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===DNA nanotechnology===
===DNA nanotechnology===
* Easy to make a certain structure
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.
* Having various functionalities
* Strong against acid or bases


===Enzymes===
===Enzymes===
* Has specific catalytic reactivity
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 pharmacucial production. The reason why enzymes have these functionalities is because of their controlled structure that would only let certain substrates bond with the enzyme; other molecules would not be able to bond because of the steric effect.
** Structure selectivity
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.
* Very vulnerable to environmental changes
In this BIMOD research project, we propose that the DNA could be used as a new material to alter enzymes.


==Binding Metals with DNA==
==Binding Metals with DNA==
* DNA Coordination bonding with different metal ions
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.
* Metal Ions play
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.
** Cofactors or Coenzymes
** Usually used as Lewis Acid centers


==Aim of Our Research==
==Aim of Our Research==

Revision as of 05:28, 2 September 2012

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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 pharmacucial production. The reason why enzymes have these functionalities is because of their controlled structure that would only let certain substrates bond with the enzyme; other molecules would not be able to bond because of the steric effect. 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

  • Building DNA device
    • Capture various molecules
    • Adjustable structures

Streptavidin and biotin

  • Binding is very strong
    • Opening and closing of the shell

Microfluidic device

  • PDMS (polydimethylsiloxane)-based microfluidic devices
  • For biochemical reaction, separation
  • Analyze target molecules by micro amount of samples
  • Part of fixed shell reacts to quenching matter
  • Fixing Shells for detecting shift of fluorescence intensity

Y-shaped Device image

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