Difference between revisions of "Team:HokkaidoU Japan/Notebook/Protocol"

 
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{{HokkaidoU_Japan}}
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<html>
 
<html>
 +
<br>
 +
<h1>Protocols</h1>
  
−
<style>
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<br>
 +
<h2 onClick="hyoji1()">PCR</h2>
  
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/********************************* DEFAULT WIKI SETTINGS  ********************************/
 
  
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#sideMenu, #top_title {display:none;}
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<div id="disp1">
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#content { padding:0px; width:1000px; margin-top:-7px; margin-left:0px;}
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<p>
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body {background-color:white; }
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  Use KOD -Plus- Neo (TOYOBO CO.,LTD) as polymerase. Mix PCR solutions and run the PCR machine in a program which is detailed below.
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#bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 { margin-bottom: 0px; }
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</p>
 +
<table>
 +
  <tr>
 +
    <th>Solution</th>
 +
    <td>template DNA</td>
 +
    <td>Primer-F 10&micro;M</td>
 +
    <td>Primer-R 10&micro;M</td>
 +
    <td>MgSO<sub>4</sub></td>
 +
    <td>dNTPs</td>
 +
    <td>10x Buffer</td>
 +
    <td>KOD Plus Neo</td>
 +
    <td>DW</td>
 +
    <td>Total</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Volume (&micro;L)</th>
 +
    <td>1</td>
 +
    <td>1</td>
 +
    <td>1</td>
 +
    <td>3</td>
 +
    <td>5</td>
 +
    <td>5</td>
 +
    <td>1</td>
 +
    <td>33</td>
 +
    <td>50</td>
 +
  </tr>
 +
</table>
 +
<p>Thermal protocol is following</p>
 +
<h3>2STEP Cycle (Tm value &gt; 63&deg;C)</h3>
 +
<table>
 +
  <tr>
 +
    <th>Sequence</th><th>Temp. (&deg;C)</th><th>Time (sec)</th>
 +
  </tr>
 +
  <tr>
 +
    <td>1</td><td>94</td><td>120</td>
 +
  </tr>
 +
  <tr>
 +
    <td>2</td><td>98</td><td>10</td>
 +
  </tr>
 +
  <tr>
 +
    <td>3</td><td>68</td><td>30sec / 1kbp</td>
 +
  </tr>
 +
  <tr>
 +
    <td>4</td><td>4</td><td>Hold</td>
 +
  </tr>
 +
</table>
 +
<p>Cycle: sequence2~3 &times; (25~45)</p>
  
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/********************************* MENU ********************************/
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<h3>3STEP Cycle (Tm value &lt; 63&deg;C)</h3>
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/* Wrapper for the menu */
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<table>
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.menu_wrapper {
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  <tr>
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width:150px;
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    <th>Sequence</th><th>Temp. (&deg;C)</th><th>Time (sec)</th>
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height:100vh;
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  </tr>
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position:fixed;
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  <tr>
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padding:0px;
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    <td>1</td><td>94</td><td>120</td>
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float:left;
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  </tr>
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background-color:#f2f2f2;
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  <tr>
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text-align:left;
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    <td>2</td><td>98</td><td>10</td>
−
}
+
  </tr>
 +
  <tr>
 +
    <td>3</td><td>Tm</td><td>30</td>
 +
  </tr>
 +
  <tr>
 +
    <td>4</td><td>68</td><td>30sec / 1kbp</td>
 +
  </tr>
 +
  <tr>
 +
    <td>5</td><td>4</td><td>Hold</td>
 +
  </tr>
 +
</table>
 +
<p>Cycle: sequence2~4 &times; (25~45)</p>
  
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/* styling for the ul that creates the buttons */
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font-weight:bold;
 
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list-style-type:none;
 
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-ms-transition: all 0.4s ease;
 
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/* styling for the submenus */
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<h2 onClick="hyoji2()">PCR Purification</h2>
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.submenu {
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width:100%;
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display: none; 
+
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font-weight:bold;
+
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cursor:pointer;
+
  
−
}
+
<div id="disp2">
  
−
/* moving the margin for the submenu ul list */
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<p>FastGene<sup>TM</sup> Gel/PCR Extraction kit (Nippon Genetics Co., Ltd)
−
ul.submenu {
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<br>Purification of PCR products</p>
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width: 100%;
+
−
margin: 10px 0px -11px 0px;
+
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list-style: none;
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}
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/*styling for the submenu buttons */
 
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.submenu li {
 
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width: 100%;
 
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margin-left: 10px;
 
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margin-bottom: 0px;
 
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}
 
  
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</script>
  
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/* hover state for the submenu buttons */
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<h2 onClick="hyoji3()">Digestion</h2>
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.submenu li a {
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<div id="disp3">
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width: 100%;
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padding: 5px 10px;
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display: inline-block;
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background-color:white;
+
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text-decoration:none;
+
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color:#000000;
+
−
}
+
  
 +
<p>Mix the following reagents in PCR tube.</p>
 +
<table>
 +
  <tr>
 +
    <th>Solution</th>
 +
    <td>DNA</td>
 +
    <td>RE1 10U/&micro;L</td>
 +
    <td>RE2 10U/&micro;L</td>
 +
    <td>Appropriate buffer</td>
 +
    <td>Total</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Volume (&micro;L)</th>
 +
    <td>16</td>
 +
    <td>1</td>
 +
    <td>1</td>
 +
    <td>2</td>
 +
    <td>20</td>
 +
  </tr>
 +
</table>
 +
<table>
 +
  <tr>
 +
    <th>Sequence</th><th>Temp. (&deg;C)</th><th>Time (min)</th>
 +
  </tr>
 +
  <tr>
 +
    <td>1</td><td>37</td><td>120</td>
 +
  </tr>
 +
  <tr>
 +
    <td>2</td><td>65</td><td>15</td>
 +
  </tr>
 +
  <tr>
 +
    <td>3</td><td>4</td><td>Hold</td>
 +
  </tr>
 +
</table>
  
 +
</div>
 +
<script>
 +
document.getElementById("disp3").style.display="none";
 +
var displaying=0;
 +
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 +
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 +
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 +
  }
 +
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 +
</script>
  
−
.submenu li a:hover  {
+
<h2 onClick="hyoji4()">Ligation</h2>
−
background-color:#000000;  
+
<div id="disp4">
−
color: #72c9b6;
+
<p>
−
}
+
  Mix the following reagents in 0.2 mL PCR tube. Use DNA Ligation Kit &lt;Mighty Mix&amp;rt; (Takara Bio Inc.) which contains ligase and buffer.
 +
</p>
 +
<table>
 +
  <tr>
 +
    <th>Solution</th><td>Vector DNA</td><td>Insert DNA</td><td>DW</td><td>Mighty Mix</td><td>Total</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Volume (&micro;L)</th><td>1</td><td>2</td><td>2</td><td>5</td><td>10</td>
 +
  </tr>
 +
</table>
 +
<p>Thermal protocol is following</p>
 +
<table
 +
  <tr>
 +
    <th>Sequence</th><th>Temp. (&deg;C)</th><th>Time (min)</th>
 +
  </tr>
 +
  <tr>
 +
    <td>1</td><td>16</td><td>30</td>
 +
  </tr>
 +
  <tr>
 +
    <td>2</td><td>65</td><td>10</td>
 +
  </tr>
 +
  <tr>
 +
    <td>3</td><td>4</td><td>Hold</td>
 +
  </tr>
 +
</table>
  
 +
</div>
 +
<script>
 +
document.getElementById("disp4").style.display="none";
 +
var displaying=0;
 +
function hyoji4()
 +
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 +
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 +
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 +
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 +
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 +
  }
 +
}
 +
</script>
  
−
/* When the screen is smaller than 680px, the menu has the option to hide/show - this button controls that */
+
<h2 onClick="hyoji5()">Electrophoresis</h2>
−
.collapsable_menu_control {
+
<div id="disp5">
−
width:100%;
+
<ol>
−
padding: 15px 0px;
+
  <li>Put gel into electrophoresis tank.</li>
−
display:none;
+
  <li>Pore 2x TBE buffer into the tank to soak gel.</li>
−
background-color:#000000;
+
  <li>Add 5  &micro;L of EtBr into cathod.</li>
−
text-align:center;   
+
  <li>Pre-migration for 30 min at 100 V.</li>
−
font-weight:bold;
+
  <li>Apply DNA solution with 6x loading dye and ladder.</li>
−
color:#72c9b6;
+
  <li>Start electrophoresis at 100 V.</li>
−
cursor:pointer;
+
</ol>
−
-webkit-transition: all 0.4s ease;
+
−
-moz-transition: all 0.4s ease;
+
−
-ms-transition: all 0.4s ease;
+
−
-o-transition: all 0.4s ease;
+
−
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+
−
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+
  
−
/* when hovering on that button */
+
</div>
−
.collapsable_menu_control:hover {
+
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−
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+
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+
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+
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 +
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 +
}
 +
</script>
  
−
/********************************* CONTENT OF THE PAGE ********************************/
 
  
−
/* Wrapper for the content */
+
<h2 onClick="hyoji6()">Gel Extraction</h2>
−
.content_wrapper {
+
<div id="disp6">
−
width: 85%;
+
−
margin-left:150px;
+
−
padding:10px 0px;
+
−
float:left;
+
−
background-color:white;
+
−
}
+
  
−
/*LAYOUT */
+
<p>FastGene<sup>TM</sup> Gel/PCR Extraction kit (Nippon Genetics Co., Ltd)
−
.column  {
+
<br>DNA extraction from gel</p>
−
padding: 10px 0px;
+
−
float:left;
+
−
background-color:white;
+
−
}
+
  
−
.full_size {
+
</div>
−
width:100%;  
+
<script>
−
}
+
document.getElementById("disp6").style.display="none";
 +
var displaying=0;
 +
function hyoji6()
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 +
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 +
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 +
</script>
  
−
.full_size img {
 
−
padding: 10px 15px;
 
−
width:96.5%;
 
−
}
 
  
−
.half_size {
+
<h2 onClick="hyoji7()">Ethanol precipitation</h2>
−
width: 50%;
+
<div id="disp7">
−
}
+
<ol>
−
.half_size img {
+
  <li>Add 1/10 volume of NaOAc, and 5/2 of 100% ethanol.</li>
−
padding: 10px 15px;
+
  <li>Leave it at room temperature for 5 min.</li>
−
width: 93%;  
+
  <li>Centrifuge at 15,000 rpm for 15 min at 25&deg;C.</li>
−
}
+
  <li>Remove supernatant and add  600 &micro;L  of 70% ethanol.</li>
 +
  <li>Centrifuge at 15,000 rpm for 5 min at 25&deg;C.</li>
 +
  <li>Remove supernatant and air-dry at room temperature with light sheilding.</li>
 +
  <li>Suspend with 10  &micro;L  of TE.</li>
 +
</ol>
  
  
−
.clear {
+
</div>
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clear:both;
+
<script>
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+
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 +
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 +
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 +
</script>
  
−
.highlight {
+
<h2 onClick="hyoji8()">Colony PCR</h2>
−
width: 90%;
+
<div id="disp8">
−
margin: auto;
+
<table>
−
padding: 15px 5px;
+
  <tr>
−
background-color: #f2f2f2;  
+
    <th>Solution</th>
−
}
+
    <td>DNA</td>
 +
    <td>Kapa-Taq (Taq polymerase)</td>
 +
    <td>EX-F primer 10&micro;M</td>
 +
    <td>PS-R primer 10&micro;M</td>
 +
    <td>Total</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Volume (&micro;L)</th>
 +
    <td>4.2</td>
 +
    <td>5</td>
 +
    <td>0.4</td>
 +
    <td>0.4</td>
 +
    <td>10</td>
 +
  </tr>
 +
</table>
  
−
.judges-will-not-evaluate {
+
<table>
−
border: 4px solid #72c9b6;
+
  <tr>
−
display: block;
+
    <th>Sequence</th><th>Temp. (&deg;C)</th><th>Time (sec)</th>
−
margin: 5px 15px;
+
  </tr>
−
width: 95%;
+
  <tr>
−
font-weight:bold;
+
    <td>1</td><td>94</td><td>120</td>
−
}
+
  </tr>
 +
  <tr>
 +
    <td>2</td><td>94</td><td>30</td>
 +
  </tr>
 +
  <tr>
 +
    <td>3</td><td>68</td><td>60 sec / 1kbp</td>
 +
  </tr>
 +
    <td>4</td><td>4</td><td>Hold</td>
 +
  </tr>
 +
</table>
 +
<p>Cycles: sequence2~3 &times; 25~45</p>
  
  
−
/*STYLING */
+
</div>
 +
<script>
 +
document.getElementById("disp8").style.display="none";
 +
var displaying=0;
 +
function hyoji8()
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  else
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 +
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 +
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 +
</script>
  
−
/* styling for the titles */
+
<h2 onClick="hyoji9()">Sequencing</h2>
−
.content_wrapper h1, .content_wrapper h2 {
+
<div id="disp9">
−
padding:5px 15px;  
+
<table>
−
border-bottom:0px;
+
  <tr>
−
color:#72c9b6;
+
    <th>Solution</th>
 +
    <td>5 x Sequencing Buffer</td>
 +
    <td>primer 1&micro;M</td>
 +
    <td>template DNA</td>
 +
    <td>Ready Reaction Premix</td>
 +
    <td>DW</td>
 +
    <td>Total</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Volume (&micro;L)</th>
 +
    <td>1.5</td>
 +
    <td>1.5</td>
 +
    <td>1</td>
 +
    <td>1</td>
 +
    <td>5</td>
 +
    <td>10</td>
 +
  </tr>
 +
</table>
  
−
}
+
<table>
−
.content_wrapper h3, .content_wrapper h4, .content_wrapper h5, .content_wrapper h6 {
+
  <tr>
−
padding:5px 15px;  
+
    <th>Sequence</th><th>Temp. (&deg;C)</th><th>Time (sec)</th>
−
border-bottom:0px;
+
  </tr>
−
color: #000000;
+
  <tr>
−
}
+
    <td>1</td><td>96</td><td>10</td>
 +
  </tr>
 +
  <tr>
 +
    <td>2</td><td>50</td><td>5</td>
 +
  </tr>
 +
  <tr>
 +
    <td>3</td><td>60</td><td>240</td>
 +
  </tr>
 +
  <tr>
 +
    <td>4</td><td>4</td><td>Hold</td>
 +
  </tr>
 +
</table>
 +
<p>Cycle: sequence2~4 &times; 25</p>
  
  
−
/* font and text */
+
<h3>Ethanol precipitation</h3>
−
.content_wrapper p {
+
<table>
−
padding:0px 15px;
+
  <tr>
−
font-size: 13px;
+
    <th>Solution</th>
−
font-family:Tahoma, Geneva, sans-serif;  
+
    <td>PCR product</td>
−
}
+
    <td>DW</td>
 +
    <td>3M NaOAc</td>
 +
    <td>Glycogen</td>
 +
    <td>100% EtOH</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Volume (&micro;L)</th>
 +
    <td>10</td>
 +
    <td>10</td>
 +
    <td>2</td>
 +
    <td>1</td>
 +
    <td>50</td>
 +
  </tr>
 +
</table>
 +
<ol>
 +
  <li>Centrifuge at 15,000 rpm for 15 min at room temprature</li>
 +
  <li>Remove supernatant ,add 100 &micro;L  of 70% EtOH and tap tubes by finger.</li>
 +
  <li>Centrifuge at 15,000 rpm for 10 min at room temprature</li>
 +
  <li>Remove supernatant and air dry at room temperature.</li>
 +
  <li>Resuspend the pellet to HiDi formamide and remove to 96-well plate.</li>
 +
  <li>Set the plate and start electrophoresis.</li>
 +
</ol>
  
−
/* Links */
+
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−
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<h2 onClick="hyoji10()">Competent Cells</h2>
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<ol>
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font-size: 13px;
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<li>Thaw original competent cells on ice.</li>
−
font-family:Tahoma, Geneva, sans-serif;  
+
<li>Add 5 &micro;L of original competent cells to 2 mL of LB.</li>
−
}
+
<li>Incubate the cells for 16 hrs at 37&deg;C.</li>
 +
<li>Add 5 &micro;L, 50 &micro;L, and 500 &micro;L of original cells to 100 mL of LB.</li>
 +
<li>Incubate the cells at 130 rpm at 20&deg;C, until OD<sub>600</sub> reach 0.5.</li>
 +
<li>Take 50 mL of incubated cells to two differnt culture tubes and centrifuge them at 3,000 rpm for 20 min at 4&deg;C.</li>
 +
<li>Remove supernatant and add 75 mL of TB to each tube.</li>
 +
<li>Bring them to a one tube and centrifuge at 3,000 rpm for 20 min at 4&deg;C.</li>
 +
<li>Remove supernatant and add 32 mL of TB.</li>
 +
<li>Add 32 &micro;L of DMSO 10 times.</li>
 +
<li>Take 50 &micro;L and freeze with liquid nitrogen.</li>
 +
</ol>
  
−
/* numbered lists */
+
</div>
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<h2 onClick="hyoji11()">Transformation</h2>
−
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<ol>
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margin:15px 10px;  
+
  <li>Add plasmid to thawed competent cells on ice.</li>
−
border: 1px solid #d3d3d3;  
+
  <li>Incubate on ice for 30 min.</li>
−
border-collapse: collapse;  
+
  <li>Add to LB.</li>
−
}
+
  <li>(Incubate the cells for 2 hrs at 37&deg;C.)</li>
 +
  <li>Spread 300  &micro;L  of the culture onto plate with LB and appropriate antibiotics.</li>
 +
  <li>Incubate the plate(s) at 37&deg;C for 16~20 hrs.</li>
 +
</ol>
  
−
/* table cells */
+
</div>
−
.content_wrapper  td {  
+
<script>
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 +
}
 +
</script>
  
−
/* table headers */
+
<h2 onClick="hyoji12()">Mini-prep</h2>
−
.content_wrapper th {
+
<div id="disp12">
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padding: 10px;
+
<p>FastGene<sup>TM</sup> Plasmid mini kit (Nippon Genetics Co., Ltd)
−
vertical-align: text-top;
+
<br>fast / standard / low copy protocol</p>
−
border: 1px solid #d3d3d3;
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border-collapse: collapse;
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/* Button class */
+
</div>
−
.button_click {
+
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margin: 10px auto;
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/* button class on hover */
+
<h2 onClick="hyoji13()">Streaking (Single colony isolation)</h2>
−
.button_click:hover { 
+
<div id="disp13">
−
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+
<ol>
−
color:#72c9b6;
+
  <li>Pick the colony with an inoculating loop from the agar plate．</li>
−
}
+
  <li>Drag the loop across on a new agar plate.</li>
 +
  <li>Re-sterilise the loop and drag it across again.</li>
 +
  <li>Repeat method 3.</li>
 +
</ol>
  
−
/********************************* RESPONSIVE STYLING ********************************/
+
</div>
 +
<script>
 +
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 +
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 +
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 +
  }
 +
}
 +
</script>
  
−
/* IF THE SCREEN IS LESS THAN 1000PX */
+
<h2 onClick="hyoji14()">PEG precipitation</h2>
 +
<div id="disp14">
 +
<ol>
 +
  <li>Add 13  &micro;L  of PEG to 20  &micro;L  of product(s).</li>
 +
  <li>Leave it at room temperature for 1 hr.</li>
 +
  <li>Centrifuge at 15,000 rpm for 20 min at 4&deg;C.</li>
 +
  <li>Remove supernatant and add  100 &micro;L  of 70% ethanol.</li>
 +
  <li>Centrifuge at 15,000 rpm for 2 min at 4&deg;C.</li>
 +
  <li>Remove supernatant and air-dry at room temperature with light sheilding.</li>
 +
  <li>Suspend with 10  &micro;L  of TE.</li>
 +
</ol>
  
−
@media only screen and (max-width: 1000px) {
+
</div>
 +
<script>
 +
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 +
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 +
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 +
</script>
  
−
#content {width:100%; }
+
<h2 onClick="hyoji15()">Gel Free System</h2>
−
.menu_wrapper {width:15%;}
+
<div id="disp15">
−
.content_wrapper {margin-left: 15%;}
+
<h3>Preparation of biotinylated DNA fragments</h3>
−
.menu_item {display:block;}
+
<p>
−
.icon {display:none;}
+
  Use KOD -Plus- Neo (TOYOBO CO.,LTD) as polymerase and 5'-biotinylated primers. Mix PCR solutions and run the PCR machine in a program which is detailed below.
−
.highlight {padding:10px 0px;}
+
</p>
−
}
+
<table>
 +
  <tr>
 +
    <th>Solution</th>
 +
    <td>template DNA</td>
 +
    <td>5'-biotinylated 100-UP primer 10&micro;M</td>
 +
    <td>5'-biotinylated 200-DN primer 10&micro;M</td>
 +
    <td>MgSO<sub>4</sub></td>
 +
    <td>dNTPs</td>
 +
    <td>10x Buffer</td>
 +
    <td>KOD Plus Neo</td>
 +
    <td>DW</td>
 +
    <td>Total</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Volume (&micro;L)</th>
 +
    <td>1</td>
 +
    <td>1.5</td>
 +
    <td>1.5</td>
 +
    <td>3</td>
 +
    <td>5</td>
 +
    <td>5</td>
 +
    <td>1</td>
 +
    <td>32</td>
 +
    <td>50</td>
 +
  </tr>
 +
</table>
 +
<p>Thermal protocol is following</p>
 +
<h3>2STEP Cycle (Tm value &gt; 63&deg;C)</h3>
 +
<table>
 +
  <tr>
 +
    <th>Sequence</th><th>Temp. (&deg;C)</th><th>Time (sec)</th>
 +
  </tr>
 +
  <tr>
 +
    <td>1</td><td>94</td><td>120</td>
 +
  </tr>
 +
  <tr>
 +
    <td>2</td><td>98</td><td>10</td>
 +
  </tr>
 +
  <tr>
 +
    <td>3</td><td>68</td><td>30sec / 1kbp</td>
 +
  </tr>
 +
  <tr>
 +
    <td>4</td><td>4</td><td>Hold</td>
 +
  </tr>
 +
</table>
 +
<p>Cycle: sequence2~3 &times; (25~45)</p>
  
 +
<h3>Preparation of magnetic beads</h3>
 +
<ol>
 +
  <li>Mix 2 &micro;L  of magnetic beads (SiMAG-Streptavidin) and 48 &micro;L  of TE by vibration using sonic-toothbrush.</li>
 +
  <li>Collect the beads by attracting them to one side in 0.2 mL  polypropylene tube using neodymium magnet.</li>
 +
  <li>Remove supernatant.</li>
 +
</ol>
  
−
/* IF THE SCREEN IS LESS THAN 680PX */
+
<h3>Fixation to magnetic beads</h3>
 +
<ol>
 +
  <li>Add 3 &micro;L  of PCR product (0.48 pmol) and 7 &micro;L  of TE to beads.</li>
 +
  <li>Mix by vibration using sonic-toothbrush.</li>
 +
  <li>Collect the beads using magnet.</li>
 +
  <li>Remove supernatant containing excess amount of free DNA fragment.</li>
 +
</ol>
  
−
@media only screen and (max-width: 680px) {
+
<h3>Double restriction digestion</h3>
−
.collapsable_menu_control { display:block;}
+
<ol>
−
.menu_item {display:none;}
+
   <li>Add Digestion Premix containing 1 &micro;L of 10x RE solution, 8 &micro;L of DW and each 0.5 &micro;L of restriction endonuclease, <I>Xba</I>I and <I>Spe</I>I, to the beads.</li>
−
.menu_wrapper { width:100%; height: 15%; position:relative;}
+
   <li>Mix by pumping using pipette.</li>
−
.content_wrapper {width:100%; margin-left:0px;}
+
   <li>Incubate at 37 &deg;C for 30 min.</li>
−
.column.half_size {width:100%; }
+
   <li>Collect the beads using magnet.</li>
−
.column img { width: 100%; padding: 5px 0px;}
+
   <li>Obtain supernatant containing digested DNA fragment.</li>
−
.icon {display:block;}
+
   <li>Purify the supernatant by ethanol precipitation.</li>
−
.highlight {padding:15px 5px;}
+
</ol>
−
}
+
−
 
+
−
</style>
+
−
 
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<div class="collapsable_menu_control"> MENU ▤ </div>
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<li class="menu_item"> <div class="icon plus"></div> HUMAN PRACTICES
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<li> <a href="https://2016.igem.org/Team:HokkaidoU_Japan/HP/Silver">  Silver </a></li>
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<li> <a href="https://2016.igem.org/Team:HokkaidoU_Japan/HP/Gold">  Gold </a></li>
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<li> <a href="https://2016.igem.org/Team:HokkaidoU_Japan/Integrated_Practices">   Integrated Practices </a></li>
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<li> <a href="https://2016.igem.org/Team:HokkaidoU_Japan/Engagement">  Engagement </a></li>
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<li> <a href="https://2016.igem.org/Team:HokkaidoU_Japan/Software">  Software </a></li>
+
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<li> <a href="https://2016.igem.org/Team:HokkaidoU_Japan/Measurement">  Measurement </a></li>
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<li> <a href="https://2016.igem.org/Team:HokkaidoU_Japan/Model">  Model </a></li>
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<div class="content_wrapper">
 
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<h1 id="team_name">  </h1>
 
−
<h4 id="page_name">  </h4>
 
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<script>
 
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document.getElementById("disp15").style.display="none";
−
// This is the jquery part of your template.  Try not modify any of this code since it makes your menu work.
+
var displaying=0;
−
 
+
function hyoji15()
−
$(document).ready(function() {
+
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+
  if (displaying==0)
−
$("#HQ_page").attr('id','');
+
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−
+
     document.getElementById("disp15").style.display="block";
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+
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−
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+
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−
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+
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−
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+
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−
 
+
    document.getElementById("disp15").style.display="none";
−
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+
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−
$("#team_name").html( wgPageName.substring( 5, wgPageName.length ) );
+
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−
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+
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+
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+
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// this adds the team's name as an h1
+
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+
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+
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// this adds the page's title as an h4
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Latest revision as of 04:42, 27 August 2016

Team:HokkaidoU Japan - 2016.igem.org

 

Team:HokkaidoU Japan

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Protocols


PCR

Use KOD -Plus- Neo (TOYOBO CO.,LTD) as polymerase. Mix PCR solutions and run the PCR machine in a program which is detailed below.

Solution template DNA Primer-F 10µM Primer-R 10µM MgSO4 dNTPs 10x Buffer KOD Plus Neo DW Total
Volume (µL) 1 1 1 3 5 5 1 33 50

Thermal protocol is following

2STEP Cycle (Tm value > 63°C)

SequenceTemp. (°C)Time (sec)
194120
29810
36830sec / 1kbp
44Hold

Cycle: sequence2~3 × (25~45)

3STEP Cycle (Tm value < 63°C)

SequenceTemp. (°C)Time (sec)
194120
29810
3Tm30
46830sec / 1kbp
54Hold

Cycle: sequence2~4 × (25~45)

PCR Purification

FastGeneTM Gel/PCR Extraction kit (Nippon Genetics Co., Ltd)
Purification of PCR products

Digestion

Mix the following reagents in PCR tube.

Solution DNA RE1 10U/µL RE2 10U/µL Appropriate buffer Total
Volume (µL) 16 1 1 2 20
SequenceTemp. (°C)Time (min)
137120
26515
34Hold

Ligation

Mix the following reagents in 0.2 mL PCR tube. Use DNA Ligation Kit <Mighty Mix&rt; (Takara Bio Inc.) which contains ligase and buffer.

SolutionVector DNAInsert DNADWMighty MixTotal
Volume (µL)122510

Thermal protocol is following

SequenceTemp. (°C)Time (min)
11630
26510
34Hold

Electrophoresis

  1. Put gel into electrophoresis tank.
  2. Pore 2x TBE buffer into the tank to soak gel.
  3. Add 5 µL of EtBr into cathod.
  4. Pre-migration for 30 min at 100 V.
  5. Apply DNA solution with 6x loading dye and ladder.
  6. Start electrophoresis at 100 V.

Gel Extraction

FastGeneTM Gel/PCR Extraction kit (Nippon Genetics Co., Ltd)
DNA extraction from gel

Ethanol precipitation

  1. Add 1/10 volume of NaOAc, and 5/2 of 100% ethanol.
  2. Leave it at room temperature for 5 min.
  3. Centrifuge at 15,000 rpm for 15 min at 25°C.
  4. Remove supernatant and add 600 µL of 70% ethanol.
  5. Centrifuge at 15,000 rpm for 5 min at 25°C.
  6. Remove supernatant and air-dry at room temperature with light sheilding.
  7. Suspend with 10 µL of TE.

Colony PCR

Solution DNA Kapa-Taq (Taq polymerase) EX-F primer 10µM PS-R primer 10µM Total
Volume (µL) 4.2 5 0.4 0.4 10
SequenceTemp. (°C)Time (sec)
194120
29430
36860 sec / 1kbp
44Hold

Cycles: sequence2~3 × 25~45

Sequencing

Solution 5 x Sequencing Buffer primer 1µM template DNA Ready Reaction Premix DW Total
Volume (µL) 1.5 1.5 1 1 5 10
SequenceTemp. (°C)Time (sec)
19610
2505
360240
44Hold

Cycle: sequence2~4 × 25

Ethanol precipitation

Solution PCR product DW 3M NaOAc Glycogen 100% EtOH
Volume (µL) 10 10 2 1 50
  1. Centrifuge at 15,000 rpm for 15 min at room temprature
  2. Remove supernatant ,add 100 µL of 70% EtOH and tap tubes by finger.
  3. Centrifuge at 15,000 rpm for 10 min at room temprature
  4. Remove supernatant and air dry at room temperature.
  5. Resuspend the pellet to HiDi formamide and remove to 96-well plate.
  6. Set the plate and start electrophoresis.

Competent Cells

  1. Thaw original competent cells on ice.
  2. Add 5 µL of original competent cells to 2 mL of LB.
  3. Incubate the cells for 16 hrs at 37°C.
  4. Add 5 µL, 50 µL, and 500 µL of original cells to 100 mL of LB.
  5. Incubate the cells at 130 rpm at 20°C, until OD600 reach 0.5.
  6. Take 50 mL of incubated cells to two differnt culture tubes and centrifuge them at 3,000 rpm for 20 min at 4°C.
  7. Remove supernatant and add 75 mL of TB to each tube.
  8. Bring them to a one tube and centrifuge at 3,000 rpm for 20 min at 4°C.
  9. Remove supernatant and add 32 mL of TB.
  10. Add 32 µL of DMSO 10 times.
  11. Take 50 µL and freeze with liquid nitrogen.

Transformation

  1. Add plasmid to thawed competent cells on ice.
  2. Incubate on ice for 30 min.
  3. Add to LB.
  4. (Incubate the cells for 2 hrs at 37°C.)
  5. Spread 300 µL of the culture onto plate with LB and appropriate antibiotics.
  6. Incubate the plate(s) at 37°C for 16~20 hrs.

Mini-prep

FastGeneTM Plasmid mini kit (Nippon Genetics Co., Ltd)
fast / standard / low copy protocol

Streaking (Single colony isolation)

  1. Pick the colony with an inoculating loop from the agar plate．
  2. Drag the loop across on a new agar plate.
  3. Re-sterilise the loop and drag it across again.
  4. Repeat method 3.

PEG precipitation

  1. Add 13 µL of PEG to 20 µL of product(s).
  2. Leave it at room temperature for 1 hr.
  3. Centrifuge at 15,000 rpm for 20 min at 4°C.
  4. Remove supernatant and add 100 µL of 70% ethanol.
  5. Centrifuge at 15,000 rpm for 2 min at 4°C.
  6. Remove supernatant and air-dry at room temperature with light sheilding.
  7. Suspend with 10 µL of TE.

Gel Free System

Preparation of biotinylated DNA fragments

Use KOD -Plus- Neo (TOYOBO CO.,LTD) as polymerase and 5'-biotinylated primers. Mix PCR solutions and run the PCR machine in a program which is detailed below.

Solution template DNA 5'-biotinylated 100-UP primer 10µM 5'-biotinylated 200-DN primer 10µM MgSO4 dNTPs 10x Buffer KOD Plus Neo DW Total
Volume (µL) 1 1.5 1.5 3 5 5 1 32 50

Thermal protocol is following

2STEP Cycle (Tm value > 63°C)

SequenceTemp. (°C)Time (sec)
194120
29810
36830sec / 1kbp
44Hold

Cycle: sequence2~3 × (25~45)

Preparation of magnetic beads

  1. Mix 2 µL of magnetic beads (SiMAG-Streptavidin) and 48 µL of TE by vibration using sonic-toothbrush.
  2. Collect the beads by attracting them to one side in 0.2 mL polypropylene tube using neodymium magnet.
  3. Remove supernatant.

Fixation to magnetic beads

  1. Add 3 µL of PCR product (0.48 pmol) and 7 µL of TE to beads.
  2. Mix by vibration using sonic-toothbrush.
  3. Collect the beads using magnet.
  4. Remove supernatant containing excess amount of free DNA fragment.

Double restriction digestion

  1. Add Digestion Premix containing 1 µL of 10x RE solution, 8 µL of DW and each 0.5 µL of restriction endonuclease, XbaI and SpeI, to the beads.
  2. Mix by pumping using pipette.
  3. Incubate at 37 °C for 30 min.
  4. Collect the beads using magnet.
  5. Obtain supernatant containing digested DNA fragment.
  6. Purify the supernatant by ethanol precipitation.