Biomod/2012/UTokyo/UT-Komaba/Experiment/Indirect Bistable

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DNA tablet

Contents

Concept

Indirect Bistable Concept

We could not get enough information from normal bistable sytem experiment so we changed the system into this indirect bistable system. Since an input of C or D indirectly increase the concentration of A or B, concentrations do not change rapidly and radically. We only input C or D, not A or B. As the diagram above shows, inputs C and D indirectly affect the cycle of the bistable system. The purpose of the experiment is to attain proper data about concentrations. This experiment is only for searching the best concentration, and we will eventually use the bistable system for the DNA tablet.

Experiment

September 28th

We could not get a good result for the bistable system so we changed several parts of the system. We introduced two types of DNA, "DII" and "NII", and two types of templates, "D to V" and "N to X" in the system. We changed the concentration of "D to V" and "N to X", which are always the same concentrations. We incubated these tubes at 42°C.

  • VII Experiment
The concept of the experiment VII

In this experiment, we first input templates CvII, CXII, V to inhX, X to inhV and starts the system with VII. After keeping them in a PCR machine at 42°C for several hours, we put DNA NII and observe the change of the concentration of VII. The purpose of the experiment is to find out the best concentration of N to X. The concentration would be introduced to the bistable system so that we can change the state from "VII" to "XII".


  • XII Experiment
The concept of the experiment XII

This one is the counterpart of the previous experiment. We first input the same templates and DNA XII. After reaching the stable state, we add DNA DII and observe the change of the concentration of XII. The purpose of the experiment is to find out the best concentration of D to V.

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October 1st

We conducted the same experiment as what we did on September 28th. We got enough information about the experiment for VII, so we only conducted that for VII. The purpose of the experiment is to find out the best conditions for XII. We changed the concentration of CvII and X to inhV and compared the results.

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October 2nd

We lowered the concentratinons of D to V, and N to X. Today, we conducted the same experiment as yesterday. We fixed the concentration of CVII, therefore the purpose of this experiment was to find out the ideal concentration of "X to inhV". We kept these tubes at 42°C, and switched states by injecting DII or NII.

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October 3rd

In the experiment, we investigated the best temperature for the bistable system. We made two solutions, one starts from "XII" and the other from "VII", and observed them at 6 different temperatures, 41.6, 42.5, 43.8, 45.6, 46.8 and 47.6°C. We successfully switched the state once, but we failed the second switch.

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