Biomod/2012/UTokyo/UT-Komaba/Experiment/Trioscillate System: Difference between revisions

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==Concept==
==Concept==


[[Image:Biomod_2012_UTokyo_UT-Komaba_Experiment_TristableConcept.png|500px|center|Trioscillate System Concept]]
[[Image:Biomod_2012_UTokyo_UT-Komaba_Experiment_TristableConcept.png|500px|center|Tristate Oscillator System Concept]]


Trioscillate system is quite similar to bistable system but it has three states, A, B and , each repressing the next one in a loop. Therefore it can never settle on any one of them and has to continuously.
This system is quite similar to bistable system but it has three states, A, B and , each repressing the next one in a loop. Therefore it can never settle on any one of them and has to continuously.
The diagram above shows the clockwise cycle of inhibition, the cycle of the states is A -> B -> C -> A -> B and it theoretically continues forever.
The diagram above shows the clockwise cycle of inhibition, the cycle of the states is A -> B -> C -> A -> B and it theoretically continues forever.
However, we can design the system with the anticlockwise cycle of inhibition so that the state changes like A -> C -> B -> A -> C and it theoretically continues forever.
However, we can design the system with the anticlockwise cycle of inhibition so that the state changes like A -> C -> B -> A -> C and it theoretically continues forever.

Revision as of 01:47, 23 October 2012

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Concept

Tristate Oscillator System Concept
Tristate Oscillator System Concept

This system is quite similar to bistable system but it has three states, A, B and , each repressing the next one in a loop. Therefore it can never settle on any one of them and has to continuously. The diagram above shows the clockwise cycle of inhibition, the cycle of the states is A -> B -> C -> A -> B and it theoretically continues forever. However, we can design the system with the anticlockwise cycle of inhibition so that the state changes like A -> C -> B -> A -> C and it theoretically continues forever. Also, Tristate oscillator system does not need input, and it changes its state by itself. Therefore, when it is introduced to the DNA modified origami, we can make the DNA tablet which change its surface autonomously and cycle between three pictures. The purpose of the experiment is to find the best conditions of trioscillate system for continuous oscillations.

Experiment

October 2nd

To investigate ideal conditions of Tristate oscillator system, we conducted experiments which checks three subparts of this system.

(µL)

BST NBI tt-RecJ DTT BSA Smix 4x inhmix dTTP XII CxII mQ Total Amount
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.10 12.44 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.20 12.34 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.30 12.24 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.40 12.14 20.00

injection: VII 0.80µL each


(µL)

BST NBI tt-RecJ DTT BSA Smix 4x inhmix dTTP VII CvII mQ Total Amount
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.10 12.44 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.20 12.34 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.30 12.24 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.40 12.14 20.00

injection: QII 0.80µL each


(µL)

BST NBI tt-RecJ DTT BSA Smix 4x inhmix dTTP QII CqII mQ Total Amount
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.10 12.44 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.20 12.34 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.30 12.24 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.50 0.20 0.10 0.40 12.14 20.00

injection: XII 0.80µL each


October 11th

Today, we tested whole trioscillate system. To investigate the ideal condition, we tested both direction of inhibition (V-|X-|Q, V-|Q-|X) and each concentration of CxII, CvII, CqII.


  • inhibit direction: V-|X-|Q

(µL)

BST NBI tt-RecJ DTT BSA Smix 4x inhmix dTTP XII VII CxII CvII CqII mQ Total Amount
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.50 0.40 0.50 11.22 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.50 0.40 1.00 10.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.50 0.40 1.50 10.22 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.50 0.40 2.00 9.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.00 0.40 0.50 10.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.00 0.40 1.00 10.22 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.00 0.40 1.50 9.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.00 0.40 2.00 8.22 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.50 0.40 0.50 10.22 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.50 0.40 1.00 9.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.50 0.40 1.50 9.22 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.50 0.40 2.00 8.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 2.00 0.40 0.50 9.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 2.00 0.40 1.00 9.22 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 2.00 0.40 1.50 8.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 2.00 0.40 2.00 8.22 20.00


  • inhibit direction: V-|Q-|X

(µL)

BST NBI tt-RecJ DTT BSA Smix 4x inhmix dTTP XII VII CxII CvII CqII mQ Total Amount
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 0.50 0.50 11.52 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 0.50 1.00 11.02 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 0.50 1.50 10.52 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 0.50 2.00 10.02 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 1.00 0.50 11.02 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 1.00 1.00 10.52 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 1.00 1.50 10.02 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 1.00 2.00 9.52 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 1.50 0.50 10.52 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 1.50 1.00 10.02 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 1.50 1.50 9.52 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 1.50 2.00 9.02 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 2.00 0.50 10.02 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 2.00 1.00 9.52 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 2.00 1.50 9.02 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.10 2.00 2.00 8.52 20.00


October 12th

We tested again the wells which worked well in before experiment.

  • inhibit direction: V-|X-|Q

(µL)

BST NBI tt-RecJ DTT BSA Smix 4x inhmix dTTP XII VII CxII CvII CqII mQ Total Amount
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.50 0.40 0.50 11.22 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.50 0.40 1.00 10.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.50 0.40 1.50 10.22 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 0.50 0.40 2.00 9.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.00 0.40 0.50 10.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.00 0.40 1.00 10.22 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.00 0.40 1.50 9.72 20.00
0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.10 0.11 0.11 1.00 0.40 2.00 8.22 20.00
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