Biomod/2011/TeamJapan/Tokyo/Project: Difference between revisions
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:To achive this mode, we needed to come up with the mechanism of walking and the way to make DNA tracks. | :To achive this mode, we needed to come up with the mechanism of walking and the way to make DNA tracks. | ||
:We chose the "Deoxyribozyme-substrate reaction" to solve the mechanism of walking. And we also chose the microchannel to solve the problem of making of DNA tracks. | :We chose the "Deoxyribozyme-substrate reaction" to solve the mechanism of walking. And we also chose the microchannel to solve the problem of making of DNA tracks. | ||
:we set three goals to achieve this mode:'''1.Confirmation of deoxyribozyme activity, 2.Construction of DNA tracks and 3.Confirmation of moving directionally.''' We show the results of these in the result page. | |||
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===The mechanism of | ===The mechanism of track walking=== | ||
:This reaction utilizes DNA ciliate’s deoxyribozyme legs and their substrates on the DNA tracks. A deoxyribozyme leg of the DNA ciliate cuts the substrate DNA at an inserted RNA base. Then, the leg dissociates from cut substrate and moves to the near uncut substrate. By repeating this reaction, DNA ciliate can walk along DNA track with substrates. | :This reaction utilizes DNA ciliate’s deoxyribozyme legs and their substrates on the DNA tracks. A deoxyribozyme leg of the DNA ciliate cuts the substrate DNA at an inserted RNA base. Then, the leg dissociates from cut substrate and moves to the near uncut substrate. By repeating this reaction, DNA ciliate can walk along DNA track with substrates. | ||
|width="450px"|[[Image:Tokyo-trackwalking2.png|Figure.1:The mechanism that DNA ciliate moves directionally.|420px|center]] | |width="450px"|[[Image:Tokyo-trackwalking2.png|Figure.1:The mechanism that DNA ciliate moves directionally.|420px|center]] | ||
|} | |} | ||
===Construction of DNA tracks=== | |||
:DNA origami can be appropriately landscape for nanometer-sized moving nanomachines because it can be designed to complex structural DNA tracks. However, as the tracks for our micrometer-sized molecular robot DNA ciliate, DNA origami is not useful because it takes enormous time to make micrometer-sized track from DNA origami that DNA ciliate can move along and we may be not able to complete constructing the tracks by this summer. Therefore, we challenged to make complex structural DNA tracks by using the technology of microfluid mechanics.(Figure.2) We show you the principle of making microchannel in the result page. (Link:) | :DNA origami can be appropriately landscape for nanometer-sized moving nanomachines because it can be designed to complex structural DNA tracks. However, as the tracks for our micrometer-sized molecular robot DNA ciliate, DNA origami is not useful because it takes enormous time to make micrometer-sized track from DNA origami that DNA ciliate can move along and we may be not able to complete constructing the tracks by this summer. Therefore, we challenged to make complex structural DNA tracks by using the technology of microfluid mechanics.(Figure.2) We show you the principle of making microchannel in the result page. (Link:) | ||
[[Image:Micrometer sized track.jpg|200px|Figure.2:The schematic diagram of microchannel.]] | [[Image:Micrometer sized track.jpg|200px|Figure.2:The schematic diagram of microchannel.]] | ||
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Project
DNA ciliate body
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1. Free moving mode
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Model
- There are two problems to moves DNA ciliate by Brownian motion. One problem is the thing which the effect of Brownian motion to large materials becomes smaller than the effect of Brownian motion to small materials. The other problem is the thing which unexpected phenomenon happens in some materials for body.
- To solve above two problems, by try and error, we designed a relevant material and size for free moving mode.
- The movement by Brownian motion is described by the right equation. The left side is the mean square displacement from the initial coordinate: x0. On the other hand, R is gas constant, T is the absolutely temperature,f is mobility and NA means Avogadro number. In those constants, f is dependent on the material’s diameter and density, so f can be changed by selecting materials. By optimization of DNA ciliate’s material, we tried to give free moving mode to DNA ciliate.
2. Track walking mode
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The mechanism of track walking
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Construction of DNA tracks
- DNA origami can be appropriately landscape for nanometer-sized moving nanomachines because it can be designed to complex structural DNA tracks. However, as the tracks for our micrometer-sized molecular robot DNA ciliate, DNA origami is not useful because it takes enormous time to make micrometer-sized track from DNA origami that DNA ciliate can move along and we may be not able to complete constructing the tracks by this summer. Therefore, we challenged to make complex structural DNA tracks by using the technology of microfluid mechanics.(Figure.2) We show you the principle of making microchannel in the result page. (Link:)
3. Light-irradiated gathering mode
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Mechanism
UV-switching system
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