Biomod/2013/Todai/Result
<html> <head> <meta name="viewport" content="width=1200">
<style> <!--
body{
font-family:Verdana; Myriad Pro; Arial; background-color: #fffc77; overflow-y:scroll; overflow-x:hidden; }
article{
background-color: #ffffff }
.Logo {
position: relative; left: -39px; }
.zairyou-heading {
font-size: 120%; position: relative; left:30px; line-height: 2.2; }
.zairyou-heading-sub {
font-size: 110%; position: relative; left:30px; line-height: 2.2; }
.zairyou-list {
font-size: 100%; position: relative; left: 40px; }
p.paragraph{
font-size :110%; line-height:1.5; margin:0 20px; text-indent: 1em; }
p.noindent-paragraph {
font-size :110%; line-height:1.5; margin:0 20px; }
p.item {
font-size :110%; line-height:1.5; margin:0px 20px; text-indent: 2em; }
h1.title a{
font-size :90%; font-style:italic; display: block; text-decoration: none; color: #000000;
font-weight:bolder;
border-left: solid 5px #e00000 }
h1.big-title a{
font-size :110%; display: block; text-decoration: none; color: #000000;
font-weight:300;
}
h1.heading a{
font-size :95%; display: block; text-decoration: none; color: #000000;
font-weight:100;
border-left: solid 7px #ffa500 }
h2.small-title a{
font-size :100%; display:block; text-decoration: none;
font-weight:bolder;
color: #e00000; }
.sidebar {
font-size: 110%; width: 110px; background-color: #ffffff; padding: 7px; position: fixed; top: 167px; left: auto; z-index: 20; margin: 0 0 0 -175px; border:solid 1.5px orange; }
.sidebar ul {
position:relative; top:-3px; left:-3px; }
.sidebar ul li ul {
list-style: none; position: relative; left: -15px }
.sidebar ul li ul li a{
font-size: 85%; }
a:link {color:#000000;} a:visited {color:#000000;} a:hover {color:#e00000;} a:active {color:#e00000;}
.Return-Logo a{
position: fixed; bottom: 10px; left: auto; margin: 0 0 0 789px; z-index: 20; display:block; width:60px; height:0px; padding-top:60px; background:url(http://openwetware.org/images/b/b1/Return-top-0828new.png); overflow:hidden; }
.Return-Logo a:hover {
background-position: left bottom; }
.reference-title a{
color:#000000; font-size:110%; font-weight:bolder; text-decoration:none; }
.reference-author {
font-size:110%; position:relative; left:30px; }
.reference-journal {
font-size:110%; font-style:italic; position:relative; left:30px; }
.ref-sup a{
vertical-align:super; color:#e00000; text-decoration:none; }
- column-one { display:none; width:0px;}
.container{background-color: #ffffff; margin-top:0px} .OWWNBcpCurrentDateFilled {display: none;}
- content { width: 0px; margin: 0 auto auto 0; padding: 0em 0em 0em 0em; align: center;}
- column-content {width: 0px; float: left; margin: 0 0 0 0;padding: 0;}
.firstHeading {display:none; width:0px;}
- globalWrapper{width:800px; background-color: #ffffff; margin-left: auto; margin-right: auto}
- column-one {display:none; width:0px;background-color: #ffffff;}
- content{ margin: 0 0 0 0;padding: 12px 12px 12px 12px; width:775px;border: 0;}
- bodyContent{ width: 730px; align: center; background-color: #ffffff;position:relative;left:20px;}
- column-content{width: 800px;background-color: #ffffff;}
- footer{position: center; width: 800px}
-->
</style> </head>
<body>
<div id="top"> <figure> <div class="Logo"> <img src="http://openwetware.org/images/9/9c/Logo-OCKver.png" width=730px height=128px> </div> </figure> </div> <br>
<div class="sidebar">
<ul> <li><a href="http://openwetware.org/wiki/Biomod/2013/Todai">Home</a> </li> <li><a href="http://openwetware.org/wiki/Biomod/2013/Todai/Project">Project</a> </li> <li><a href="http://openwetware.org/wiki/Biomod/2013/Todai/Design">Design</a> </li> <li><a href="http://openwetware.org/wiki/Biomod/2013/Todai/Result">Result</a> </li> <li><a href="http://openwetware.org/wiki/Biomod/2013/Todai/Experiment">Experiment</a> <ul style="list-style-type: none;">
<li>
<a href="http://openwetware.org/wiki/Biomod/2013/Todai/Experiment#Contents"> Contents</a></li> <li> <a href="http://openwetware.org/wiki/Biomod/2013/Todai/Experiment#PilotStudy"> Pilot Study</a></li> <li> <a href="http://openwetware.org/wiki/Biomod/2013/Todai/Experiment#Protocols"> Protocols</a></li> </ul> </li> <li><a href="http://openwetware.org/wiki/Biomod/2013/Todai/Team">Team</a> </li> <li><a href="http://openwetware.org/wiki/Biomod/2013/Todai/Sponsors">Sponsors</a> </li> </ul>
</div>
<div class="Return-Logo">
<a href="#TOP"> <figure> <img src="http://openwetware.org/images/b/b1/Return-top-0828new.png" width:60px height:60px> </figure> </a>
</div>
</body> </html>
<html> <head> <title>Result-Todai nanORFEVRE-</title> <style>
figure.figure-left {
position:relative; left:-35px; }
.res-conclusion {
font-size:120%; font-weight:bolder; color:blue; position:relative; left:30px; margin-top:10px; }
</style>
</head>
<body>
<!--◆◆Result◆◆-->
<h1 class="big-title"><a name="Result"> Result</a></h1>
<!--◆◆A.Cylinder in barrel by DNA origami◆◆-->
<h1 class="heading"><a name="A.Cylinder in barrel by DNA origami"> Oligomeric Cell Killer (OCK)</a></h1>
<!--◆◆
DNA strands assemble to form designed structures.◆◆-->
<article> <h2 class="small-title"><a name="STEP0"> STEP 1: DNA strands assemble to form designed structures.</a></h2>
<h3>1)Optimize the condition to assemble OCK</h3> <!--Method-->
<div class="zairyou-heading">[Method]</div> <figure class="figure-left"> <img style="float:left; margin:0;margin-right:-10px;margin-bottom:10px;" src="http://openwetware.org/images/1/1e/OCKnaname-Todai.png" width="200px" height="200px" > </figure>
<div id ="step0_1)"> <p class="paragraph"> The DNA nanostructure, <a target="_bramk" href="http://openwetware.org/wiki/Biomod/2013/Todai/Design#Oligomeric_Cell_Killer " style="color:#e00000"> "Oligomeric Cell Killer" </a> , was designed to achieve our goal(--><a href="http://openwetware.org/wiki/Biomod/2013/Todai/Project">Project</a>). </p>
<p class ="paragraph">
To know the optimum condition of the structure assembly, we did experiments in three conditions as follows. <ul style="position:relative;left:30px;"> <li>At different concentration of MgCl<sub>2</sub></li> <li>At different incubate temperature</li> <li>At different length of incubate time</li>
</ul> (<a target="_blank" href="http://openwetware.org/wiki/Biomod/2013/Todai/Experiment#Protocols" style="color:#e00000;"> protocols </a> ) </p> </div> <br> <br>
<!--Result&Discussion1-->
<div class="zairyou-heading">[Result & Discussion]</div>
<div class="res-conclusion"> Optimum concentration of MgCl<sub>2</sub> </div>
<figure> <center> <img src="http://openwetware.org/images/a/af/OOCK_Optimize_MgConc.png" width=640px height=360px> <figcaption> <b>Agarose-gel electrophoresis to research the optimum concentration of MgCl<sub>2</sub>
</b>
</figcaption> </center> </figure>
<p class="paragraph">
Fast-migrating species upon agarose-gel electrophoresis was yielded at 10~20mM MgCl<sub>2</sub> condition. At higher MgCl<sub>2</sub> concntration, a sub-band which might be a dimer band appeared.
</p> <div class="res-conclusion"> --->> Optimum concentration of MgCl<sub>2</sub>: 10mM </div>
<br> <br>
<!--Result&Discussion2-->
<div class="res-conclusion"> Optimum incubate temparature </div> <figure> <center> <img src="http://openwetware.org/images/9/95/OOCK_Optimize_Temp-Todai.png" width=640px height=360px > <figcaption> <b>Agarose-gel electrophoresis to research the optimum temperature</b> </figcaption> </center> </figure>
<p class="paragraph">
Fast-migrating species upon agarose-gel electrophoresis was yielded at 52.0 °C.
</p> <div class="res-conclusion"> --->> Optimum temparature : 52.0 °C </div> <br> <br>
<!--Result&Discussion2-->
<div class="res-conclusion"> To decide optimum length of incubate time </div>
<figure> <center> <img src="http://openwetware.org/images/9/94/OOCK_Optimize_Time-Todai.png" width=640px height=360px > <figcaption> <b>Agarose-gel electrophoresis to research the optimum time</b> </figcaption> </center> </figure>
<p class="paragraph">
The band for 3h is fast migrated and sharp.
</p>
<div class="res-conclusion"> --->> Optimum incubate time : 3h </div>
<br> <h3>2)Conformation of the 3D structure of OCK by TEM</h3> <!--Method--> <div class="zairyou-heading">[Method]</div>
<div id ="step0_2)"> <p class="paragraph">
Gel electro phoresis cannot visualize the 3D structure of OCK, so it was confirmed by Transmission electron microscopy (TEM)
(<a target="_blank" href="http://openwetware.org/wiki/Biomod/2013/Todai/Experiment#Protocols" style="color:#e00000;"> protocols </a> ) </p> </div> <br> <br>
</article> <br>
<!--Result&Discussion1-->
<div class="zairyou-heading">[Result & Discussion]</div>
<div class="res-conclusion"> </div>
<figure> <center> <img src="" width=640px height=360px> <figcaption> <b></b> </figcaption> </center> </figure>
<p class="paragraph"> </p> <div class="res-conclusion"> </div> </article>
<!--◆◆STEP 2: The formed subunits oligomerize in solution.◆◆-->
<article> <h2 class="small-title"><a name="STEP2"> STEP 2: The formed subunits oligomerize in solution.</a></h2> <h3>1) Oligomerization by streptavidin-biotin complex</h3> <!--Method--> <div class="zairyou-heading">[Method]</div>
<div id ="step2_1)"> <p class="paragraph"> Biotins are devised to OCK for oligomerization. The experiment which confirmed that streptavidins induced oligomeriation was done. (<a target="_blank" href="http://openwetware.org/wiki/Biomod/2013/Todai/Experiment#Protocols" style="color:#e00000;"> protocols </a> ) </p> </div> <br> <br>
</article> <br>
<!--Result&Discussion1-->
<div class="zairyou-heading">[Result & Discussion]</div>
<div class="res-conclusion"> Streptavidins induced oligomerization </div>
<figure> <center> <img src="http://openwetware.org/images/5/5b/Streptavidin_dimer-Todai.png" width=600px height=450px>
</center> </figure> </article>
<!--◆◆Optimum concentration of CuSO4◆◆-->
<article> <h3>2) Oligomerization by Clik reaction</h3> <!--Method--> <div class="zairyou-heading">[Method]</div>
<div id ="step2_2)"> <p class="paragraph"> Azide and alkyne, which function as a linker by click reaction, are also equiped to OCK. It demands Cu<sup>1+</sup> as catalyst, but too high concentration of Cu<sup>1+</sup> (cation) might denaturate OCK like Mg<sup>2+</sup>. Therefore, we optimized the concentration of Cu<sup>1+</sup> to OCK first, and then the optimum Cu<sup>1+</sup> concentration to click reaction was investigated. (<a target="_blank" href="http://openwetware.org/wiki/Biomod/2013/Todai/Experiment#Protocols" style="color:#e00000;"> protocols </a> ) </p> </div> <div class="res-conclusion"> a) Optimum concentration of CuSO<sub>4</sub> to OCK </div> <figure> <center> <img src="http://openwetware.org/images/5/5e/CuAlive-Todai.png" width=600px height=450px>
</center> </figure> <div class="res-conclusion"> -->Optimum concentration of CuSO<sub>4</sub>: 625 uM or less </div> <br> <br> </div> <div class="res-conclusion"> b) Optimum concentration of CuSO<sub>4</sub> to click reaction </div> <figure> <center> <img src="http://openwetware.org/images/9/94/ClickResult-Todai.png" width=600px height=450px>
</center> </figure> <p class ="paragraph"> Product of click reaction appeared over 375 uM CuSO<sub>4</sub> concentration. Combining with the stability data, we decided to use 625 uM CuSO<sub>4</sub> condition. <div class="res-conclusion"> --> Optimum concentration of CuSO<sub>4</sub>: 625 uM </div> </article> <br>
<!--Result&Discussion1-->
<div class="zairyou-heading">[Result & Discussion]</div>
<div class="res-conclusion"> </div>
<figure> <center> <img src="" width=640px height=360px> <figcaption> <b></b> </figcaption> </center> </figure>
<p class="paragraph"> </p> <div class="res-conclusion"> </div> <br> <br> <br> <br> <br> <br> <br> <br>
<footer style="position:relative;left:400px"> <small> Copyright © Todai nanORFEVRE, all rights reserved. </small> </footer>
</body> </html>