USTC/Inputs and Outputs

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Revision as of 08:51, 23 October 2007

PoPS (the flow of RNA Polymerase molecules along DNA) means the current of gene expression. Our logic gates accept PoPS input signals, but we cannot input a PoPS signal directly. We decide to add something into our system as input signal, such as cheminal ligands and light. So a convertor must be built firstly to convert these signals to PoPS signals.

Candidates of input signals

Light

We decide not to use light signals as the inputs of our system for the following two reasons.

For one, it would be rather difficult to dynamically control the light intensity in real experiments. Compared with simply adding reagents to the solutions, controlling the input level of light is far more complicated. Still unpleasant is the requirement for the techniques of keeping the light sensors on the cell membrane from frequent exposure.

For another, since light has seldom been applied as input signals before, there is little relative background knowledge and experience to help us.

IPTG

IPTG is actually the RESET signal of the whole system. Once added, it will let all the repressor-operator pairs in the system no longer function. All the outputs will consequently become 1 as well as all the input signals being automatically ignored.

aTc

ATC is a well studied and widely used inducer of celluar communication. We take a fancy to its stable properties and reasonable price.

AHL

We consider AHL a well-qualified input signal that is normally used in quorum sensing. Actually, we choose 3OC6HSL, a member of AHL family to be the input signal, and its according receptor LuxR to be the sensor.

Arabinose

Considering that the promoter of arabinose requires to match and is too much limited by the genotype of the host strain, we finally give up the idea that arabinose would serve as an input signal.

Design of PoPS converters

The figure above shows the basic structure of our input device. It functions to convert the input chemical signals to the PoPS (the flow of RNA Polymerase molecules along DNA) signals of the lac repressor A and B, the wires that will actually connect the two main parts of our system together.

PoPS-converter parts

Figure 2 The first design of [aTc]->PoPS converter (BBa_I732014).

Figure 2 is the first design of our [aTc]->PoPS converter. Fluorescent reporters was added behind. However, we found that the background expression could not be ignored under the fluorescent microscope. It might be due to the LVA tag of Tet repressor which served to help TetR degrade. Therefore, we decide to remove the LVA tag of the Tet repressor like the one shown in Figure 3.

We take [http://partsregistry.org/Part:BBa_J09855 BBa_J09855] directly from the registry as [AHL]->PoPS converter. Fluorescent expression under different [3OC6HSL] has been tested and the results show that this part is a perfect input device in this study.

Figure 3 The second design of [aTc]->PoPS converter (BBa_I732083).

Figure 4 [AHL]->PoPS converter (BBa_J09855).