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In the strand displacement reaction, when a DNA is input, another DNA is released.
In the strand displacement reaction, when a DNA is input, another DNA is released.


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=== Design of Logical Gates on the DNA Shell===
=== Design of Logical Gates on the DNA Shell===
We will attach a biotin to the non-binding site of the DNA that is released in the strand displacement reaction.
We will attach a biotin to the non-binding site of the DNA that is released in the strand displacement reaction.
   
   
[[Image:Fig.4-6.jpg|center|500px]]
[[Image:Fig.4-6.jpg|thumb|500px]]
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Without the input DNA, streptavidin cannot combine with biotins because of the steric hindrance. However, once the DNA is input, the combination between streptavidin and biotins can be formed. The combination is formed only when 2, 3, or 4 biotin monomers are binding. We will make the 2 strand displacement reaction devices on both sides of the Shell (total 4 devices).  
Without the input DNA, streptavidin cannot combine with biotins because of the steric hindrance. However, once the DNA is input, the combination between streptavidin and biotins can be formed. The combination is formed only when 2, 3, or 4 biotin monomers are binding. We will make the 2 strand displacement reaction devices on both sides of the Shell (total 4 devices).  


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Each device catches the different input DNA. When the more than two biotins on the different Shell sides are gathering, the DNA Shell will be closed (i.e., biotins on the A and B, or C and D gathering, the Shell will not be closed).
Each device catches the different input DNA. When the more than two biotins on the different Shell sides are gathering, the DNA Shell will be closed (i.e., biotins on the A and B, or C and D gathering, the Shell will not be closed).
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We will check it by the fluorophotometry.
We will check it by the fluorophotometry.


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=== Practical application===
=== Practical application===

Revision as of 04:55, 22 October 2012

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Confirmation of the flexibility of the bond of the DNA Shell

In order to "catch" some kind of a substrate, the bonding between the lid and the bottom must be flexible enough to bend. Before we catch the target molecule (Streptavidin) by the DNA Shell, we have to make it clear whether the DNA Shell can be closed or not.


The next picture shows the part of the DNA Shell.


①DNA binding to the fluorescent molecule

②DNA binding to the quencher

③DNA binding to the biotin( no.1)

④DNA binding to the biotin( no.2)

⑤DNA with the fluorescent molecule

⑥DNA with the quencher

⑦DNA with biotin (no.1)

⑧DNA with biotin (no.2)

⑨streptavidin

⑩complementary DNA for the DNA binding to the biotin

In the experiment of folding the shell by the combination of DNA for the fixation of streptavidin and biotin, we will use ③, ④, and ⑩ (like in the scheme below).


In the experiment of folding by the combination between streptavidin and biotin, we will use ⑦, ⑧, and ⑨ (like below).



Observing the shape of the Shell before and after closing

We will use the Gel Electrophoresis, fluorophotometry, and AFM for detection.

In fluorophotometer, ①, ②, ⑤, and ⑥ are also needed.


Shell with the DNA Hybridization Circuits

DNA Shell with the toehold medicated strand displacement reaction device

To get more advanced DNA Shell with a logical circuit, we will make the toehold medicated strand displacement reaction device on the DNA Shell. In the strand displacement reaction, when a DNA is input, another DNA is released.


Design of Logical Gates on the DNA Shell

We will attach a biotin to the non-binding site of the DNA that is released in the strand displacement reaction.



Without the input DNA, streptavidin cannot combine with biotins because of the steric hindrance. However, once the DNA is input, the combination between streptavidin and biotins can be formed. The combination is formed only when 2, 3, or 4 biotin monomers are binding. We will make the 2 strand displacement reaction devices on both sides of the Shell (total 4 devices).


Each device catches the different input DNA. When the more than two biotins on the different Shell sides are gathering, the DNA Shell will be closed (i.e., biotins on the A and B, or C and D gathering, the Shell will not be closed). Output is expected like the diagram below. The probability of the output is 9/16. We will check it by the fluorophotometry.


Practical application

This circuit consists of two OR gates and one AND gate, and the number of inputs must be less than 4. Therefore, this circuit might be applied to a drug delivery system under such condition, or medical examinations using the blood types (that has just 4 inputs).

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork">Progress & Beyond</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#Variety_of_Target_Substances">Target Variety</a></li> 

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement">Acknowledgement</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Mentor">Mentor</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Professors">Professors</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Sponsors">Sponsors</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Special_Thanks">Special Thanks</a></li> </ul> 

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