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#Realize the DNA shell structure
#Realize the DNA shell structure
#Confirm the three possible functionalities through experiments
#Confirm the three possible functionalities through experiments


After we had finished the experiments, assessment of how well we did was made.  
After we had finished the experiments, assessment of how well we did was made.  
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As for the detection, we were able to confirm that by using more than one pair of fluorescent and quencher molecules, we were able to get a higher signal of the capturing. We also confirmed in the experiment of using DNA Shell to protect the HRP-Streptavidin that the activity of streptavidin could be retained even if it was in a captured state. Finally, the experiments showed that the attachment of DNA shell to the microfluidics device was also achieved.
As for the detection, we were able to confirm that by using more than one pair of fluorescent and quencher molecules, we were able to get a higher signal of the capturing. We also confirmed in the experiment of using DNA Shell to protect the HRP-Streptavidin that the activity of streptavidin could be retained even if it was in a captured state. Finally, the experiments showed that the attachment of DNA shell to the microfluidics device was also achieved.


To improve and give a more sound result, these experiments below should be conducted.
<br>
----
<br>
 
To improve and give a more useful result to verify our idea, these experiments below should be conducted.


*Finding the length of each fluorescent and quencher molecules where self-absorption does not occur
*Finding the length of each fluorescent and quencher molecules where self-absorption does not occur

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<li class="toppage"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo">Top</a></li> <li class="motives"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro">Motives</a></li> <!-- <li class="design"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Function">Design</a></li> --> <li class="result"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly">Design & Results</a> <ul class="submenu"> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Assembly_of_the_DNA_Shell">Assembly of the DNA Shell</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Capturing_ability">Capturing Ability</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Immobilizing_on_microfluidic_device">Immobilizing on microfluidic device</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Supporting_Enzyme">Supporting Enzyme</a></li> </ul> </li> <li class="method"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Method">Method</a></li> <li class="futurework"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork">Progress & Beyond</a></li> <li class="team"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Team">Team</a></li> <li class="acknowledgement"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement">Acknowledgement</a></li> 

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Progress of Our Research

We gave set the goal as below.

  1. Realize the DNA shell structure
  2. Confirm the three possible functionalities through experiments

After we had finished the experiments, assessment of how well we did was made.

Goal 1. Not only was the building of the DNA shell confirmed using the AFM but also the captured state was analysed geometrically. Therefore, we think that this goal was fully accomplished.

Goal 2. As for the detection, we were able to confirm that by using more than one pair of fluorescent and quencher molecules, we were able to get a higher signal of the capturing. We also confirmed in the experiment of using DNA Shell to protect the HRP-Streptavidin that the activity of streptavidin could be retained even if it was in a captured state. Finally, the experiments showed that the attachment of DNA shell to the microfluidics device was also achieved.



To improve and give a more useful result to verify our idea, these experiments below should be conducted.

  • Finding the length of each fluorescent and quencher molecules where self-absorption does not occur

When we added 12 equiv. pairs of fluorescent and quencher molecules, there was no difference in the change in fluorescence. This is thought to be caused by a phenomena called self-absorption, where the emitted fluorescence is captured by another fluorescent molecule. This can be prevented by enlarging the distance between the fluorescent molecules. Finding the length this phenomena will not be troubling would be a method to make this more device useful.

  • Protection experiment using new Trypsin reagent and also with different groups of proteases

Our experiment with Trypsin seemed not to work because of the failure in Trypsin activity. Therefore, we would like to do the experiment again with a new Trypsin. Also, it would be better to try with different proteases.

Future Works

From the results of our experiments, we confirmed that the proposed ideas were realized. To give ideas on a more broader span of ideas, we also thought of places this new nano-device could work in handy.

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


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


Shell with the DNA Hybridization Circuits

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. If you design two or more these structures, the Shell works like OR gate (Fig.5).

Fig.5


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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<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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