Biomod/2012/UTokyo/UT-Hongo/FutureWork
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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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1. Closing the DNA Shell.
1.1 Confirming that the bond of the DNA Shell is flexible
Before we catch the target molecule by DNA Shell, we have to make it clear whether the DNA Shell can be closed, or the bond of the Shell is enough flexible to move smoothly.
1.2 How to close the Shell
We will close the Shell using DNA with the quencher and the fluorescent molecule, and the very strong combination between streptavidin and biotin. Streptavidin forms tetramer and each monomer binds to a biotin.
The design of the Shell is like below.
red: DNA binding to the functional molecule
yellow: DNA binding to the quencher and the fluorescent molecule
The next picture shows the part of the DNA Shell.
①DNA binding to the fluorescent molecule ②DNA binding to the quencher ③DNA binding to the biotin( no.1) ④DNA binding to the biotin( no.2) ⑤DNA with the fluorescent molecule ⑥DNA with the quencher ⑦DNA with biotin (no.1) ⑧DNA with biotin (no.2) ⑨streptavidin ⑩complementary DNA for the DNA binding to the biotin
In the experiment of folding by the combination of DNA for the fixation of streptavidin and biotin, we will use ③, ④, and ⑩ (like below).
In the experiment of folding by the combination between streptavidin and biotin, we will use ⑦, ⑧, and ⑨ (like below).
1.3 Observing the shape of the Shell before and after closing
We will use the Gel Electrophoresis, fluorophotometry, and AFM. In fluorophotometr, ①, ②, ⑤, and ⑥ are also needed.
2. Shell with the DNA Hybridization Circuits
2.1 DNA Shell with the toehold medicated strand displacement reaction device
To get more advanced DNA Shell with a logical circuit, we will make the toehold medicated strand displacement reaction device on the DNA Shell. In the strand displacement reaction, when a DNA is input, another DNA is released.
2.2 Toehold medicated strand displacement reaction device with biotin
We will 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. The combination is formed only when 2, 3, or 4 biotin monomers is gathering. We will make the 2 strand displacement reaction devices on both sides of the Shell (total 4 devices).
Each device catches the different input DNA. When the more than two biotins on the different Shell sides are gathering, the DNA Shell will be closed (i.e., biotins on the A and B, or C and D gathering, the Shell will not be closed). Output is expected like the diagram below. The probability of the output is 9/16. We will check it by the fluorophotometry
2.3 Practical application
This circuit consists of two OR gates and one AND gate, and the number of inputs must be less than 4. Therefore, this circuit might be applied to a drug delivery system under such condition, or medical examinations using the blood types (that has just 4 inputs).
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