Revision as of 11:23, 14 October 2014

iGEM ETH Zurich 2014

XOR Gate

Model

After binding to DNA, integrases can flip the fragment and thus compute the output of the XOR logic gate.

XOR Logic Gate

The logic gate we consider has two binary inputs and one binary output.

Truth table of the XOR logic gate.

Biological Principles

The fragment integrases can flip is a terminator. Thus, the terminator can either be on or off.

T_on: terminator is on, transcription is blocked.

T_off: terminator is off, transcription is active. It corresponds to one flipping of the terminator.

In our design, we are interested in a double flipping. That is to say that two pairs of binding sites surrounds the fragment to be flipped. One pair of binding sites can be bound by DBxb1 and the other one by ΦC31.

The terminator can be flipped once if either DBxb1 or ΦC31 is present. The state T_off can be caused by two reasons. We further decompose it into two different states: T_offBxb1(flipping due to presence of Bxb1) and T_offΦC31(flipping due to presence of ΦC31).
Insert Image of two states

Flipping by integrases is irreversible. The initial state, in which the terminator is on, is different from the state after two switches. From this last state, no further evolution of the system is possible. Therefore, we decompose the T_on into two different states: T_on,i(initial state of the system, no flipping) and T_on,f(final state of the system after two flips).
Insert Image of two states

XOR biologic gate

Other Chemical Species

Name	Description
mRNA_GFP	mRNA for Green fluorescent protein which is produced when the cells are ON.
GFP	Green fluorescent protein which is produced when the cells are ON.
mRNA_LuxI	mRNA for LuxI which is produced when the cells are ON.
LuxI	Enzyme catalysing the production of LuxAHL from SAM and ACP.
mRNA_LasI	mRNA for LasI which is produced when the cell are ON.
LasI	Enzyme catalysing the production of LasAHL from SAM and ACP.

Reactions

The following reactions are valid for the strain producing LasAHL as output (It corresponds to the blue cells here).

$$\begin{align*} SA_{Bxb1}+SA_{Bxb1}+T_{on,i}& \rightarrow T_{offBxb1}+ SF_{Bxb1}+SF_{Bxb1}\\ T_{offBxb1} &\rightarrow T_{offBxb1} + mRNA_{GFP} + mRNA_{LasI} \\ SA_{\phi C31}+SA_{\phi C31}+T_{on,i}& \rightarrow T_{off\phi C31}+SF_{\phi C31}+SF_{\phi C31}\\ T_{off\phi C31} &\rightarrow T_{off\phi C31} + mRNA_{GFP} + mRNA_{LasI} \\ SA_{Bxb1}+SA_{Bxb1}+T_{off\phi C31}& \rightarrow T_{on,f}+SF_{Bxb1}+SF_{Bxb1}\\ SA_{\phi C31}+SA_{\phi C31}+T_{offBxb1}& \rightarrow T_{on,f}+SF_{\phi C31}+SF_{\phi C31}\\ mRNA_{GFP} &\rightarrow GFP\\ mRNA_{LasI} &\rightarrow LasI\\ mRNA_{GFP} &\rightarrow \emptyset\\ mRNA_{LasI}&\rightarrow \emptyset\\ GFP &\rightarrow \emptyset\\ LasI&\rightarrow \emptyset \end{align*}$$

To have the equivalent for the strain producing LuxAHL as output, it suffices to remplace every occurence of LasI by LuxI.

Transfer Function

== We modeled the XOR gate module deterministically. Thus, we considered a continuous approximation of variables, like the number of integrases-DNA binding sites or the number of terminator. We wrote them as concentration. The transfer function obtained

The behaviour of XOR module as a function of activated Bxb1 sites (SABxb1) and ΦC31 sites (SAΦC31). The XOR behaviour is continuous since we modelled it deterministically.

@@ Line 86: / Line 86: @@
 To have the equivalent for the strain producing LuxAHL as output, it suffices to remplace every occurence of LasI by LuxI.
+<html></article></html>
+<html><article></html>
+== Transfer Function ==
+==
+We modeled the XOR gate module deterministically. Thus, we considered a continuous approximation of variables, like the number of integrases-DNA binding sites or the number of terminator. We wrote them as concentration. The transfer function obtained
+[[File:ETHZ_XORmodule.png|center|600px|thumb|The behaviour of XOR module as a function of activated Bxb1 sites (SABxb1) and ΦC31 sites (SAΦC31). The XOR behaviour is continuous since we modelled it deterministically.]]
 <html></article></html>

Team:ETH Zurich/modeling/xor

From 2014.igem.org