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<title>Result-Todai nanORFEVRE-</title>
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<body>
<body>


    <h1>&nbsp;Result</a></h1>
<!--◆◆ライトバー◆◆-->
 
<div class="rightbar-res">
  <ul>
    <li><a href="#A.Cylinder in barrel by DNA origami">A. Cylinder in barrel</a>
        <ul>
          <li>STEP&nbsp;</a>
          </li>
          <li><a href="#StepA-1">1&nbsp;</a>
          </li>
          <li><a href="#StepA-2">2&nbsp;</a>
          </li>
          <li><a href="#StepA-3">3&nbsp;</a>
          </li>
          <li><a href="#StepA-4">4&nbsp;</a>
          </li>
          <li><a href="#StepA-5">5</a>
          </li>
        </ul>
    </li>
  </ul>
</div>
 
<!--◆◆Result◆◆-->
 
  <h1 class="big-title"><a name="Result">&nbsp;Result</a></h1>
  <br>
    <div style="position:relative;left:30px;">
      <h3>We focus on pilot study now, so please visit
      <a target="_blank"
      href="http://openwetware.org/wiki/Biomod/2013/Todai/Experiment#PilotStudy" 
      style="color:#e00000">
      Pilot Study
      </a>
      ,too.
      </h3>
    </div>
    <br>
 
<!--◆◆A.Cylinder in barrel by DNA origami◆◆-->
 
  <h1 class="heading"><a name="A.Cylinder in barrel by DNA origami">&nbsp;A. Cylinder in barrel by DNA origami</a></h1>
 
<!--◆◆1.BarrelMaking◆◆-->
 
    <article>
      <h2 class="small-title"><a name="STEPA-1">&nbsp;STEP1. DNA strands assemble to form designed structures.</a></h2>
 
<!--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/7/79/BarrelSize-Todai.png" width="200px" height="200px" >
      </figure>
 
    <div id ="step1Introduction">
      <p class="paragraph">
      First, the DNA nanostructure,
      <a target="_bramk" href="http://openwetware.org/wiki/Biomod/2013/Todai/Design#2.Cylinder in barrel by DNA origami" style="color:#e00000">
      "Cylinder in barrel"
      </a>
      , was used for pilot study.
      </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">
    To decide optimum concentration of MgCl<sub>2</sub>
    </div>
 
      <figure>
        <center>
        <img src="http://openwetware.org/images/a/a9/Result-SA1-MgCl2-Todai-new.png" width=480px 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 20mM MgCl<sub>2</sub> condition.
Correctly folded structures were yielded at 20mM of MgCl<sub>2</sub>, because they were more compact than misfolded versions.
(The structures at high concentration (30 and 40mM) of MgCl<sub>2</sub> tend to aggregate because of positive charge.)
    </p>
    <div class="res-conclusion">
    --->> Optimum concentration of MgCl<sub>2</sub>: 20mM 
    </div>
 
    <br>
    <br>
 
<!--Result&Discussion2-->
 
    <div class="res-conclusion">
    To decide optimum incubate temparature
    </div>
 
    <figure>
        <center>
          <img src="http://openwetware.org/images/3/3b/Result-SA1-Temp-Todai-new.png" width=480px 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 47.7 or 51.6 degree C. The
band at 47.7 degree C is more clear than that of at 51.6 degree C.
The band of 47.7 degree C is fast migrated and strong.
    </p>
    <div class="res-conclusion">
    --->> Optimum temparature : 47.7 degree 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/d/d2/Result-StepA1-Time-Todai.png" width=480px height=360px >
          <figcaption>
          <b>Agarose-gel electrophoresis to research the optimum time</b>
          </figcaption>
        </center>
      </figure>
 
    <p class="paragraph">
The structure assembled for 4h becomes most compact. The band for 4h is fast migrated and strong. 
    </p>
 
    <div class="res-conclusion">
    --->> Optimum incubate time : 4h
    </div>
 
    <br>
    </article>
    <br>
 
<!--◆◆2.溶液中、バレルで多量体できるか◆◆-->
 
    <article>
      <h2 class="small-title"><a name="STEPA-2">&nbsp;STEP2-5.</a></h2>
      <br>
    <div style="font-size:150%;font-weight:bolder;">
    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Coming Soon...!!!
    </div>
    </article>
    <br>


    </article>
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Revision as of 07:13, 31 August 2013

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 <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>
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<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>
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<body>

<!--◆◆ライトバー◆◆-->

<div class="rightbar-res"> 

 <ul>
    <li><a href="#A.Cylinder in barrel by DNA origami">A. Cylinder in barrel</a>
       <ul>
         <li>STEP&nbsp;</a>
         </li>
         <li><a href="#StepA-1">1&nbsp;</a>
         </li>
         <li><a href="#StepA-2">2&nbsp;</a>
         </li>
         <li><a href="#StepA-3">3&nbsp;</a>
         </li>
         <li><a href="#StepA-4">4&nbsp;</a>
         </li>
         <li><a href="#StepA-5">5</a>
         </li>
       </ul>
    </li>
 </ul>

</div>

<!--◆◆Result◆◆--> 

  <h1 class="big-title"><a name="Result">&nbsp;Result</a></h1>
  <br>
    <div style="position:relative;left:30px;">
      <h3>We focus on pilot study now, so please visit 
      <a target="_blank" 
      href="http://openwetware.org/wiki/Biomod/2013/Todai/Experiment#PilotStudy"   
      style="color:#e00000">
      Pilot Study
      </a>
      ,too.
      </h3>
    </div>
    <br>

<!--◆◆A.Cylinder in barrel by DNA origami◆◆--> 

  <h1 class="heading"><a name="A.Cylinder in barrel by DNA origami">&nbsp;A. Cylinder in barrel by DNA origami</a></h1>

<!--◆◆1.BarrelMaking◆◆--> 

    <article>
     <h2 class="small-title"><a name="STEPA-1">&nbsp;STEP1. DNA strands assemble to form designed structures.</a></h2>

<!--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/7/79/BarrelSize-Todai.png" width="200px" height="200px" >
      </figure>

    <div id ="step1Introduction">
      <p class="paragraph">
      First, the DNA nanostructure,
      <a target="_bramk" href="http://openwetware.org/wiki/Biomod/2013/Todai/Design#2.Cylinder in barrel by DNA origami" style="color:#e00000">
      "Cylinder in barrel"
      </a>
      , was used for pilot study. 
      </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">
    To decide optimum concentration of MgCl<sub>2</sub>
    </div>

      <figure>
       <center>
        <img src="http://openwetware.org/images/a/a9/Result-SA1-MgCl2-Todai-new.png" width=480px 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 20mM MgCl<sub>2</sub> condition. Correctly folded structures were yielded at 20mM of MgCl<sub>2</sub>, because they were more compact than misfolded versions. (The structures at high concentration (30 and 40mM) of MgCl<sub>2</sub> tend to aggregate because of positive charge.) 

    </p>
    <div class="res-conclusion">
    --->> Optimum concentration of MgCl<sub>2</sub>: 20mM   
    </div>

    <br>
    <br>

<!--Result&Discussion2--> 

    <div class="res-conclusion">
    To decide optimum incubate temparature
    </div>
  
    <figure>
       <center>
          <img src="http://openwetware.org/images/3/3b/Result-SA1-Temp-Todai-new.png" width=480px 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 47.7 or 51.6 degree C. The band at 47.7 degree C is more clear than that of at 51.6 degree C. The band of 47.7 degree C is fast migrated and strong. 

    </p>
    <div class="res-conclusion">
    --->> Optimum temparature : 47.7 degree 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/d/d2/Result-StepA1-Time-Todai.png" width=480px height=360px >
          <figcaption>
          <b>Agarose-gel electrophoresis to research the optimum time</b>
          </figcaption>
       </center>
      </figure>

   <p class="paragraph">
The structure assembled for 4h becomes most compact. The band for 4h is fast migrated and strong.   
    </p>

    <div class="res-conclusion">
    --->> Optimum incubate time : 4h 
    </div>

    <br>
    </article>
    <br>

<!--◆◆2.溶液中、バレルで多量体できるか◆◆--> 

    <article>
     <h2 class="small-title"><a name="STEPA-2">&nbsp;STEP2-5.</a></h2>
     <br>
    <div style="font-size:150%;font-weight:bolder;">
    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Coming Soon...!!!
    </div>
    </article>
    <br>

    </article>
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