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==Project overview==
:<br><i>TeamJapan Tokyo developed an autonomous micrometer-sized molecular robot, “DNA ciliate”, toward the construction of a highly functional molecular robot like a living cell.</i><br><br>
=Project overview=
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&nbsp;&nbsp;A living cell is an ultimate highly functional molecular robot. The high functionality results from not only its various functional molecules but also its “micrometer-sized” body that has enough space to possess the molecules. However, the sizes of already-developed molecular nanomachines are too small to include many functional molecules. Toward the construction of highly functional molecular machines and molecular robots, it is required to construct molecular robots with large (i.e., micrometer-sized) bodies. Here, we propose an autonomous micrometer-sized molecular robot “DNA ciliate”.
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<br><center>This is our YouTube video.</center>
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<i>We developed an autonomous micrometer-sized molecular robot,“DNA ciliate,toward a highly functional molecular robot like living cells.</i><br><br>
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&nbsp;A living cell is an ultimate highly functional molecular robot. The high functionality is caused by not only its various nanometer-sized functional molecules but also its “micrometer-sized” body that has enough space to possess the molecules. However, the size of already-developed molecular nano-robots is too small to include multiple functions. Toward highly functional molecular robots, it is required to construct molecular robots with micrometer-sized body. Here, we propose an autonomous DNA-based molecular robot “DNA ciliate”. A natural ciliate has a micrometer-sized body with cilia and achieves various functions such as autonomous motion with the cilia, phototaxis, etc. DNA ciliate has a micrometer-sized body with many DNAs as cilia, and it can switch three different modes in response to its external environment: the free moving mode, tracks walking mode, and light-irradiated gathering mode. We believe our concept will promote the construction of highly functional molecular robots like cells in future.</td>
<a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project"><img src="http://openwetware.org/images/2/2c/Biomod2011_Team_Tokyo_111101Biomod_three_mode_02_R.jpg" border=1 width="470" height="353"></a><br> 
　　<td align="top"><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Over_view"><img src="http://openwetware.org/images/9/9c/DNA_ciliate概念図.png" border=1 width="400" height="300"></a>
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<font size="3" color="#009933">“DNA ciliate”</font>is an autonomous micrometer-sized molecular robot that has three independent functional modes.
<font size="3" color="#00ff66">“DNA ciliate”</font> has three independent functional modes.
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==DNA ciliate==
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“DNA ciliate” is an autonomous micrometer-sized molecular robot, which is inspired by water microorganisms, ciliates. A natural ciliate has a micrometer-sized body with cilia and achieves various functions such as autonomous motion with the cilia, phototaxis, etc. Similarly,<B> the DNA ciliate has a micrometer-sized body with many DNAs as cilia</B>, and it can<B> switch three different modes</B> in response to its external environment:<B> the free moving mode, the track walking mode, and the light-irradiated gathering mode.</B> (See below)
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<!--<h2>Abstract</h2>
==Three independent functional modes of DNA ciliate==
{|
|A living cell is an ultimate highly-functional molecular robot. The high functionality is caused by not only their various nanometer-sized functional molecules but also its “micrometer-sized” body that has enough space to possess the molecules. However, the size of already-developed molecular nano-robots is too small to include multiple functions. Toward highly-functional molecular robots, it is required to construct molecular robots with micrometer-sized body. Here, we propose an autonomous DNA-based molecular robot “DNA ciliate”. A natural ciliate has a micrometer-sized body with cilia and achieves various functions such as autonomous motion with the cilia, phototaxis, etc. DNA ciliate has a micrometer-sized body with many DNAs as cilia, and it can switch three different modes in response to its external environment: the free moving mode, tracks walking mode, and light-irradiated gathering mode. We believe our concept will promote the construction of highly-functional molecular robots like cells in future.
|}
 
 
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  <td><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Over_view"><img src="http://openwetware.org/images/9/9c/DNA_ciliate概念図.png" border=1 width=420 height=315></a></td>
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<a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project#1._Free_moving_mode"><img src="http://openwetware.org/images/d/d4/Biomod2011_Team_Tokyo_111101Biomod_FreeMovingMode_3_title.gif" border=1 width="300"></a>
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<a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project#3._Light-irradiated_gathering_mode"><img src="http://openwetware.org/images/9/9e/Biomod2011_Team_Tokyo_111101Biomod_Right-irradiatedGatheringMode_3_title.gif" border=1 width="300"></a>
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The DNA ciliate can move around in a broad range of space using the free moving mode. This mode utilizes the Brownian motion of the DNA ciliate.
<br>[[Biomod/2011/TeamJapan/Tokyo/Project#1. Free moving mode|See more]]
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In the track walking mode, the DNA ciliate walk directionally along a single-stranded DNA track on a plate using the cleaving activity of deoxyribozymes attached on the body of the DNA ciliate. The deoxyribozymes cleave substrate DNA strands arrayed as the track, and help the DNA ciliate move to the region of uncleaved substrate DNA step-by-step.
<br>[[Biomod/2011/TeamJapan/Tokyo/Project#2. Track walking mode|See more]]
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The DNA ciliates gather at a specific area where an ultraviolet (UV) light is irradiated; this is the light-irradiated gathering mode. To achieve this mode, a UV-switching DNA system based on the cis-trans isomerization of azobenzenes was designed.
<br>[[Biomod/2011/TeamJapan/Tokyo/Project#3. Light-irradiated gathering mode|See more]]
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-------------------------------
==DNA ciliate body==
{|
|-
|width="320px"|[[Image:DNA ciliate body.jpg|light|250px|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.<br> Threfore,we made DNA ciliate by using polystyrene beads which were attached a lot of covalently-immobilized DNA strands.(Figure.1)
|}
[[Image:Biomod2011 Team Tokyo 111030 111030Biomod Construction of DNA ciliate body.png|thumb|center|none|500px|Figure.1:The pattern diagram of creating DNA ciliate]]
-----------------------
==1. Free moving mode==
{|
|-
|width="300px" valign="top"|
[[Image:Free moving mode figure.jpg|250px|center]]
|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.
|}
<!--:Free Movingモードでは、DNA ciliateは空間の中をrandomly and freelyに動き回ります。私たちは、このFree movingモードにおけるDNA ciliateの動作原理としてブラウン運動を採用しました。DNA ciliateにブラウン運動をさせるにあたって、2つの課題があります。１つは、大きい物体にはブラウン運動の影響が小さくなってしまうのではないかということです。もう1つは、ボディに採用した素材によっては、予期しない現象が起こってしまうのではないかということです。
:以上の2つの課題を解決するため、私たちは試行錯誤しつつFree movingに適したDNA ciliateの素材、大きさをdesignしました。-->
===Model===
[[image:Tokyo-freemoving1.png|right|300px|The equation of Brownian motion.]]
: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: x<sub>0</sub>. On the other hand, R is gas constant, T is the absolutely temperature,f is mobility and N<sub>A</sub> 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.
<!--:ブラウン運動に従う物体の動きは右の方程式で記述されます。左辺は開始点x0からのmean square displacement、Rは気体定数、Tは絶対温度、fはmobilityをrepresentしています。これらの定数のうち、fは物体の直径と密度に依存しています。したがって、fはDNA ciliateの材料や直径を変化させることによって変えることができます。DNA ciliateの材料や直径を最適化することによって、マイクロサイズの体を持つDNA ciliateにFree movingモードを実装します。-->
==2. Track walking mode==
{|
|-
|width="300px"|[[Image:Track walking mode figure.jpg|left|280px]]
|
:The purpose of the track walking mode is to move DNA ciliate directionally<br>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.
|}
<!--
Track walking modeでは、DNA trackに沿って、
DNA ciliateを一方向的に歩かせることを目的としている。
その達成のためには、当然ながら、
「歩行に用いる機構(mechanism,reactionとか)」と、
「DNA trackの作りかた」を考える必要がある。
我々は、
「歩行に用いる機構」として「Deoxyribozyme-substrate」反応を選び、
「DNA tracksの作り方」としてマイクロ流路を用いることにした。
-->
<h3>・The mechanism of "Deoxyribozyme-substrate reaction"</h3>
: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.(Figure.1)
[[Image:BIOMOD Tokyo20111101Deoxyribozyme.png‎|Figure.1:The mechanism that DNA ciliate moves directionally.|600x1200px]]
<h3>・The motivation of using microchannel to make the landcape</h3>
: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:) 
:Thus,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. (Link:)
[[Image:Micrometer sized track.jpg|200px|Figure.2:The schematic diagram of microchannel.]]
==3. Light-irradiated gathering mode==
{|
|-
|width="320px"|[[image:Tokyo-gathering1.png|300px|center]]
|
: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 and observation of gathering DNA ciliates.
: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 DNA’s movement can be controlled.
|}
===Mechanism===
------------------------
{|
|-
|width="450px"|[[Image:Tokyo-gathering2.png|450px|center]]
|
====UV-switching system====
:Deoxyribozyme, blocking DNA, and UV-switching DNA are used in this system. The UV-switching DNA hybridizes with blocking DNA and DNA ciliate’s deoxyribozyme legs doesn’t hybridize. This structure is closed state. By UV irradiation, the stem-loop of UV-switching DNA becomes open and branch migration starts, so DNA ciliate’s deoxyribozyme legs 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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|}

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TeamJapan Tokyo developed an autonomous micrometer-sized molecular robot, “DNA ciliate”, toward the construction of a highly functional molecular robot like a living cell.

Project overview

　

  A living cell is an ultimate highly functional molecular robot. The high functionality results from not only its various functional molecules but also its “micrometer-sized” body that has enough space to possess the molecules. However, the sizes of already-developed molecular nanomachines are too small to include many functional molecules. Toward the construction of highly functional molecular machines and molecular robots, it is required to construct molecular robots with large (i.e., micrometer-sized) bodies. Here, we propose an autonomous micrometer-sized molecular robot “DNA ciliate”.

<html><body> <iframe width="450" height="263" src="http://www.youtube.com/embed/aze2N57tcng" frameborder="0" allowfullscreen></iframe> <br><center>This is our YouTube video.</center> </body></html>

<html> <a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project"><img src="http://openwetware.org/images/2/2c/Biomod2011_Team_Tokyo_111101Biomod_three_mode_02_R.jpg" border=1 width="470" height="353"></a><br> <font size="3" color="#000066"><i><strong> <font size="3" color="#009933">“DNA ciliate”</font>is an autonomous micrometer-sized molecular robot that has three independent functional modes. </strong></i></font><br><br> </html>

DNA ciliate

<html><Center> <a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project#The_body_of_the_DNA_ciliate"><img src="http://openwetware.org/images/8/8c/DNA_ciliate_body.jpg" border=1 width="250px"></a> </Center></html>

“DNA ciliate” is an autonomous micrometer-sized molecular robot, which is inspired by water microorganisms, ciliates. A natural ciliate has a micrometer-sized body with cilia and achieves various functions such as autonomous motion with the cilia, phototaxis, etc. Similarly, the DNA ciliate has a micrometer-sized body with many DNAs as cilia, and it can switch three different modes in response to its external environment: the free moving mode, the track walking mode, and the light-irradiated gathering mode. (See below)

Three independent functional modes of DNA ciliate

<html> <td style="padding: 0px 10px"> <a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project#1._Free_moving_mode"><img src="http://openwetware.org/images/d/d4/Biomod2011_Team_Tokyo_111101Biomod_FreeMovingMode_3_title.gif" border=1 width="300"></a> </td> <td style="padding: 0px 10px"> <a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project#2._Track_walking_mode"><img src="http://openwetware.org/images/a/a5/Biomod2011_Team_Tokyo_111101Biomod_TrackWalkingMode_3_title.gif" border=1 width="300"></a> </td> <td style="padding: 0px 10px"> <a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project#3._Light-irradiated_gathering_mode"><img src="http://openwetware.org/images/9/9e/Biomod2011_Team_Tokyo_111101Biomod_Right-irradiatedGatheringMode_3_title.gif" border=1 width="300"></a> </td> </html>

The DNA ciliate can move around in a broad range of space using the free moving mode. This mode utilizes the Brownian motion of the DNA ciliate.
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In the track walking mode, the DNA ciliate walk directionally along a single-stranded DNA track on a plate using the cleaving activity of deoxyribozymes attached on the body of the DNA ciliate. The deoxyribozymes cleave substrate DNA strands arrayed as the track, and help the DNA ciliate move to the region of uncleaved substrate DNA step-by-step.
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The DNA ciliates gather at a specific area where an ultraviolet (UV) light is irradiated; this is the light-irradiated gathering mode. To achieve this mode, a UV-switching DNA system based on the cis-trans isomerization of azobenzenes was designed.
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