Biomod/2012/UTokyo/UT-Hongo/FutureWork

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(The Number of the Inputs)
(The Number of the Inputs)
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Output is expected like the diagram below (Fig.8).  
Output is expected like the diagram below (Fig.8).  
The probability of the output is 9/16.
The probability of the output is 9/16.
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[[Image:5-7.jpg|730px|thumb|center|Fig.8]]
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[[Image:5-7.jpg|730px|border|center|Fig.8]]
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Revision as of 11:34, 27 October 2012

The University of Tokyo

Contents

Variety of Target Substances

We made DNA Shell like below (Fig.1), and additional DNA that specifically binds to a certain substance can be constructed on the Shell. By changing the arrangement of the DNA, you can capture whatever substance you like. As example, we experimented with biotin and streptavidin (Fig.2).

Fig.1
Fig.1
Fig.2
Fig.2


We thought of capturing ATP (Fig.3) or thrombin. We could not experiment because of the shortage of time, but we made arrangements of the DNA that bind to ATP or thrombin. Thrombin solidifies the blood, so the Shell that specifically binds to thrombin can prevent a blood clot. Like these, you can change the arrangement of the DNA on the Shell, and capture many kinds of substances. It makes DNA Shell a more useful device.

Fig.3
Fig.3


DNA Shell with Functionality

By putting DNA Shell and an enzyme together, you can use the Shell as a more functional device. As example, we experimented with tetramethylbenzidine(TMB), horseradish peroxidase(HRP), and trypsin. Like that experiment, by capturing the substrate, you can use the Shell as an inhibitor for enzyme (Fig.4).

Fig.4
Fig.4


Shell with the DNA Hybridization Circuits

DNA Shell with the toehold medicated strand displacement reaction device

Fig.5
Fig.5


To get more advanced DNA Shell with a logical circuit, you can make the toehold medicated strand displacement reaction device on the Shell. In the strand displacement reaction, when a DNA is input, another DNA is released (Fig.5)

Design of the Logical Gates on DNA Shell

Fig.6
Fig.6



When you 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 (Fig.6).

Fig.7
Fig.7


The combination is formed only when 2, 3, or 4 biotin monomers are binding. Two strand displacement reaction devices can be constructed on both sides of the Shell (total four devices) (Fig.7).

The Number of the Inputs

Each device catches the different input DNA. When the more than two biotins on the different Shell sides are gathering, The Shell will be closed (i.e., biotins on the A and B, or C and D gathering, the Shell will not be closed). So the number of the inputs is less than four. Output is expected like the diagram below (Fig.8). The probability of the output is 9/16.

Fig.8


A Device more than Shell and Enzyme

When you combine the features of the above 1. ~3., you can get the more advanced DNA Shell. For example, in the case of using the Shell with the logical circuit, the Shell captures a substrate only when all the four kinds of input DNA are exist.


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