Biological Modules

Logic Gates

An electronic full adder is composed of 5 logic gates (2 XOR, 2 AND and 1 OR)


To transpose these logic gates into biological gates, two publications published this year inspired us (Siuti and al. 2013, Bonnet and al. 2013). These two publications were using recombinases to create biological gates. The E.calculus full adder uses different recombinases: TP901.1, Bxb1, PhiC31 and FimE. Each recombinase is a one way recombinase, it means that its recombination sites have been designed to ensure an one-way switch only. When a sequence between two recombination sites has been switched, the sites are not retained and the recombinase can not switch a second time.

The two AND gates

In a biological way, with the use of recombinases, an AND gate can be represented by different ways. The E.calculus full adder uses two different AND gates.

The first one is composed of one promoter followed by two transcriptional terminators, each one surounded by recombination sites. Each terminator is surrounded by a different recombination site, recognized by two different recombinases: Bxb1 and TP 901.1.
Those two terminators are then followed by the downstream gene (with its own rbs and terminator).


If there is one input, the corresponding recombinase will be produced (the red one or the blue one), so one or the other terminator will be switched off and can then let the polymerase go.
It needs both recombinases production to transcript the downstream gene.

Move the mouse over the figure to see how it works!

For the other AND gate, it works the same way but does not use terminators. The entire gene has been put between recombiation sites.
At first, both the promoter and the gene (with its own rbs and terminator) are on the wrong way and are not fonctionnal. Both are surrounded by recombination sites recognized by two different recombinases (Phic31 and FimE)


It needs both recombinases (the purple one and the green one) to transcript the gene.

Move the mouse over the figure to see how it works!

The two XOR gates

As for the AND gates, the E.calculus full adder uses two different XOR gates.
The first one works the same way as the first AND gate. It is composed of one terminator surrounded by two different recombination sites (Bxb1 and TP901.1). The used sites are the same as for the first AND gate because the input are the same.


If there is one input, the corresponding recombinase will be produced (the red one or the blue one), so the terminator will be switched off and the downstream gene can be transcripted.
When there are two inputs, the terminator is switched twice and does not let the polymerase go.

Move the mouse over the figure to see how it works!

The second XOR gate works the same way as the second AND gate.
The gene is put the wrong way and surrounded by two different recombination sites (PhiC31 and FimE)


The gene needs to be switched only once to be transcripted.

Move the mouse over the figure to see how it works!

The full adder combined those 4 logic gates. (See Full adder)