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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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Background Story
DNA nanotechnology
Technologies to use DNA to form nanostructures with controlled structure has developed over the years. By controlling various features of DNA molecules such as hybridization, various functions could be built in the composite. One of the most remarkable feature DNA molecules possesses is the strong stability against acid or base, which is in the opposite of enzymes which will be depicted below.
Enzymes
Enzymes are known to have specific catalytic activity and specific bonding with the substrate. These features are exploited socially as biosensers and biocatalysts, which are often used for medical check-ups and pharmaceutical production. The reason why enzymes have these functionalities is because of their controlled structure that would only let certain substrates bond with the enzyme. Substrate must be the same size with its active site. If it is big, it can’t combine by the steric effect and if it is small, it enters the active site but hydrophobic inverse-square phenomenon and dispersion force can’t affect to make combination together. Substrate specificity of enzyme is regarding as ‘key and lock’ relationship. But it has to satisfy not only shape but also many physical and chemical factors such as hydrogen bond, Coulomb's inverse-square law, Hydrophobic inverse-square law.
The problem with the enzyme is its vulnerability and its cost for production. Most enzyme's activity is optimized at temperatures around 37 degrees celsius, which is the temperature of the human body, and discrepancy from this temperature leads to decrease in the catalytic activity. Also, the structure of the enzymes could be easily destroyed by acids and bases, which also limits the conditions which it could be used. Also, the yield of producing enzymes is very low compared to the fee. This make enzymes very expensive materials for usage. For these reasons, it could be said that even though enzymes have fabulous features, there are possibilities for a better substituting material.
In this BIMOD research project, we propose that the DNA could be used as a new material to alter enzymes.
Binding Metals with DNA
In the case of enzymes, metal ions, considered as coenzymes or cofactors in molecular biology, play the main role in catalysing reactions as the Lewis acid center. Several researches have shown that coordination bonding between DNA and metallic ions occur between certain base pairs. By fixing the array so that there would be some binding sites for metal ion bonding, we could incorporate metal ions inside the DNA structure, so that it may similarly work as a lewis acid site.
Aim of Our Research
The great scope of our research is to make a DNA origami structure that has functionalities similar to that of enzymes... however, that is far too much for students to do in one summer. Therefore, we chose to narrow down to making a structure which can bind to certain molecules and capture it, just like enzymes makes specific bondings to make ES complex.
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 (Fig. 1) 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.
