Biomod/2011/TeamJapan/Tokyo/Project: Difference between revisions

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[[image:Tokyo-freemoving2.png|center|130px|The equation of Brownian motion.]]
[[image:Tokyo-freemoving2.png|center|130px|The equation of Brownian motion.]]
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==2. Track walking mode==
==2. Track walking mode==
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|width="330px"|[[Image:Tokyo-trackwalking3.png|280px|center|Figure.2:The schematic diagram of microchannel.]]
|width="330px"|[[Image:Tokyo-trackwalking3.png|280px|center|Figure.2:The schematic diagram of microchannel.]]
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==　　3. Light-irradiated gathering mode==
==　　3. Light-irradiated gathering mode==
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|width="450px"|[[Image:Tokyo-gathering2.png|450px|center]]
|width="450px"|[[Image:Tokyo-gathering2.png|450px|center]]
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<div id="navigation"> <div id="menu" style="position:static"> <ul> <li><a class="aMain" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo">Home</a></li> <li><a class="aTeam" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Team/Students">Team</a></li> <li><a class="aProject" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Project</a> <!-- <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Overview</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/introduction">Introduction</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Model">Model</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Devices">Devices</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Modes">Modes</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Results</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> </ul> --> <li><font color="#ffffff">Results</font> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Experiments</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Design</a></li> </ul></li> <!-- <li><a class="Simulation" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a class="DNA design" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Designs</a></li> --> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Protocols">Protocols</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Lab.notebook">Notes</a></li> <li><a class="aNotebook" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sponsors/">Sponsors</a></li> <li><a class="aSitemap" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sitemap">Sitemap</a></li>

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Project

light
We designed micrometer-sized molecular robot: DNA ciliate. DNA ciliate is made by attaching DNA to a micrometer-sized material. DNA ciliate has three independent modes: free moving mode, track walking mode, and light-irradiated gathering mode. In free moving mode, DNA ciliate moves freely and at random by Brownian motion. In track walking mode, DNA ciliate walks on “DNA track”. In light-irradiated gathering mode, DNA ciliate gathers at a specific point by using “UV-switching system” when UV is spotted. Furthermore, DNA ciliate can change a mode. In this page, we explain DNA ciliate and three modes in detail.

The body of the DNA ciliate

DNA ciliates'body
DNA ciliates'body
We made micrometer-sized molecular robot:DNA ciliate. To create DNA ciliate, a micrometer-sized body and its motor are indispensable. We chose DNA as a material for the motor because DNA is the most suitable material that is nanometer-sized and easy to be attached to micrometer-sized objects by various surface modifications. The micrometer-sized body is required to be micrometer-sized, homogeneous, and easy to attach DNA. We use micrometer-sized polystyrene beads as the micrometer-sized bodies because their forms are homogeneous and their carboxylic acid is useful for attaching molecular.
Threfore,we made DNA ciliate by using polystyrene beads which were attached a lot of covalently-immobilized DNA strands.
Figure.1:The pattern diagram of creating DNA ciliate
Figure.1:The pattern diagram of creating DNA ciliate

Three independent modes of the DNA ciliate

　　1. Free moving mode
To realize functional autonomous molecular robot, the robot needs to be able to move at all times because it guarantees the molecular robot not to stop and become uncontrollable. Furthermore, this characteristic is very useful for moving molecular robot to the area. We make “free moving mode” to give DNA ciliate the character. In free moving mode, DNA ciliate moves freely and at random in almost all the space. We use Brownian motion to move DNA ciliate in this mode.
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 principle of free moving

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 diameter and density of the material, so f can be changed by selecting materials. By optimization of material of the DNA ciliate, we gave free moving mode to DNA ciliate.
The equation of Brownian motion.
The equation of Brownian motion.

The equation of Brownian motion.
The equation of Brownian motion.

2. Track walking mode
The mechanizm of track walking is to move DNA ciliate directionally on the track.
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 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.

The mechanism of track walking

This reaction utilizes 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.
Figure.1:The mechanism that DNA ciliate moves directionally.
Figure.1:The mechanism that DNA ciliate moves directionally.

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.(The light figure) We show you the principle of making microchannel in the result page. (Link:here)
Figure.2:The schematic diagram of microchannel.
Figure.2:The schematic diagram of microchannel.

　　3. Light-irradiated gathering mode
In the light-irradiated gathering mode, DNA ciliates gather at a specific area responding to UV irradiation. This mode is achieved by UV-switching DNA devices.
The UV-switching DNA device has the stem-loop structure which has UV-responsive bases, azobenzenes. Before UV-irradiattion, this DNA device doesn’t trap deoxyribozyme legs of DNA ciliate. After UV irradiation, azobenzenes are isomerized and the DNA device traps deoxyribozyme legs of DNA ciliate. By this reaction, DNA ciliates gather at UV-irradiated area. By using this system, we think movement of DNA ciliates can be controlled.

UV-switching system

Deoxyribozyme, blocking DNA, and UV-switching DNA are used in this system. The UV-switching DNA hybridizes with blocking DNA and deoxyribozyme legs of DNA ciliates don’t hybridize with blocking DNA. This structure is closed state. By UV irradiation, the stem-loop of UV-switching DNA becomes open and branch migration starts, so deoxyribozyme legs of DNA ciliates become trapped by UV-switching-DNA. This structure is open state.
UV-switching DNA has a stem-loop structure which contains two azobenzenes. By spotting UV, azobenzenes are isomerized and this loop becomes open. This opened loop has a complementary part for deoxyribozyme. This UV-switching DNA is complimentary for blocking DNA.
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