Biomod/2012/UTokyo/UT-Komaba/Idea: Difference between revisions

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The DNA tablet will also be able to show a short movie by using a n-oscillate system. Look at the figure below.
The DNA tablet will also be able to show a short movie by using a n-oscillate system. Look at the figure below.


[[Image:BIOMOD-2012-UTokyo-UTKomaba-trioscillate_system_model_1]]
[[Image:BIOMOD-2012-UTokyo-UTKomaba-trioscillate_system_model_1.png|200px]]


The figure is a model of a trioscillate system. The difference between this figure and the one of a tristable system is tha each of A, B and C produces inhibitions of production of only C, B and A(therefore, inhibitions are not mutual).
The figure is a model of a trioscillate system. The difference between this figure and the one of a tristable system is tha each of A, B and C produces inhibitions of production of only C, B and A(therefore, inhibitions are not mutual).
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In this case, the state does clockwise change, like A to B to C to A, or A1 to A2 to...to An to A1.
In this case, the state does clockwise change, like A to B to C to A, or A1 to A2 to...to An to A1.


[[Image:BIOMOD-2012-UTokyo-UTKomaba-trioscillate_system_simplemodel|200px]]
[[Image:BIOMOD-2012-UTokyo-UTKomaba-trioscillate_system_simplemodel.png|200px]]
[[Image:BIOMOD-2012-UTokyo-UTKomaba-noscillate_system_simlemodel|380px]]
[[Image:BIOMOD-2012-UTokyo-UTKomaba-noscillate_system_simlemodel.png|380px]]


Now we are ready to make the DNA tablet play a short movie. If we prepare slightly different images (like film frames), they change automatically and look like a movie.
Now we are ready to make the DNA tablet play a short movie. If we prepare slightly different images (like film frames), they change automatically and look like a movie.

Revision as of 19:33, 20 October 2012

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<div id="title"><img src="http://openwetware.org/images/4/47/Biomod_2012_UTokyo_UT-Komaba_Top.png" alt="DNA tablet" width="800" height="120" onClick="this.src='http://openwetware.org/images/7/7d/BIOMOD_2012_UTokyo_UT-Komaba_title-animation.gif'"/></div>

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 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba">Home</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Idea">Idea</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Simulation">Simulation</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment">Experiment</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Progress">Progress</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Episode">Episode</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Team">Team</a></li>
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Mission

Now that there are many tablet computers, our goal is to create the world's smallest tablet ! We are designing and constructing 9x12 pixel display made of DNA origami. We aim to show animation on that display, using bistable system.

Bistable System

What is Bistable System?

network of bistable system

The bistable system enables us to express two exclusive states, using network of chemical reactions.

For example, we represent two states by materials A and B. The picture on the right side shows how the bistable system uses reaction networks. In this network, A promotes production of A itself and iB(i means inhibition), and B promotes B itself and iA. On the other hand, iA inhibits production of A and iB inhibits production of B. There are also reactions that decompose A, B, iA, and iB.

If the amount of A is a little bit more than that of B, this network promotes production of A and decomposition of B (details are shown in Simulation). Afterwards, there remains only A and vice versa. Thus, thank for the bistable system, we can make the two conditions easily; "There is only A" and "There is only B".ation

Method

We design the bistable system with DNA.

  • Production of A,B,iA,iB

　　

B and iA are also produced in the same way.


  • Inhibition of production of A,B

The production of B is also inhibited in the same way by iB.


  • Decomposition of A,B,iA,iB

DNA tablet

What is DNA tablet ?

The mechanics of displaying pixel

The DNA tablet shows the two different pictures in response to its environmental changes. We observe the response by AFM.


There are four kinds of pixels:

  • Θ always can be observed.
  • Φ always can not be observed.
  • [math]\displaystyle{ \overline{A} }[/math] can be observed when there are a lot of A near the pixels.
  • [math]\displaystyle{ \overline{B} }[/math] can be observed when there are a lot of B near the pixels.


These pixels are made of DNA strands. They stand on DNA origami, and can be observed when they are hybridized. Please note that both [math]\displaystyle{ \overline{A} }[/math] and [math]\displaystyle{ \overline{B} }[/math] can not be observed at the same time because the bistable system only makes the two condition; "There is only A" or "There is only B".

These four kinds of pixels enable us to switch pictures (The simulation can be seen here). How to switch? It is very easy. If you put B enough into the test tube, the bistable system decompose A, and the picture B appear. Also, if you put A enough, the picture A appear on the tablet.

Example: design of 5x5 tablet

How to see it

We use AFM to see DNA tablet. Generally an AFM detects the difference between hybridized staple strands and non-hybridized ones on DNA origami. However, even if the single strands on the DNA tablet are hybridized, they are not strong enough to be seen by an AFM. So, we apply hammerhead structures as the pixels.

Look at the figure below. When they are hybridized, they compose a hammerhead and become strong.

Hammerhead structure

Future Works

More pictures ～ DNA tablet with a n-stable system

We are sure that the size of the library can be extended by using a n-stable system. Look at the figure below.


The figure is a model of a tristable system. Each of A, B and C produces itself and inhibitions of the production of the others. Also, all of the production(A,B,C,iA,iB,iC) are decomposed by exonuclease. The decomposition processes are not shown in the picture. We can change the picture which the DNA tablet is showing since this system can realize the condition "There is only A, B or C" in the same way as the bistable system.

In a similar way, the DNA tablet can show many pictures, by applying the n-stable system. In this system, each of A1, A2, A3......A(n-1) and An produces itself and inhibitions of all the self-production of the others. This system can realize the condition "There is only Ak (k = 1,2,...n)".

We can represent the n-stable system by a n-sided polygon in order to make the diagram simpler. Look at the diagrams below. Mutual inhibition between each two of A1, A2...and An is expressed by red line. There are decomposition processes but not shown in these figures.


The characteristics of the DNA-tablet with n-stable system is that we can freely switch(or preserve) the picture it is showing to another one by changing the condition.


Simulation of the n-stable system is here.

Play a movie ～ DNA tablet with a n-oscillate system

The DNA tablet will also be able to show a short movie by using a n-oscillate system. Look at the figure below.

The figure is a model of a trioscillate system. The difference between this figure and the one of a tristable system is tha each of A, B and C produces inhibitions of production of only C, B and A(therefore, inhibitions are not mutual). In this system, the condition change makes a circle through "there is only A", "there is only B" and "there is only C", and the DNA tablet switch the pictures automatically:if A is dominant, the inhibition to C from A becomes strong, then the inhibition to B from C gets weaken, and B increases, then inhibition to A from B gets strong, and as a result B becomes dominant. Here we don't have to input some specific strands to change the pictures.

The figures below are simplified models of trioscillate and n-oscillate system. The difference these and those of the tristable or n-stable system is quite simple, the sides of the polygon are blue. The blue lines represent non-mutual inhibition(A inhibits all of the self-productions except B's, and B does so except C's, and....), while red ones do mutual inhibition. In this case, the state does clockwise change, like A to B to C to A, or A1 to A2 to...to An to A1.

Now we are ready to make the DNA tablet play a short movie. If we prepare slightly different images (like film frames), they change automatically and look like a movie.

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