Overview.
Our project aims to construct a synthetic biological device based on a digital circuit called a multiplexer. Our system is designed to generate
a response dependent solely on the provided input signals. As multiple input signals were needed, we had to test multiple inducible promoters. Activities
of these promoters are induced by presence or absence of various monosaccharides: xylose, arabinose, rhamnose and disaccharide melibiose.
Thus, their concentrations were equivalent to analog signals that could be converted to expression of serine recombinases (phage integrases)
in an 'all-or-none' way, providing us with a digital control over the system.
Using the interases' ability to recognize nonidentical sites and invert or excise identified sequence, one may make DNA editable in vivo.
One of the possible uses of such a sub-system is to create a biological equivalent of a transistor - dubbed a transcriptor - that uses DNA polimerase flow as an analogue of the electric current,
while exploiting the integrase as a control signal. That suffices to build an SR-latch - the simplest memory cell, being one of the basic units of the Von Neumann computer architecture.
The resultant DNA-based memory storage can be propagated when cells divide.
We envision that the abilities of integrases could allow switching expression
on and off, targeting various genetic components.
Inspiration.
We were inspired by a digital circuit - a multiplexer - allowing to choose an arbitrary input signal x and send it to the output y using adressing signal a. Strobe signal S forces the original device to ignore the inputs producing 0 as an output.
Our modifications of the circuit include a multiple rewritable memory cell functionality - the device is designed to comprise of three SR-latches (each memorizing one bit of information). The strobe signal resets them to 0 state. The output has 8 cumulative states while still remaining digital - one may choose more than one input to be included independently.
Implementation.
Input signals are concentrations of saccharides rhamnose, xylose and melibiose, and the strobe signal is the concentration of arabinose. Each of them induces expression of a corresponding integrase. We have decided to use standard reporting genes - fluorescent proteins - as an output, but in theory, any protein could be an output. The signals to be included/ignored are chosen by trasformation with a proper vector and tratment with a corresponding antibiotic.
References.
J. Bonnet et al. (2012), Rewritable digital data storage in live cells via engineered control of recombination directionality, PNAS.
J. Bonnet et al. (2013), Amplifying genetic logic gates, Science.
P. Siuti et al. (2013), Synthetic circuits integrating logic and memory in living cells, Nature.
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