Biomod/2012/UTokyo/UT-Hongo/Intro

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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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Focus

Fig.1

Our focus was to use DNAs with some other functional molecules so that new unprecedented devices could be made.

Enzymes are widely used for their specific binding and catalytic abilities. However, they are difficult to fully exploit the advantages for two reasons. The first reason is that they can easily be deactivated by external factors such as the presence of proteases. Also, even though it is getting easier, it is still difficult to adjust the structure of the enzyme for purposes such as adding a new function. This is because the enzymes structure can be changed by the modification. By overcoming these difficulties, the enzyme could be used in a wider field.

We focused on the DNA molecules for they are the optimum materials to compliment such difficulties. DNAs are stable in various environmental conditions, and by making a rigid structure, it can also be relieved from DNAnases. The structure of DNA can also be easily adjusted and modified to add new functionalities. By combining enzymes and DNAs, we sought to make a nanodevice that can be used for a wider field of application.


Idea of DNA Shell

fig.2

To make a DNA device which can connect with some other matter, we need a mechanizm to connect the two components. We thought it wise to add the connection ability on the DNA, for we could use the same system on all the substrates. The most simplest idea that came to us was the shell. By adding molecules that are capable of binding with other substrates, we can capture the substrate selectively.

For the Biomod, we focused on capturing streptavidin using biotin functionalized DNAs.


Areas of Application

Our DNA shell opened up new various applications in various fields.

  1. High-Resolution Molecular Sensing
  2. Substrate Protection
  3. Attachment to solid surface



High-Resolution Molecular Sensing

fig.3

The molecular detection with higher sensitivity could be achieved by the DNA Shell. This is because of the capturing mechanizm. Conventional DNA devices only used one fluorescent molecule and quencher molecule. This way, the difference in the fluorescence is very small. However, since the DNA shell captures the molecules using the DNA surface, we can add more fluorescent and quenching molecules. With more of each molecules, we can expect a larger change in the fluorescence when the device captures the substrate. This feature could be used to manipulate the


Substrate Protection

fig.4

Just like shellfish use their shells for protection in the nature, we can use the DNA shell to protect the substrate inside. When an enzymes gets decomposed, it is usually done by proteases, another group of enzymes that break down other enzymes. Proteases decompose the enzymes by capturing it inside the protease's structure. When the substrate is "wearing" the DNA shell, the structure would be too big for the protease to capture.

One of the problems with using enzymes is that they can be easily decomposed by the presence of unnecessary proteases which is often called contamination. This application enalbles us to do the following things.

1.The use of Enzymes in the presence of enzymes
2.The longer usage of bioreactors


Attachment to solid surfaces

Attachment to a solid surface is very important for practical application. When the enzymes are floating in the solution with the substrates for reactions, they will also be washed away with the flow. However, by attaching it to a solid surface, we can keep the enzyme from being washed away. This way, not only can we keep the reactor working longer, but also retain the purity of the products at the downstream. Usually, it is difficult to attach enzymes onto a solid surface. The reason is because the structure of the enzymes could change easily by solid, and leads to the deacitivation of the catalytic point. However, by using DNA shell, we can neglect such problems because they are strong against environmental changes.

We experimented this feature using the microfluidics device, a device which has a high surface to volume ratio, and therefore is practical when using bioreactors.

We named our DNA origami Medical DNA Shell because the structure is like a seashell capturing some kind of a prey, and we have a wish that it would be applied to medical usage. The scheme above depicts the way it could be used to capture thrombin, a protein that causes thrombiosis. The Medical DNA Shell is comprised of three domains, the upper lid and the bottom part of the shell, and the linker to some surface. On each sides of the shell, there are either flourescent molecules or quenching molecules connected to the structure. For the purpose of measuring the strength of bonding or for some quantitative analysis, there are A LOT of them. The more we have the florescent and quenching molecules, the larger the difference between in the florescence observed when the shell is “open” and “closed”, leading us to detect the capture of substrates in molecular level.


Streptavidin and biotin

We chose the bonding between Streptavidin and biotin as the model bonding. This bonding is one of the strongest specific bonding, strong enough to assure that the mechanism of closing of the shell when capturing takes place would occur.


Microfluidic device

Microfluidic technologies provide numbers of advantageous features especially for biological applications. Researchers have been working on PDMS (polydimethylsiloxane)-based microfluidic devices for microscale biochemical operations. It pours liquid to microscopic channels and operates the biochemical reaction, separation. In micro space, the ratio of the surface area to the volume of fluid is remarkably large compared with the usual scale. Therefore, walls and fluid interface exert a large influence on reaction. So we can analyze target molecule by micro amount of samples using microfluidic. Also it can form laminar flow. Then we use the device in order that only a part of fixed shell reacts to quenching matter. The reason of fixing Shell is that a shift of fluorescence intensity becomes intelligible by observing the time variation of a specific portion.

　


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   <h2 style="border-bottom: none;">BIOMOD 2012 Team UT-Hongo</h2>
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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo">Top</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo#description">Abstract</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo#youtube">YouTube</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo#navi">Links</a></li> </ul> 

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro">Motives</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Focus">Focus</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Idea_of_DNA_Shell">Idea</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Functionalities_Exhibited">Funcitonalities</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Conceptual_Blueprint_of_the_Structure">Blueprint</a></li>

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly">Design & Results</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Design">Design</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Adding_functionality">Function</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Result">Result</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Assembly_of_the_DNA_Shell">Experiments</a></li>

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method">Method</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#AFM">AFM</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Photometer">Photometer</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Electrophoresis">Electrophoresis</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Ultraviolet_Irradiation">Others</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Reagent">Reagent</a></li> </ul> 

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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> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#DNA_Shell_with_Functionality">Functionalization</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#Shell_with_the_DNA_Hybridization_Circuits">Circuits</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#A_Device_more_than_Shell_and_Enzyme">Conclusion</a></li>

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team">Team</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Info">Info</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Team_members">Members</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Graduate_and_Post-Doctoral_Mentors">Mentors</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Team_Photos">Photos</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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     Copyright (C) 2012 | Design by Yuichi Nishwiaki | BIOMOD Team UT-Hongo
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