Team:Tsinghua-A/Project/Design

What is ‘programmable‘?

Logic, which tends to be presented in the form of truth tables, shows a relationship between inputs and outputs. Below are the truth tables of the two basic gates: the And gate and the Or gate. So we quickly find the difference lies in the outputs when only one of the inputs is true. In the And gate if there are only one true input, either A or B, the output is false. But in the Or gate it’s to the contrary. So if we can control the output when only one input is true, we can successfully make the switch between the And gate and the Or gate, which can be called a programmable device.

AND Gate	OR Gate
A B Output 0 0 0 1 0 0 0 1 0 1 1 1	A B Output 0 0 0 1 0 1 0 1 1 1 1 1

How we make it happen?

We accomplish the design of the switch between the two gates with the help of the site-specific recombination system.
Cre-Lox system is a typical kind of site-specific recombination system. The system consists of two components: Cre recombinase and LoxP site. It is a site-specific recombinase technology widely used to carry out excisions, insertions, translocations and inversions in the DNA of cells. It allows the DNA modification targeted to a specific cell type or be triggered by a specific external stimulus.
We make use of the cre-lox site-specific system to accomplish the inversions in the DNA. When the external stimulus comes, the Cre recombinase will be expressed and then flip the sequence between the two LoxP sites.

After the flip, the direction of the signal stream is altered, which results in changes of logic on the physical layer. Through controlling the direction of the signal stream we can achieve our goal to make a logic-flexible device. Now let’s come to a simple example.
We replace the Gene of Interest with a kind of promoter. Under the initial condition, the promoter is able to induce the Output. But once the external signal comes, the expression of the Cre recombinase will be activated and it will lead to the flip between the two LoxP sites. Consequently, the promoter cannot bring out the output.

What we exactly want and how?

Without loss of generality, we decide to start our project with the conversion of the two basic gates mentioned above: the And gate and the Or gate. And when it comes to the situation with 2 inputs, we construct our design like this.

Before Reverse

A	B	Y	X	Output
0	0	0	0	0
1	0	1	0	0
0	1	0	1	0
1	1	1	1	1

After Reverse

A	B	Y	X	Output
0	0	0	0	0
1	0	1	1	1
0	1	1	1	1
1	1	1	1	1

Between the LoxP site there’re promoter A&B. Initially promoter A can only induce signal X, and promoter B signal Y. The Output is under the regulation which can only be induced by X AND Y.So only when both promoter A&B are activated can we get the expression of the Output. Definitely it serves as an And gate.
In response to the external stimulus we’ve given, the Cre recombinase come out and start the flip. After the flip either promoter A or promoter B can activate the expression of both signal X and signal Y. Then we can get the Output. So the system works as an Or gate. That’s how we construct the switch between the And gate and the Or gate.

An Introduction to Cre-LoxP System

The system consists of two components: Cre recombinase and LoxP site. Cre-Lox recombination is a site-specific recombinase technology widely used to carry out deletions, insertions, translocations and inversions in the DNA of cells. It allows the DNA modification to be targeted to a specific cell type or be triggered by a specific external stimulus. It is implemented both in eukaryotic and prokaryotic systems.

I．Cre recombinase

Cre recombinase is a 38-kDa monomeric protein encoded by bacteriophage P1. Cre binds cooperatively to loxP sites ( which remains to be elucidated later ), with one Cre monomer contacting each of two 13-bp recombinase binding elements arranged as inverted repeats around a central strand-exchange region (Fig. 1) . Cre promotes the synapsis of loxP-containing DNA substrates and catalyzes recombination between the sites, as shown in Fig. 2.