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{{Biomod/2012/UTokyo/UT-Hongo}}
1. Confirming that the bond of the DNA Shell is flexible.
1.1 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 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 a biotin.
1.3
4. Shell with the DNA Hybridization Circuits
4.1 DNA Shell with the logical circuit is more useful, so we will make the toehold medicated strand displacement reaction device on the DNA Shell.
In a toehold medicated strand displacement reaction, when a DNA is input, another DNA is released.
4.2 We will attach the biotin to the non-binding site of the DNA that is released in the strand displacement reaction.
Without the input DNA , Streptavidin can not combine with the biotin because of the steric hindrance. However, once the DNA is input, the combination between Streptavidin and biotin can be formed. The combination is only formed when 2, 3, or 4 biotin monomer is gathering. We will make the 2 strand displacement reaction devices on both side of the Shell (total 4 devices). Each device catch different input DNA. Output is expected like the diagram below. The probability of the output is 9/16.
We will check it by the fluorophotometry.






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1. Confirming that the bond of the DNA Shell is flexible. 1.1 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 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 a biotin.

1.3


4. Shell with the DNA Hybridization Circuits 4.1 DNA Shell with the logical circuit is more useful, so we will make the toehold medicated strand displacement reaction device on the DNA Shell. In a toehold medicated strand displacement reaction, when a DNA is input, another DNA is released.

4.2 We will attach the biotin to the non-binding site of the DNA that is released in the strand displacement reaction.

Without the input DNA , Streptavidin can not combine with the biotin because of the steric hindrance. However, once the DNA is input, the combination between Streptavidin and biotin can be formed. The combination is only formed when 2, 3, or 4 biotin monomer is gathering. We will make the 2 strand displacement reaction devices on both side of the Shell (total 4 devices). Each device catch different input DNA. Output is expected like the diagram below. The probability of the output is 9/16. We will check it by the fluorophotometry.


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