Biomod/2011/TeamJapan/Tokyo
<html> <!--<head>--> <!-- We refer to the wiki of team iGEM Heidlberg 2009. -->
<style type="text/css">
/* ====================
主に全体に関わるCSS
==================== */
body {behavior: url(http://www.xs4all.nl/~peterned/htc/csshover3-source.htc);}
.clear {clear:both;}
body.mediawiki {
font-size: 14px;
background-color:#707070; background-position: center center; background-attachment: fixed; background-repeat: no-repeat; font-family: Calibri, Verdana, helvetica, sans-serif; }
h1 { padding: 0px 20px 5px 20px; font-size: 34px; font-weight: bold; } h2 { padding: 20px 20px 5px 20px; font-size: 25px; color: #0083eb; text-decoration: none; font-weight: bold;} border: none; h2 a { color: #eb8300; } h3 { padding: 20px 20px 5px 20px; font-size: 20px; color: #000; font-decoration: none; font-weight: bold; } h1.firstHeading {
display: none;
}
p { text-align: justify; } a:link { color: #00a5ea; text-decoration: none } a:visited { color:#00a5ea; text-decoration: none } a:hover {
color: #eb8300;
text-decoration: none } a:active { color:#f29400; text-decoration: none } #bodyContent {
width: 970px; margin: 0px 0px 0px; background-color:#ffffff; border-width: 0px 1px 0px 1px; border-color: #000000; } #content { padding-left: 0px; width: 970px; }
table#team_members {
text-align: justify; border: 0; }
table#team_members h2, table#team_members h3 {
clear: both; }
#content * a:hover {
text-decoration:none; }
#main_wrapper {
position:absolute; left:0px; top:20px;
margin-top: 0; width: 969px; height: 221px; align: center; border-style: solid;
border-color: white;
} /* ====================
メニューの画像を変更できる部分 ==================== */
#header {
position:relative; left:0px; top:0px;
margin-top: 0; width: 969px; height: 221px; align: left; background-color: #FFFFFF;
background-image: url(http://openwetware.org/images/e/e0/NEW_header.jpg);
} /* ====================
以下、特殊なclassに適用される ==================== */
#navigation { position:absolute;
left:18px; top:155px; width:1200px; height:69px;
z-index:100;
background-color: transparent; float: left;
color: #0000FF; } #super_main_wrapper {
position:absolute; left:0px; top:227px;
width: 975px; align: center; background-color: #ede8e2;
heigth: auto; } #SubWrapper { width: 645px; padding: 0px; border-left:4px solid #ede8e2; float: left; margin-top: 0px; background-color: #ede8e2; } #SubWrapper * p, #SubWrapper p { padding: 0 20px; text-align: justify; font-size: 12px; } #SubWrapper * h3, #SubWrapper h3 { padding-top: 10px; font-size: 18px; } #news { width: 322px; margin-top: 0px; float: left; background-color: #d8d5d0; border-right:4px solid #ede8e2; } #news p { padding: 0 20px 20px 20px; text-align: justify; font-size: 12px; } #news h3 { padding: 10px 20px; font-size: 18px; } #mission_box { width:650px; float: left; } #team_box, #heartbeat_box, #notebook_box, #parts_box, #gallery_box, #sponsors_box, .boxy { width:215px; float: left; padding: 10px 0 0 0; } div.tleft { border-width: 0px; margin:0; padding:0; border-color:transparent; }
/* ====================
ここからプルダウン周辺のデザイン ==================== */
- menu * {
margin: 0; padding: 0; }
- menu {
behavior: url(http://www.xs4all.nl/~peterned/htc/csshover3-source.htc); <!-- fuer ie6 --> font-family: calibri, verdana, sans-serif;
font-color: #ffffff;
font-size: 19px; background-color: transparent; float:left; padding: 12px 0 0 0; }
- menu ul {
float: left; list-style: none; }
- menu ul li {
background-color:transparent;
position:relative;
float:left; list-style: none; padding: 10px 20px 0 0;
font-weight: bold; width: auto;
}
- menu a {
color: #FFFFFF; display: inline; text-decoration: none; }
- menu a:visited {
color:#FFFFFF; text-decoration: none }
- menu a:hover {
color: #00a5ea; }
- menu ul li ul {
display: none; position: absolute; left: 0px;
width: 155px; heigth: 1%;
font-size: 19px; opacity: 0.8; list-style: none;
top: 30px; padding-top: 20px; z-index:500;
}
- menu ul li:hover ul {
display: inline;
background-position: bottom;
}
- menu ul li ul li {
width: 100%; list-style: none;
background-color: #000; margin: -1px; padding: 0px 0 0 5px; display: inline;
}
</style> <!-- </head> -->
<!-- ############################# BODY!!!!! #################################### -->
<!-- <body> --> <!--[if IE]> <style type="text/css">
- SubWrapper {width: 645px;}
- news {width: 317px;}
- super_main_wrapper {position:static;}
- navigation {left: 15px;}
- menu ul li ul {left: -2px; top: 22px;}
</style> <![endif]--> <div id="main_wrapper">
<div id="header">
<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>
</ul> </div><!-- end drop menu --> </div> <!-- end navigation --> </div> </div> <!-- For IE 6 --> <script type="text/javascript">
/***********************************************
- CSS Vertical List Menu- by JavaScript Kit (www.javascriptkit.com)
- Menu interface credits: http://www.dynamicdrive.com/style/csslibrary/item/glossy-vertical-menu/
- This notice must stay intact for usage
- Visit JavaScript Kit at http://www.javascriptkit.com/ for this script and 100s more
- /
var menuids=new Array("verticalmenu") //Enter id(s) of UL menus, separated by commas var submenuoffset=-2 //Offset of submenus from main menu. Default is -2 pixels.
function createcssmenu(){ for (var i=0; i<menuids.length; i++){
var ultags=document.getElementById(menuids[i]).getElementsByTagName("ul") for (var t=0; t<ultags.length; t++){ var spanref=document.createElement("span")
spanref.className="arrowdiv" spanref.innerHTML=" " ultags[t].parentNode.getElementsByTagName("a")[0].appendChild(spanref)
ultags[t].parentNode.onmouseover=function(){ this.getElementsByTagName("ul")[0].style.left=this.parentNode.offsetWidth+submenuoffset+"px" this.getElementsByTagName("ul")[0].style.display="block" } ultags[t].parentNode.onmouseout=function(){ this.getElementsByTagName("ul")[0].style.display="none" } } }
}
if (window.addEventListener)
window.addEventListener("load", createcssmenu, false)
else if (window.attachEvent)
window.attachEvent("onload", createcssmenu)
</script>
<!-- </body> -->
</html>
Project overview
<html><body> <table width="100%">
<tr> <td>
<i>We developed an autonomous micrometer-sized molecular robot,“DNA ciliate,toward a highly functional molecular robot like living cells.</i><br><br> 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> <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>
<font size="3" color="#000066"><i><strong>
<font size="3" color="#00ff66">“DNA ciliate”</font> has three independent functional modes. </strong></i></font></td>
</tr>
</table> <center> <iframe width="420" height="315" src="http://www.youtube.com/embed/uejCuQWG07A" frameborder="0" allowfullscreen></iframe> </center> </body></html>
<html> <!--<head>--> <!-- We refer to the wiki of team iGEM Heidlberg 2009. -->
<style type="text/css">
/* ====================
主に全体に関わるCSS
==================== */
body {behavior: url(http://www.xs4all.nl/~peterned/htc/csshover3-source.htc);}
.clear {clear:both;}
body.mediawiki {
font-size: 14px;
background-color:#707070; background-position: center center; background-attachment: fixed; background-repeat: no-repeat; font-family: Calibri, Verdana, helvetica, sans-serif; }
h1 { padding: 0px 20px 5px 20px; font-size: 34px; font-weight: bold; } h2 { padding: 20px 20px 5px 20px; font-size: 25px; color: #0083eb; text-decoration: none; font-weight: bold;} border: none; h2 a { color: #eb8300; } h3 { padding: 20px 20px 5px 20px; font-size: 20px; color: #000; font-decoration: none; font-weight: bold; } h1.firstHeading {
display: none;
}
p { text-align: justify; } a:link { color: #00a5ea; text-decoration: none } a:visited { color:#00a5ea; text-decoration: none } a:hover {
color: #eb8300;
text-decoration: none } a:active { color:#f29400; text-decoration: none } #bodyContent {
width: 970px; margin: 0px 0px 0px; background-color:#ffffff; border-width: 0px 1px 0px 1px; border-color: #000000; } #content { padding-left: 0px; width: 970px; }
table#team_members {
text-align: justify; border: 0; }
table#team_members h2, table#team_members h3 {
clear: both; }
#content * a:hover {
text-decoration:none; }
#main_wrapper {
position:absolute; left:0px; top:20px;
margin-top: 0; width: 969px; height: 221px; align: center; border-style: solid;
border-color: white;
} /* ====================
メニューの画像を変更できる部分 ==================== */
#header {
position:relative; left:0px; top:0px;
margin-top: 0; width: 969px; height: 221px; align: left; background-color: #FFFFFF;
background-image: url(http://openwetware.org/images/e/e0/NEW_header.jpg);
} /* ====================
以下、特殊なclassに適用される ==================== */
#navigation { position:absolute;
left:18px; top:155px; width:1200px; height:69px;
z-index:100;
background-color: transparent; float: left;
color: #0000FF; } #super_main_wrapper {
position:absolute; left:0px; top:227px;
width: 975px; align: center; background-color: #ede8e2;
heigth: auto; } #SubWrapper { width: 645px; padding: 0px; border-left:4px solid #ede8e2; float: left; margin-top: 0px; background-color: #ede8e2; } #SubWrapper * p, #SubWrapper p { padding: 0 20px; text-align: justify; font-size: 12px; } #SubWrapper * h3, #SubWrapper h3 { padding-top: 10px; font-size: 18px; } #news { width: 322px; margin-top: 0px; float: left; background-color: #d8d5d0; border-right:4px solid #ede8e2; } #news p { padding: 0 20px 20px 20px; text-align: justify; font-size: 12px; } #news h3 { padding: 10px 20px; font-size: 18px; } #mission_box { width:650px; float: left; } #team_box, #heartbeat_box, #notebook_box, #parts_box, #gallery_box, #sponsors_box, .boxy { width:215px; float: left; padding: 10px 0 0 0; } div.tleft { border-width: 0px; margin:0; padding:0; border-color:transparent; }
/* ====================
ここからプルダウン周辺のデザイン ==================== */
- menu * {
margin: 0; padding: 0; }
- menu {
behavior: url(http://www.xs4all.nl/~peterned/htc/csshover3-source.htc); <!-- fuer ie6 --> font-family: calibri, verdana, sans-serif;
font-color: #ffffff;
font-size: 19px; background-color: transparent; float:left; padding: 12px 0 0 0; }
- menu ul {
float: left; list-style: none; }
- menu ul li {
background-color:transparent;
position:relative;
float:left; list-style: none; padding: 10px 20px 0 0;
font-weight: bold; width: auto;
}
- menu a {
color: #FFFFFF; display: inline; text-decoration: none; }
- menu a:visited {
color:#FFFFFF; text-decoration: none }
- menu a:hover {
color: #00a5ea; }
- menu ul li ul {
display: none; position: absolute; left: 0px;
width: 155px; heigth: 1%;
font-size: 19px; opacity: 0.8; list-style: none;
top: 30px; padding-top: 20px; z-index:500;
}
- menu ul li:hover ul {
display: inline;
background-position: bottom;
}
- menu ul li ul li {
width: 100%; list-style: none;
background-color: #000; margin: -1px; padding: 0px 0 0 5px; display: inline;
}
</style> <!-- </head> -->
<!-- ############################# BODY!!!!! #################################### -->
<!-- <body> --> <!--[if IE]> <style type="text/css">
- SubWrapper {width: 645px;}
- news {width: 317px;}
- super_main_wrapper {position:static;}
- navigation {left: 15px;}
- menu ul li ul {left: -2px; top: 22px;}
</style> <![endif]--> <div id="main_wrapper">
<div id="header">
<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>
</ul> </div><!-- end drop menu --> </div> <!-- end navigation --> </div> </div> <!-- For IE 6 --> <script type="text/javascript">
/***********************************************
- CSS Vertical List Menu- by JavaScript Kit (www.javascriptkit.com)
- Menu interface credits: http://www.dynamicdrive.com/style/csslibrary/item/glossy-vertical-menu/
- This notice must stay intact for usage
- Visit JavaScript Kit at http://www.javascriptkit.com/ for this script and 100s more
- /
var menuids=new Array("verticalmenu") //Enter id(s) of UL menus, separated by commas var submenuoffset=-2 //Offset of submenus from main menu. Default is -2 pixels.
function createcssmenu(){ for (var i=0; i<menuids.length; i++){
var ultags=document.getElementById(menuids[i]).getElementsByTagName("ul") for (var t=0; t<ultags.length; t++){ var spanref=document.createElement("span")
spanref.className="arrowdiv" spanref.innerHTML=" " ultags[t].parentNode.getElementsByTagName("a")[0].appendChild(spanref)
ultags[t].parentNode.onmouseover=function(){ this.getElementsByTagName("ul")[0].style.left=this.parentNode.offsetWidth+submenuoffset+"px" this.getElementsByTagName("ul")[0].style.display="block" } ultags[t].parentNode.onmouseout=function(){ this.getElementsByTagName("ul")[0].style.display="none" } } }
}
if (window.addEventListener)
window.addEventListener("load", createcssmenu, false)
else if (window.attachEvent)
window.attachEvent("onload", createcssmenu)
</script>
<!-- </body> -->
</html>
Project
DNA ciliate body
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. |
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
|
・The mechanism of "Deoxyribozyme-substrate reaction"
- 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)
・The motivation of using microchannel to make the landcape
- 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:)
3. Light-irradiated gathering mode
|
Mechanism
UV-switching system
| |