand acts as the main wire in a circuit but instead of conducting electrons, this strand conducts molecules of RNA-P using the integrases as the “gate” mechanism that controls how many may pass at any given time. One final step: the insertion of a “terminator” — a short sequence of DNA — into the middle of the main DNA strand. This terminator sequence rejects the RNA-P molecules — “kicking” them off the strand — but only when they are moving in a particular direction (like left to right, etc.). This action turns the circuit “off”.
To reverse this, the integrase proteins come back into play; the integrating enzymes cut out the terminator sequence, flip it around, and splice it back onto the DNA strand (turning the sequence into a promoter). This then allows the RNA-Ps to stay attached to the DNA and move down the DNA circuit without impediment, continuing to the endpoint of the circuit where they transcribe their RNA messages (thus making the circuit “on”).
In their tests, the researchers used RNA-Ps that transcribe the gene that encodes green fluorescent protein (GFP). When the RNA-Ps completed the open circuit, the cell lit up (glowed green). This process could be readily reversed, turning cell fluorescence off.
Towards More Complex Cell Programming
Following this proof of principle, the team demonstrated that they could assemble multiple transcriptors to carry out extended logic functions. Using the molecular circuit components, they were able to create standard (“Boolean”) logic circuit functions such as AND gates, OR gates, and XOR gates. These functions are able to combine or segregate circuits according to their logic rules (similar to a computer processor, although less complex).
Most importantly, the team showed that their circuits could produce signals of high amplification (so they don’t get lost in the background noise of the cell) and up-regulate target gene expression (like the GFP genes used to confirm the circuit’s activation and the cell “program”).
Although the team is not the first to use these genetic components to build bio-synthetic logic circuits (see Lu et al, MIT, Nature Biotechnology, February, 2013), it is the first effort to conclusively show that this method can be used to control transcription rates through amplifying signals. This advance could also aid future designs for intracellular and intercellular circuity to detect signaling molecules within and between cells.
This capability of turning weak signals into strong ones means that such signals can be more readily detected — possibly before a cell completely malfunctions or becomes cancerous.
Results of the experiments were reported in the on-line edition of Science, under the title ‘Amplifying Genetic Logic Gates’ (Bonnet et al)
Some source material for this post came from the Science NOW article ‘A Computer Inside a Cell’ by Robert F. Service
Top Image: Binary tunnel and DNA Strand /Image ID: 45347221 / Copyright: Bruce Rolff via shutterstock.com