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==Concept==
==Concept==
[[Image:Biomod_2012_UTokyo_UT-Komaba_Idea_concept.png|left|240px|border|concept of DNA tablet]]
Now that there are many tablet computers, our goal is to create '''the world's smallest tablet''' ! We designed and constructed a 9x12 pixels display made of DNA origami. Our tablet shows multiple pictures autonomously, corresponding to its environment.


To realize this idea, we combined two technology, '''DNA origami''' and '''Bistable system'''. Detail is written in latter section.
[[Image:Biomod_2012_UTokyo_UT-Komaba_Idea_concept.png|left|240px|border|The Concept of the DNA Tablet]]
 
Now that there are many tablet computers, our goal is to create '''the world's smallest tablet'''!! We designed and structured a 9x12 pixels display made of DNA origami. Our tablet shows multiple pictures autonomously, corresponding to its environment.
 
To realize this idea, we combined two technology, '''DNA origami''' and '''Bistable system'''. Detailed information is written in latter section.
 


==Bistable System==
==Bistable System==
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===What is the Bistable System?===
===What is the Bistable System?===


[[Image:Biomod-2012-UTokyo-UT-Komaba-bistable-network.png|300px|thumb|right|network of bistable system]]
[[Image:Biomod-2012-UTokyo-UT-Komaba-bistable-network.png|300px|thumb|right|The Network of the Bistable System]]


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


For example, we represent two states by materials A and B. The picture on the right side shows a reaction network implementing a bistable system using those two materials. In this network, A promotes the production of A itself and iB (i meaning inhibition), and B promotes B itself and iA. On the other hand, iA inhibits the production of A and iB inhibits production of B. There are also reactions that continuously degrade A, B, iA, and iB.
For example, we represent two states by materials A and B. The picture on the right side shows a reaction network implementing a bistable system using those two materials. In this network, A promotes the production of A itself and iB ("i" means inhibition), and B promotes B itself and iA. On the other hand, iA inhibits the production of A and iB inhibits production of B. There are also reactions that continuously degrade the number A, B, iA, and iB.


If the system is started with a larger amount of A than B, this network promotes more the production of A, which in turn will induce a decrease of B (Detailed information is written in [[Biomod/2012/UTokyo/UT-Komaba/Simulation|Simulation]]). Afterwards, there remains only A and vice versa if the initial conditions are opposite. Thus, thanks to the bistable system, we can make two states easily: "only A" or "only B". Any intermediate state cannot be stable and will go toward one of these two exclusive states.
If the system is started with a larger amount of A than B, this network promotes more the production of A, which in turn will induce a decrease of B (Detailed information is written in [[Biomod/2012/UTokyo/UT-Komaba/Simulation|Simulation|Simulation section]]). Afterwards, there remains only A, and vice versa if the initial conditions are opposite. Thus, thanks to the bistable system, we can make two states easily: "only A" or "only B". Any intermediate state cannot be stable and will go toward one of these two exclusive states.




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We design the bistable system with DNA. [[Biomod/2012/UTokyo/UT-Komaba/Supplementary#References|[3]]]
We design the bistable system with DNA. [[Biomod/2012/UTokyo/UT-Komaba/Supplementary#References|[3]]]


*Production of A,B,iA,iB
*The Production of A,B,iA,iB
[[Image:Biomod-2012-UTokyo-UT-Komaba-product-a.png|350px|border|Production of A]]　　[[Image:Biomod-2012-UTokyo-UT-Komaba-product-ib.png|350px|border|Production of B]]
[[Image:Biomod-2012-UTokyo-UT-Komaba-product-a.png|350px|border|The Production of A]]　　[[Image:Biomod-2012-UTokyo-UT-Komaba-product-ib.png|350px|border|The  Production of B]]


B and iA are also produced in the same way.
B and iA are also produced in the same way.




*Inhibition of Production of A,B
*The Inhibition of Production of A,B
[[Image:Biomod-2012-UTokyo-UT-Komaba-inhibit-a.png|350px|border|Inhibition of A]]
[[Image:Biomod-2012-UTokyo-UT-Komaba-inhibit-a.png|350px|border|The Inhibition of A]]


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




*Decomposition of A,B,iA,iB (nothing means dNMPs a non-reactive monomer of DNA)
*The Decomposition of A,B,iA,iB (nothing means dNMPs a non-reactive monomer of DNA)


[[Image:Biomod-2012-UTokyo-UT-Komaba-decompose.png|350px|border|Decomposition of DNA]]
[[Image:Biomod-2012-UTokyo-UT-Komaba-decompose.png|350px|border|The Decomposition of DNA]]




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===What is the DNA tablet ?===
===What is the DNA tablet ?===


[[Image:Biomod-2012-UTokyo-UT-Komaba-Dna-tablet1.png|400px|thumb|The mechanics of displaying pixel]]
[[Image:Biomod-2012-UTokyo-UT-Komaba-Dna-tablet1.png|400px|thumb|The Mechanics of Displaying Pixels]]
 
The DNA tablet shows two different pictures in response to its environmental changes.
The DNA tablet shows two different pictures in response to its environmental changes.
We observe those pictures by AFM.
We observe those pictures by AFM.
Line 63: Line 67:




These pixels are made of hammerhead-like structures. They stand on DNA origami, and can be observed when they are hybridized.
These pixels are made of hammerhead-like structures. They stand on DNA origami and can be observed when they are hybridized.
Please note that both <math>\overline{A}</math> and <math>\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".
Please note that both <math>\overline{A}</math> and <math>\overline{B}</math> can not be observed at the same time because the bistable system only makes the two condition; "only A" or "only B".


These four kinds of pixels enable us to switch pictures (The simulation can be seen [[Biomod/2012/UTokyo/UT-Komaba/Simulation#The_Change_Between_Two_Pictures|here]]). Switching is very easy: you just need to switch the state of the bistable system. If you were observing the image A, then all A will disappear and B will be produced making the B image appear. Then you can switch again to come back to image A. Note that if you don't have the bistable system and you just add A (or B) strands when you want A (or B) image, after a few rounds you will end up with a concentrated mixture of A and B strands, and the images will be blurred. On the contrary the bistable keeps everything clear and reversible.
These four kinds of pixels enable us to switch pictures (You can see the simulation [[Biomod/2012/UTokyo/UT-Komaba/Simulation#The_Change_Between_Two_Pictures|here]]). The way of switching is very simple: you just need to switch the state of the bistable system. If you put enough B when you are observing the image A, all A will disappear, and B will be produced, which makes the image B appear. Then you can switch again to come back to image A just by putting enough A. Note that if you don't have the bistable system and you just add A (or B) strands when you want to see the image A (or B), the solution will end up with a concentrated mixed one of A and B strands, and the image on the surface will be blurred after a few changes of states. On the contrary the bistable keeps the picture clear and reversible in any time.


[[Image:Biomod-2012-UTokyo-UT-Komaba-dna-tablet-example.png|thumb|600px|Example: design of 5x5 tablet|center]]


[[Image:Biomod-2012-UTokyo-UT-Komaba-dna-tablet-example.png|thumb|600px|Example: design of 5x5 tablet|center|The Example of the DNA Tablet Design]]


===How to See It===


We use AFM to see the DNA tablet. Generally an AFM detects the difference between hybridized  and single-stranded ends of the staple strands  on the DNA origami surface.
===How to See===
However, even if the single strands on the DNA tablet are hybridized, they do not produce enough contrast to be seen by AFM.  Hammerhead structures are sometime used as pixels with higher AFM contrast. However, they cannot be dynamically updated by hybridization-dehybridization reactions. So, we propose to use open hammerheads (pseudo-hammerheads) to produce enough contrast and still be updatable.


When the strands produced by the bistable system are hybridized, they compose a stable hammerhead and produce a good signal (figure below).
We use AFM to see the DNA tablet. Generally, AFM detects the difference between hybridized and single-stranded ends of the staple strands on the DNA origami surface.
However,　even if the single strands on the DNA tablet are hybridized, they do not produce enough contrast to be seen by AFM.  Therefore, we applied hammerhead structures to the DNA tablet because the structures can be observed as pixels with higher AFM contrast. However, they cannot be dynamically updated by hybridization-dehybridization reactions. Therefore, we introduced open hammerheads (pseudo-hammerheads) stuructures to produce enough contrast and make themselves updatable.


When the strands produced by the bistable system are hybridized, they compose stable hammerhead structures and produce visible pixels.


[[Image:Biomod-2012-UTokyo-UT-Komaba-hammerhead_structure_3.png|500px|center|thumb|Pseudo-Hammerhead structure]]
 
[[Image:Biomod-2012-UTokyo-UT-Komaba-hammerhead_structure_3.png|500px|center|thumb|The Pseudo-Hammerhead structure]]




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===DNA Tablet with a N-stable System: More Pictures===
===DNA Tablet with a N-stable System: More Pictures===


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


[[Image:Biomod-2012-UTokyo-UTKomaba-tristable_model.png|300px|center|n-oscillator system]]
[[Image:Biomod-2012-UTokyo-UTKomaba-tristable_model.png|300px|center|The Tristable System]]




This figure depicts a model of a tristable system. Each of A, B and C produces itself and inhibits the production of the others. Also, all of the products (A,B,C,iA,iB,iC) are degraded by the exonuclease. The degradation processes are not shown in the picture.
The figure above depicts a model of the tristable system. Each of A, B and C produces itself and inhibits the production of the others. Also, the number of the all products (A,B,C,iA,iB,iC) are degraded by the exonuclease. The decreasing 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 "only A" or "only B" or "only C" in the same way as the bistable system.
We can change the picture which the DNA tablet shows while this system realizes the condition of "only A" or "only B" or "only C" in the same way as the bistable system.


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


We can represent such n-stable system by an n-sided polygon in order to make the diagram simpler (figure below). Mutual inhibition between each two of A1, A2...and An is expressed by a red line. The degradation and self-production processes are not shown.
We can represent such n-stable system by an n-sided polygon in order to make the diagram simpler. Mutual inhibitions between each two of A1, A2...and An are expressed by red lines. The degradation and self-production processes are not shown in the figure.


{|class="noborder center"  
{|class="noborder center"  
|[[Image:Biomod-2012-UTokyo-UTKomaba-tristable_simple_model.png|200px]]  
|[[Image:Biomod-2012-UTokyo-UTKomaba-tristable_simple_model.png|200px|The Simple Model of the Tristable System]]  
|[[Image:Biomod-2012-UTokyo-UTKomaba-nstable_simple_model.png|380px]]
|[[Image:Biomod-2012-UTokyo-UTKomaba-nstable_simple_model.png|380px|The Simple Model of the n-stable System]]
|}
|}


The characteristics of the DNA-tablet with n-stable system is that we can freely switch (or preserve) the picture it is showing to any other one by changing the conditions.
The characteristics of the DNA-tablet with n-stable system is that we can freely switch the pictures.
 
Simulation of the n-stable system is [[Biomod/2012/UTokyo/UT-Komaba/Simulation#n-stable_system_simulation|here]].


If you want to see  the simulation of n-stable system, please click [[Biomod/2012/UTokyo/UT-Komaba/Simulation#N-stable_System_Simulation|here]].


===DNA Tablet with an N-oscillator System: Play a Movie===
===DNA Tablet with an N-oscillator System: Play a Movie===


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




[[Image:BIOMOD-2012-UTokyo-UTKomaba-trioscillate_system_model_1.png|300px|center]]
[[Image:BIOMOD-2012-UTokyo-UTKomaba-trioscillate_system_model_1.png|300px|center|The Trioscillator System]]




The figure is a model of a trioscillator system. The difference between this system and a tristable one is that each of A, B and C inhibits the production of only C, B and A respectively (therefore, inhibitions are not mutual).
The figure above is the model of the trioscillator system. The difference between this system and the tristable one is that each of A, B and C inhibits the production of only one of the other DNA so that inhibitions are not mutual.
In this system, the condition change makes a circle through "only A", "only B" and "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 weaker, and B increases, then inhibition to A from B gets strong, and as a result B becomes dominant.
In this system, the condition changes make a circuit of "only A", "only B" and "only C", and the DNA tablet switches its pictures automatically: if A is dominant, the inhibition of A to C becomes strong, then the inhibition of C to B gets weaker so that B increases. Then inhibition to A from B gets strong, and as a result B becomes dominant. In the same way, the circuit continues to go around.
Here we don't have to input some specific strands to change the pictures.  
Here we don't have to input some specific strands to change the pictures.  


The figures below are simplified models of tristate oscillator and n-oscillator systems.
The figures below are simplified models of the tristate oscillator and n-oscillator systems.
The difference between these and those of the tristable or n-stable systems 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 so on), while red ones mean mutual inhibition.
The difference between these models and those of the tristable and n-stable systems is quite simple: the sides of the polygon are blue. The blue lines represent non-mutual inhibition while red ones mean mutual inhibition. For example, A inhibits all of the self-productions except B's, and B does so except C's, and so on.  
In this case, the state does clockwise change: A to B to C to A, or A1 to A2 to...to An to A1.
In this case, the change of the states is clockwise: A to B to C to A, or A1 to A2 to...to An to A1.


{| class="center noborder"
{| class="center noborder"
|[[Image:BIOMOD-2012-UTokyo-UTKomaba-trioscillate_system_simplemodel.png|200px]]
|[[Image:BIOMOD-2012-UTokyo-UTKomaba-trioscillate_system_simplemodel.png|200px|The Simple Model of the Trioscillator system]]
|[[Image:BIOMOD-2012-UTokyo-UTKomaba-noscillate_system_simlemodel.png|380px]]
|[[Image:BIOMOD-2012-UTokyo-UTKomaba-noscillate_system_simlemodel.png|380px|The Simple Model of the n-oscillator System]]
|}
|}


This allows the DNA tablet to play a short movie. If we prepare slightly different images (like film frames), they change automatically and look like a movie. If you want to look at the movie in the reverse direction, you just need to change the direction of the inhibition loop.
This system enables the DNA tablet to play a short movie. If we prepare slightly different images like film frames, and they change automatically, we can observe a movie on the surface of the tablet. If you want to look at the movie in the reverse direction, you just need to change the direction of the inhibition circuit.


{| class="noborder" style="margin-left: auto; margin-right: auto;"
{| class="noborder" style="margin-left: auto; margin-right: auto;"
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|}
|}


Simulation of the n-oscillator system is [[Biomod/2012/UTokyo/UT-Komaba/Simulation#N-oscillate_System_Simulation|here]].
If you want to see  the simulation of oscillator system, please click [[Biomod/2012/UTokyo/UT-Komaba/Simulation#N-oscillator_System_Simulation|here]].
 
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Idea

Concept

The Concept of the DNA Tablet
The Concept of the DNA Tablet

Now that there are many tablet computers, our goal is to create the world's smallest tablet!! We designed and structured a 9x12 pixels display made of DNA origami. Our tablet shows multiple pictures autonomously, corresponding to its environment.

To realize this idea, we combined two technology, DNA origami and Bistable system. Detailed information is written in latter section.


Bistable System

What is the Bistable System?

The Network of the Bistable System

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

For example, we represent two states by materials A and B. The picture on the right side shows a reaction network implementing a bistable system using those two materials. In this network, A promotes the production of A itself and iB ("i" means inhibition), and B promotes B itself and iA. On the other hand, iA inhibits the production of A and iB inhibits production of B. There are also reactions that continuously degrade the number A, B, iA, and iB.

If the system is started with a larger amount of A than B, this network promotes more the production of A, which in turn will induce a decrease of B (Detailed information is written in Simulation|Simulation section). Afterwards, there remains only A, and vice versa if the initial conditions are opposite. Thus, thanks to the bistable system, we can make two states easily: "only A" or "only B". Any intermediate state cannot be stable and will go toward one of these two exclusive states.


Method

We design the bistable system with DNA. [3]

  • The Production of A,B,iA,iB

The Production of A　　The Production of B

B and iA are also produced in the same way.


  • The Inhibition of Production of A,B

The Inhibition of A

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


  • The Decomposition of A,B,iA,iB (nothing means dNMPs a non-reactive monomer of DNA)

The Decomposition of DNA


DNA tablet

What is the DNA tablet ?

The Mechanics of Displaying Pixels

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


There are four kinds of pixels:

  • Θ is always on (it can always be observed).
  • Φ is always off (it can not be observed).
  • [math]\displaystyle{ \overline{A} }[/math] can be observed when there is a lot of A in the solution.
  • [math]\displaystyle{ \overline{B} }[/math] can be observed when there is a lot of B in the solution.


These pixels are made of hammerhead-like structures. 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; "only A" or "only B".

These four kinds of pixels enable us to switch pictures (You can see the simulation here). The way of switching is very simple: you just need to switch the state of the bistable system. If you put enough B when you are observing the image A, all A will disappear, and B will be produced, which makes the image B appear. Then you can switch again to come back to image A just by putting enough A. Note that if you don't have the bistable system and you just add A (or B) strands when you want to see the image A (or B), the solution will end up with a concentrated mixed one of A and B strands, and the image on the surface will be blurred after a few changes of states. On the contrary the bistable keeps the picture clear and reversible in any time.


The Example of the DNA Tablet Design


How to See

We use AFM to see the DNA tablet. Generally, AFM detects the difference between hybridized and single-stranded ends of the staple strands on the DNA origami surface. However,　even if the single strands on the DNA tablet are hybridized, they do not produce enough contrast to be seen by AFM. Therefore, we applied hammerhead structures to the DNA tablet because the structures can be observed as pixels with higher AFM contrast. However, they cannot be dynamically updated by hybridization-dehybridization reactions. Therefore, we introduced open hammerheads (pseudo-hammerheads) stuructures to produce enough contrast and make themselves updatable.

When the strands produced by the bistable system are hybridized, they compose stable hammerhead structures and produce visible pixels.


The Pseudo-Hammerhead structure


Future Works

DNA Tablet with a N-stable System: More Pictures

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

The Tristable System
The Tristable System


The figure above depicts a model of the tristable system. Each of A, B and C produces itself and inhibits the production of the others. Also, the number of the all products (A,B,C,iA,iB,iC) are degraded by the exonuclease. The decreasing processes are not shown in the picture. We can change the picture which the DNA tablet shows while this system realizes the condition of "only A" or "only B" or "only C" in the same way as the bistable system.

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

We can represent such n-stable system by an n-sided polygon in order to make the diagram simpler. Mutual inhibitions between each two of A1, A2...and An are expressed by red lines. The degradation and self-production processes are not shown in the figure.

The Simple Model of the Tristable System The Simple Model of the n-stable System

The characteristics of the DNA-tablet with n-stable system is that we can freely switch the pictures.

If you want to see the simulation of n-stable system, please click here.

DNA Tablet with an N-oscillator System: Play a Movie

The DNA tablet will also be able to show a short movie by using an n-oscillator system.


The Trioscillator System
The Trioscillator System


The figure above is the model of the trioscillator system. The difference between this system and the tristable one is that each of A, B and C inhibits the production of only one of the other DNA so that inhibitions are not mutual. In this system, the condition changes make a circuit of "only A", "only B" and "only C", and the DNA tablet switches its pictures automatically: if A is dominant, the inhibition of A to C becomes strong, then the inhibition of C to B gets weaker so that B increases. Then inhibition to A from B gets strong, and as a result B becomes dominant. In the same way, the circuit continues to go around. Here we don't have to input some specific strands to change the pictures.

The figures below are simplified models of the tristate oscillator and n-oscillator systems. The difference between these models and those of the tristable and n-stable systems is quite simple: the sides of the polygon are blue. The blue lines represent non-mutual inhibition while red ones mean mutual inhibition. For example, A inhibits all of the self-productions except B's, and B does so except C's, and so on. In this case, the change of the states is clockwise: A to B to C to A, or A1 to A2 to...to An to A1.

The Simple Model of the Trioscillator system The Simple Model of the n-oscillator System

This system enables the DNA tablet to play a short movie. If we prepare slightly different images like film frames, and they change automatically, we can observe a movie on the surface of the tablet. If you want to look at the movie in the reverse direction, you just need to change the direction of the inhibition circuit.

If you want to see the simulation of oscillator system, please click here.


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