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 tyrosine recombinases to create biological gates. The E.calculus full adder uses different recombinases: TP901.1 integrase, Bxb1 integrase, PhiC31 integrase and FimE. The first AND and XOR gate have been design from Bonnet and al. 2013, the second ones have been design from Siuti and al. 2013. 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 integrase and TP 901.1 integrase.
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.

We design a BioBricks with this gate (BBa_K1132001).

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 integrase and FimE)


If there is one input, the corresponding recombinase will be produced (the purple one and the green one), so one the promoter or the gene will be switched on the right. The transcription of the output gene will occur in presence of the both recombinases, when the promoter and the gene are in the right way.

We design a BioBricks with this gate (BBa_K1132003).

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 has the same design than 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 inputs (the recombinases) 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 the two recombinases, the terminator is switched twice and does not let the polymerase go. This system is designed to be activated (transcription of the output gene) only in the presence of both recombinases.

We design a BioBricks with this gate (BBa_K1132002).

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

The second XOR gate has the same design than the second AND gate.
The gene is inserted on the wrong way and surrounded by two different recombination sites (PhiC31 and FimE). To transcript the gene, the gene will need to be in the right way, to have been switched one time only by one of the both recombinases.


If there is one input only, the corresponding recombinase will be produced (the purple one or the green one), the gene will be in the right way, therefore transcripted. When there are two inputs, the gene is switched twice and stay in the wrong way. To be transcripted, the gene has to be switched one time only by one of the both recombinases.

We design a BioBricks with this gate (BBa_K1132002).

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

All of these gates (XOR and AND) can be used in any regulation system, provided that the recombinases are assembled following the promoter of your choice with your specific regulations requirements.

Resetting these gates to its basal state require a series of excisases capable of switching back the sequences to their native state.

The OR gates

The OR gate is in our adder an implicit gate. To be activated, an OR gate has to have one input or both. We just have the both promoter activated by the input below the same output, then if we have one input, the other one or both the output would be product.

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