Project

Biological Construction

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 (2013) 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 differents 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 have 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 terminators is surrounded by a differents recombination sites, recognized by two differents recombinases : Bxb1 and TP 901.1.
Those two terminators are then followed by the downstream gene (with its own rbs and terminator). As in this diagram.

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.

For the other AND gate, it works the same way but does not use terminators because the recombinase used can not switch short sequence. 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 recognize by two differents recombinases (Phic31 and FimE)

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

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