Team:EPF Lausanne/Protocol

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<!-- ABSTRACT -->
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                  <li class="active"><span><i class="glyphicon glyphicon-th"></i> Protocols</span></li>
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</div>
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<h1 class="center">PROTOCOLS</h1>
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<div class="row">
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<p>In this page you will find the protocols that worked well for us.</p>
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<div class="col col-md-9">
 +
<div class="whitebg box">
 +
<!-- ce serait cool de faire un menu vertical qui reste tjrs là (sur le protocol page) ac la liste des protocols -->
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<h3 id="gel_protocol">Agarose Gel Preparation</h3> <!-- name of protocol -->
-
<!-- AGAROSE GEL -->
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-
 
+
-
<h3>Agarose Gel Preparation</h3> <!-- name of protocol -->
+
<p>Materials</p>
<p>Materials</p>
-
<ul class="list-unstyled">
+
<ul>
  <li>TAE 1X</li>
  <li>TAE 1X</li>
  <li>Agarose</li>
  <li>Agarose</li>
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<!-- END AGAROSE GEL -->
<!-- END AGAROSE GEL -->
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 +
</div>
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<div class="whitebg box">
 +
 +
<!-- AMINO ACID SOLUTIONS -->
 +
 +
 +
<h3 id="amino_acid_solution">Amino acid solutions Protocol</h3> <!-- name of protocol -->
 +
<p>Materials</p>
 +
<ul>
 +
<li>Histidine-Hcl</li>
 +
<li>Uracil</li>
 +
<li>Leucine</li>
 +
<li>Tryptophan</li>
 +
</ul>
 +
<p>Procedure</p>
 +
<table id="assembly mix" class="table table-striped table-hover">
 +
  <thead>
 +
  <tr>
 +
    <th> Stock concentration </th>
 +
    <th> Final concentration </th>
 +
    <th> Total quantity for 50 mL</th>
 +
  </tr>
 +
  </thead>
 +
  <tbody>
 +
  <tr>
 +
    <td>100 mM Histidine-Hcl(209g/mol)</td>
 +
    <td>20.9 g/l</td>
 +
    <td>0.418 g</td>
 +
  </tr>
 +
  <tr>
 +
    <td>20 mM Uracil (112 g/mol)</td>
 +
    <td>2.24 g/l</td>
 +
    <td>0.0448 g</td>
 +
  </tr>
 +
  <tr>
 +
    <td> 100 mM Leucine (131 g/mol)</td>
 +
    <td>13.1 g/l</td>
 +
    <td>0.262 g</td>
 +
  </tr>
 +
  <tr>
 +
    <td> 40 mM Tryptophan (204 g/mol) </td>
 +
    <td>8.16 g/l</td>
 +
    <td>0.1632g</td>
 +
  </tr>
 +
  </tbody>
 +
  </table>
 +
 +
<ol>
 +
<li>Filter and sterilize the solutions</li>
 +
<li>Add 8 mL per liter of selective medium or spread 500 µl on top of a selective plate </li>
 +
</ol>
 +
 +
 +
 +
 +
<!-- END AMINO ACID SOLUTIONS -->
 +
 +
 +
</div>
 +
<div class="whitebg box">
 +
 +
<!-- COLONY PCR -->
 +
 +
 +
<h3 id="colony_pcr">Colony PCR</h3> <!-- name of protocol -->
 +
<h4></h4> <!-- sub-part -->
 +
<p>Materials</p>  <!-- Materials -->
 +
<ul>
 +
<li>Petri dish with transformed colonies</li>
 +
<li>Taq Polymerase PCR material (see protocol for Taq polymerase)</li>
 +
<li>Nuclease free water</li>
 +
</ul>
 +
<p>Procedure</p>  <!-- Procedure -->
 +
<ol>
 +
<li> Inoculate a single colony from the plate with a tip and agitate the tip into 10uL of nuclease free water into a PCR tube</li>
 +
<li> Heat shock the tubes at 95°C for 10 min.</li>
 +
<li> Transfer 1uL of the heatshocked solution into a new PCR tube and perform a Taq PCR according to the protocol for Taq polymerase (considering 1uL of DNA and for 25uL final product).</li>
 +
</ol>
 +
 +
<p></p> <!-- protocol source -->
 +
 +
<!-- END COLONY PCR -->
 +
 +
 +
</div>
 +
<div class="whitebg box">
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<h3>Gibson Assembly Protocol</h3> <!-- name of protocol -->
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<h3 id="gibson_protocol">Gibson Assembly Protocol</h3> <!-- name of protocol -->
<h4></h4> <!-- sub-part -->
<h4></h4> <!-- sub-part -->
<p>Materials</p>
<p>Materials</p>
-
<ul class="list-unstyled">
+
<ul>
  <li>Plasmids of interest (miniprep)</li>
  <li>Plasmids of interest (miniprep)</li>
  <li>NEB Gibson assembly Kit (Gibson Assembly Master Mix (2X) and chemically competent cells)</li>
  <li>NEB Gibson assembly Kit (Gibson Assembly Master Mix (2X) and chemically competent cells)</li>
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</ul>
</ul>
<p>Procedure</p>
<p>Procedure</p>
 +
 +
<table id="assembly mix" class="table table-striped table-hover">
 +
<thead>
 +
  <tr>
 +
    <th> </th>
 +
    <th>2-3 Fragments assembly* (X uL)</th>
 +
    <th>4-6 Fragments assembly* (X uL)</th>
 +
  </tr>
 +
</thead>
 +
<tbody>
 +
  <tr>
 +
    <td>Total Amount of Fragments</td>
 +
    <td>0.02-0.5 pmols</td>
 +
    <td>0.2-1 pmols*</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Gibson Assembly Master Mix (2X)</td>
 +
    <td>10 uL</td>
 +
    <td>10 uL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Deionized H2O</td>
 +
    <td>10-X uL</td>
 +
    <td>10-X uL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Total Volume</td>
 +
    <td>20 uL</td>
 +
    <td>20 uL</td>
 +
  </tr>
 +
  </tbody>
 +
  </table>
 +
<ol>
<ol>
  <li>Set up the following reaction on ice:</li>
  <li>Set up the following reaction on ice:</li>
-
  <table id="assembly mix" style="width:40%">
+
<p>*Optimized cloning efficiency is 50-100ng of vectors with 2-3 fold of excess inserts. Use 5 times more of inserts if size is less than 200 bps.</p>
 +
<li>Incubate samples in a thermocycler at 50C for 15 minutes when 2 or 3 fragments are being assembled or 60 minutes when 4-6 fragments are being assembled. Following incubation, store samples on ice or at -20°C for subsequent transformation.</li>
 +
<li>Transform 50 uL of competent cells (provided with the kit) with 2 μl of the assembly reaction, following the transformation protocol.</li>
 +
</ol>
 +
 
 +
<p>You can find the original NEB Gison Assembly Protocol <a target="_blank" href="http://www.neb.com/protocols/2012/12/11/gibson-assembly-protocol-e5510">here</a></p> <!-- protocol source -->
 +
 
 +
 
 +
<!-- END GIBSON ASSEMBLY -->
 +
 
 +
 
 +
</div>
 +
<div class="whitebg box">
 +
 
 +
 
 +
 
 +
<!-- MINIPREP -->
 +
 
 +
 
 +
<h3 id="miniprep_protocol">Miniprep – with QlAprep Spin Miniprep kit</h3> <!-- name of protocol -->
 +
<h4></h4> <!-- sub-part -->
 +
<p>Materials</p>  <!-- Materials -->
 +
<ul>
 +
<li>Ovenight liquid cell cultures (5-8 mL)</li>
 +
<li>QlAprep Spin Miniprep kit</li>
 +
</ul>
 +
<p>Procedure</p>  <!-- Procedure -->
 +
<ol>
 +
<li>Pellet bacterial cells from overnight 5-8 mL culture (4000 rpm, 10 min) and discard the medium.</li>
 +
<li>Resuspend pelleted bacterial cells in 250 μL Buffer P1 (stored at 4°C). Ensure that RNase A has been added to Buffer P1. No cells clumps should be visible after resuspension of the pellet. Transfer the resuspended cells into a 1.5 microcentrifuge tube.</li>
 +
<li>Add 250 μL Buffer P2 and gently invert the tube 4-6 times to mix (do not vortex). If necessary, continue inverting the tube until the solution becomes viscous and slightly clear. Let stand for 2-4 minutes; never more than 5.</li>
 +
<li>Add 350 μL Buffer N3 and invert the tube immediately but gently 4-6 times. The solution should become cloudy.</li>
 +
<li>Centrifuge for 10 min at 13,000 rpm in a table-top microcentrifuge. A compact pellet will form.</li>
 +
<li>Apply the supernatant from step 5 to the QlAprep Spin Column by pipetting.</li>
 +
<li>Centrifuge for 1 min at 13,000 rpm. Discard the flow-through.</li>
 +
<li>Wash QlAprep Spin Column by adding 750 μL Buffer PE and centrifuge for 1 min at 13,000 rpm.</li>
 +
<li>Discard the flow-through, and centrifuge for an additional 1 min to remove residual wash buffer.</li>
 +
<li>Place the QlAprep column in a clean 1.5 ml microcentrifuge tube. To elute DNA, add 50 μL Buffer EP (10 mM Tris-Cl, pH 8.5) to the center of each QlAprep Spin Column, let stand for 1 min, and centrifuge for 1 min at 13,000 rpm.</li>
 +
</ol>
 +
 
 +
<p>You can find the original Qiagen Miniprep Protocol <a target="_blank" href="http://public.wsu.edu/~kahn_sci/Flow/E2-QIAprep_Miniprep_Handbook.pdf">here</a>.</p> <!-- protocol source -->
 +
 
 +
<!-- END MINIPREP -->
 +
 
 +
 
 +
</div>
 +
<div class="whitebg box">
 +
 
 +
 
 +
<!-- PCR -->
 +
 
 +
 
 +
<h3 id="pcr_protocol">PCR Protocol</h3> <!-- name of protocol -->
 +
 
 +
<h4>Phusion PCR</h4> <!-- sub-part -->
 +
<p>Materials</p>  <!-- Materials -->
 +
<ul>
 +
<li>Phusion® High-Fidelity DNA Polymerase PCR Kit</li>
 +
<li>Nuclease-free Water</li>
 +
<li>Primers</li>
 +
<li>Template DNA</li>
 +
</ul>
 +
<p>Procedure</p>  <!-- Procedure -->
 +
<ol>
 +
<li>Setup the following reaction in a 0.5 mL PCR tube:
 +
  <table id="chemicals" class="table table-striped table-hover">
 +
  <thead>
   <tr>
   <tr>
-
     <th> </th>
+
     <th>Component</th>
-
     <th>Recommended Amout of Fragments Used for Assembly</th>
+
     <th>20 µL Reaction</th>
 +
    <th>50 µL Reaction</th>
 +
    <th>Final Concentration</th>
   </tr>
   </tr>
 +
  </thead>
 +
  <tbody>
   <tr>
   <tr>
-
     <th> </th>
+
     <td>5X Phusion HF or GC Buffer</td>
-
     <th>2-3 Fragments assembly* (X uL)</th>
+
     <td>4 µL</td>
-
     <th>4-6 Fragments assembly* (X uL)</th>
+
     <td>10 µL</td>
 +
    <td>1X</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th>Total Amount of Fragments</th>
+
     <td>10 mM dNTPs</td>
-
     <th>0.02-0.5 pmols</th>
+
     <td>0.4 µL</td>
-
     <th>0.2-1 pmols*</th>
+
     <td>1 µL</td>
 +
    <td>200 µM</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th>Gibson Assembly Master Mix (2X)</th>
+
     <td>10 µM Forward Primer</td>
-
     <th>10 uL</th>
+
     <td>1 µL</td>
-
     <th>10 uL</th>
+
     <td>2.5 µL</td>
 +
    <td>0.5 µM</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th>Deionized H2O</th>
+
     <td>10 µM Reverse Primer</td>
-
     <th>10-X uL</th>
+
     <td>1 µL</td>
-
     <th>10-X uL</th>
+
     <td>2.5 µL</td>
 +
    <td>0.5 µM</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th>Total Volume</th>
+
     <td>Template DNA</td>
-
     <th>20 uL</th>
+
     <td>variable</td>
-
     <th>20 uL</th>
+
     <td>variable</td>
 +
    <td>&lt;250 ng</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th>*Optimized cloning efficiency is 50-100ng of vectors with 2-3 fold of excess inserts. Use 5 times more of inserts if size is less than 200 bps.</th>
+
     <td>DMSO (optional)</td>
 +
    <td>(0.6 µL)</td>
 +
    <td>(1.5 µL)</td>
 +
    <td>3 %</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Phusion DNA Polymerase</td>
 +
    <td>0.2 µL</td>
 +
    <td>0.5 µL</td>
 +
    <td>1.0 units/50 µl PCR</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Nuclease-free Water</td>
 +
    <td>To 20 µL</td>
 +
    <td>To 50 µL</td>
 +
  </tr>
 +
  </tbody>
 +
  </table></li>
 +
<li>Gently mix the reaction. Collect all liquid to the bottom of the tube by a quick spin if necessary. Overlay the sample with mineral oil if using a PCR machine without a heated lid.</li>
 +
<li>Transfer PCR tubes from ice to a PCR machine with the block preheated to 98°C and begin thermocycling:
 +
<table id="chemicals" class="table table-striped table-hover">
 +
<thead>
 +
  <tr>
 +
    <th>STEP</th>
 +
    <th>TEMP</th>
 +
    <th>TIME</th>
 +
  </tr>
 +
  </thead>
 +
  <tbody>
 +
  <tr>
 +
    <td>Initial Denaturation</td>
 +
    <td>98 °C</td>
 +
    <td>30 seconds</td>
 +
  </tr>
 +
  <tr>
 +
    <td>25-35 Cycles</td>
 +
    <td>98°C</td>
 +
    <td>5-10 seconds</td>
 +
  </tr>
 +
  <tr>
 +
    <td> </td>
 +
    <td>45-72 °C Annealing Temp</td>
 +
    <td>20 seconds</td>
 +
  </tr>
 +
  <tr>
 +
    <td> </td>
 +
    <td>72 °C Elongation Temp</td>
 +
    <td>15-30 seconds per kb </td>
 +
  </tr>
 +
  <tr>
 +
    <td>Final Extension</td>
 +
    <td>72 °C</td>
 +
    <td>5-10 minutes</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Hold</td>
 +
    <td>4-10 °C </td>
 +
  </tr>
 +
  </tbody>
 +
  </table></li>
 +
</ol>
 +
 
 +
<p>You can find the original PCR Protocol for Phusion® High-Fidelity DNA Polymerase (M0530) <a target="_blank" href="https://www.neb.com/protocols/1/01/01/pcr-protocol-m0530">here</a>.</p> <!-- protocol source -->
 +
 
 +
 
 +
<h4 id="taq">Taq PCR</h4> <!-- sub-part -->
 +
<p>Materials</p>  <!-- Materials -->
 +
<ul>
 +
<li>ThermoPol Buffer 10X</li>
 +
<li>dNTPs</li>
 +
<li>Taq Polymerase</li>
 +
<li>Template DNA</li>
 +
<li>Primers</li>
 +
<li>Nuclease-free water</li>
 +
</ul>
 +
<p>Procedure</p>  <!-- Procedure -->
 +
<ol>
 +
<li>Prepare the following reaction in a 0.5 mL PCR tube on ice:
 +
  <table id="chemicals" class="table table-striped table-hover">
 +
  <thead>
 +
  <tr>
 +
    <th>Component</th>
 +
    <th>25 µL Reaction</th>
 +
    <th>50 µL Reaction</th>
 +
    <th>Final Concentration</th>
 +
  </tr>
 +
  </thead>
 +
  <tbody>
 +
  <tr>
 +
    <td>10X ThermoPol or Standard Taq Reaction Buffer</td>
 +
    <td>2.5 µL</td>
 +
    <td>5 μL</td>
 +
    <td>1X</td>
 +
  </tr>  
 +
  <tr>
 +
    <td>10 mM dNTPs</td>
 +
    <td>0.5 µL</td>
 +
    <td>1 µL</td>
 +
    <td>200 µM</td>
 +
  </tr>
 +
  <tr>
 +
    <td>10 µM Forward Primer</td>
 +
    <td>0.5 µL</td>
 +
    <td>1 µL</td>
 +
    <td>0.2 µM</td>
 +
  </tr>
 +
  <tr>
 +
    <td>10 µM Reverse Primer</td>
 +
    <td>0.5 µL</td>
 +
    <td>1 µL</td>
 +
    <td>0.2 µM</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Template DNA</td>
 +
    <td>variable</td>
 +
    <td>variable</td>
 +
    <td>&lt;1000 ng</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Taq DNA Polymerase</td>
 +
    <td>0.125 µL</td>
 +
    <td>0.25 µL</td>
 +
    <td>1.25 units/50 µL PCR</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Nuclease-free Water</td>
 +
    <td>To 25 µL</td>
 +
    <td>To 50 µL</td>
 +
    <td></td>
 +
  </tr>
 +
  </tbody>
   </table>
   </table>
-
  <li></li>
+
* Due to the difficulties in pipetting small volumes of enzyme, Taq DNA Polymerase can be diluted in 1X reaction buffer. For example, 1 µl of Taq DNA Polymerase is mixed with 4 µl of 1X reaction buffer and 1 µl of that mixture is added to the reaction. Enzyme diluted 1X reaction buffer should not be stored for future use.</li>
-
  <li></li>
+
  <li>Gently mix the reaction and spin down in microcentrifuge.
-
<li></li>
+
If the thermocycler does not have a heated cover, add one drop of mineral oil to the reaction tube to prevent evaporation.</li>
-
<li></li>
+
  <li>Cycling Conditions for a Routine PCR:
-
<li></li>
+
<table id="chemicals" class="table table-striped table-hover">
-
<li></li>
+
<thead>
-
<li></li>
+
  <tr>
-
<li></li>
+
    <th>STEP</th>
 +
    <th>TEMP</th>
 +
    <th>TIME</th>
 +
    <th>CYCLES</th>
 +
  </tr>
 +
  </thead>
 +
  <tbody>
 +
  <tr>
 +
    <td>Initial Denaturation</td>
 +
    <td>95 °C</td>
 +
    <td>30 seconds</td>
 +
    <td>1</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Denaturation</td>
 +
    <td>95 °C</td>
 +
    <td>15-30 seconds</td>
 +
    <td>30</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Annealing</td>
 +
    <td>45-68 °C</td>
 +
    <td>15-60 seconds</td>
 +
    <td> </td>
 +
  </tr>
 +
  <tr>
 +
    <td>Extension</td>
 +
    <td>68 °C</td>
 +
    <td>1 minute per kb</td>
 +
    <td> </td>
 +
  </tr>
 +
  <tr>
 +
    <td>Final Extension</td>
 +
    <td>72 °C</td>
 +
    <td>5 minutes</td>
 +
    <td> </td>
 +
  </tr>
 +
  <tr>
 +
    <td>Hold</td>
 +
    <td>4-10°C </td>
 +
    <td></td>
 +
    <td> </td>
 +
  </tr>
 +
  </tbody>
 +
  </table></li>
</ol>
</ol>
-
<p>You can find the original NEB Gison Assembly Protocol <a href="https://www.neb.com/protocols/2012/12/11/gibson-assembly-protocol-e5510">here</a></p> <!-- protocol source -->
+
<p>You can find the original NEB Taq PCR <a target="_blank" href="https://www.neb.com/protocols/1/01/01/protocol-for-a-routine-taq-pcr-reaction">here</a>.</p> <!-- protocol source -->
 +
 
 +
 
 +
<!-- END PCR -->
 +
 
 +
 
 +
</div>
 +
<div class="whitebg box">
 +
 
 +
 
 +
<!-- PCR PURIFICATION -->
 +
 
 +
<h3 id="purification_protocol">PCR Product Purification Protocol</h3> <!-- name of protocol -->
 +
<h4></h4> <!-- sub-part -->
 +
<p>Materials</p>  <!-- Materials -->
 +
<ul>
 +
<li>PCR products</li>
 +
<li>Qiagen QlAquick PCR kit</li>
 +
</ul>
 +
<p>Procedure</p>  <!-- Procedure -->
 +
<ol>
 +
<li>Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.</li>
 +
<li>To bind DNA, apply the sample to the QlAquick column and centrifuge for 1 min at 13,000 rpm.</li>
 +
<li>Discard the flow-through. Place the QlAquick column back into the same tube.</li>
 +
<li>To wash, add 750 uL Buffer PE to the QlAquick column and centrifuge for 1 min at 13,000 rpm.</li>
 +
<li>Discard flow-through and place the QlAquick column back in the same tube. Centrifuge the column for an additional 1 min.</li>
 +
<li>Place QlAquick column in a clean 1.5 mL microcentrifuge tube.</li>
 +
<li>To elute DNA, add 30 uL Buffer EP (10 mM Tris-Cl, pH 8.5) to the center of the QlAquick membrane, let the column stand for 1 min and then centrifuge for 1 min at 13,000 rpm.</li>
 +
</ol>
 +
 
 +
<p>You can find the original Qiagen PCR Product Purification Protocol <a target="_blank" href="https://static.igem.org/mediawiki/2012/a/a3/QIAquick_PCR-purification.pdf">here</a>.</p> <!-- protocol source -->
 +
 
 +
 
 +
<!-- END PCR PURIFICATION -->
 +
 
 +
 
 +
</div>
 +
<div class="whitebg box">
 +
 
 +
 
 +
<!-- PEG/LiAc solution-->
 +
<h3 id="PEG_LiAc_solution">PEG/LiAc solution protocol</h3> <!-- name of protocol -->
 +
 
 +
<p>Prepare fresh just prior to use.</p>
 +
<p>Materials</p>
 +
<ul>
 +
<li>50% PEG 3350 (Polyethylene glycol, avg. mol. wt. = 3,350; Sigma Cat No. P-3640) prepare
 +
with sterile deionized H2O; if necessary, warm solution to 50°C to help the PEG go into
 +
solution</li>
 +
<li>10X TE buffer: 0.1 M Tris-HCl, 10 mM EDTA, pH 7.5. Autoclaved.</li>
 +
<li>10X LiAc: 1 M lithium acetate (Sigma Cat No. L-6883) Adjust to pH 7.5 with dilute acetic
 +
acid and autoclaved.</li>
 +
</ul>
 +
 
 +
<p>Prepare the PEG/LiAc solution as follows: </p>
 +
 
 +
<table id="chemicals" class="table table-striped table-hover">
 +
<thead>
 +
  <tr>
 +
    <th>Final Concentration</th>
 +
    <th>Stock solution Concentration</th>
 +
    <th>Volume to add to prepare 10mL of solution</th>
 +
  </tr>
 +
  </thead>
 +
  <tbody>
 +
  <tr>
 +
    <td>PEG 4000 40%</td>
 +
    <td>50% PEG</td>
 +
    <td>8mL</td>
 +
  </tr>  
 +
  <tr>
 +
    <td>TE buffer 1X</td>
 +
    <td>10X TE</td>
 +
    <td>1mL</td>
 +
  </tr>
 +
 
 +
 
 +
  <tr>
 +
    <td>LiAc 1X </td>
 +
    <td>10X LiAc</td>
 +
    <td>1mL</td>
 +
   
 +
  </tr>
 +
</tbody>
 +
  </table>
 +
 
 +
<p></p>
 +
 
 +
<p>You can download the Yeast Protocol Handbook (Clontech) containing the original procedure <a target="_blank" href="http://www.clontech.com/xxclt_ibcGetAttachment.jsp?cItemId=17602">here</a>.</p>
 +
 
 +
<!-- END PEG/LiAc solution-->
 +
 
 +
 
 +
</div>
 +
<div class="whitebg box">
 +
 
 +
 
 +
<h3 id="sdmedium_protocol"> SD Medium </h3> <!-- name of protocol -->
 +
<p>Materials</p>  <!-- Materials -->
 +
<ul>
 +
<li>Amino Acid Power</li>
 +
<li>yeast nitrogen base</li>
 +
<li>ammonium sulphate</li>
 +
<li>adenine sulphate</li>
 +
<li>water</li>
 +
<li>NaOH</li>
 +
<li>agar</li>
 +
<li>glucose</li>
 +
</ul>
 +
<p>Procedure</p>  <!-- Procedure -->
 +
<ol>
 +
<li>Place a stirrer bar in a 2 liters Erlenmeyers</li>
 +
<li>Add 2.6g amino acid powder, 3.4g yeast nitrogen base, 10g ammonium sulphate, adenine sulphate(+/- 1g) and 950mL water.</li>
 +
<li>adjust pH to 5.9 by adding a few drops of 10 M NaOH</li>
 +
<li>In a new erlenmeyer, add 35g agar and 900 ml water</li>
 +
<li>Autoclave the 2 flasks</li>
 +
<li>Transfer the bottle of medium to the agar bottle.</li>
 +
<li>Cool to 55°C</li>
 +
<li>Before pouring add 100ml 40% glucose (in 2l final)</li>
 +
<li>before pouring add 16ml* of the required amino acids (in 2L final)</li>
 +
<li>Pour plates</li>
 +
</ol>
-
<!-- END GIBSON ASSEMBLY -->
 
<!-- COMPETENT CELLS -->
<!-- COMPETENT CELLS -->
-
<h3>Thermocompetent E coli cells preparation</h3> <!-- name of protocol -->
+
 
 +
</div>
 +
<div class="whitebg box">
 +
 
 +
 
 +
<h3 id="competent_protocol">Thermocompetent <i>E. coli</i> cells preparation</h3> <!-- name of protocol -->
<p>Materials</p>
<p>Materials</p>
-
<ul class="list-unstyled">
+
<ul>
  <li>Bacterial colony from plate (day 1)</li>
  <li>Bacterial colony from plate (day 1)</li>
  <li>LB medium (day 1)</li>
  <li>LB medium (day 1)</li>
Line 206: Line 732:
</ol>
</ol>
-
<h4>Inoue Transformation Buffer</h4> <!-- sub-part -->
+
<h4 id="inouebuffer">Inoue Transformation Buffer</h4> <!-- sub-part -->
<p>Materials</p>
<p>Materials</p>
-
<ul class="list-unstyled">
+
<ul>
  <li>MnCl2 · 4H2O</li>
  <li>MnCl2 · 4H2O</li>
  <li>CaCl2 · 2H2O</li>
  <li>CaCl2 · 2H2O</li>
Line 225: Line 751:
   </ol>
   </ol>
  <li>Dissolve solutes as follows in 800 mL of Milli-Q water.</li>
  <li>Dissolve solutes as follows in 800 mL of Milli-Q water.</li>
-
   <table id="chemicals" style="width:30%">
+
   <table id="chemicals" class="table table-striped table-hover">
 +
  <thead>
   <tr>
   <tr>
     <th>Reagent</th>
     <th>Reagent</th>
Line 231: Line 758:
     <th>Final Conc.</th>
     <th>Final Conc.</th>
   </tr>
   </tr>
 +
  </thead>
 +
  <tbody>
   <tr>
   <tr>
-
     <th>MnCl2 · 4H2O</th>
+
     <td>MnCl2 · 4H2O</td>
-
     <th>10.88 g</th>
+
     <td>10.88 g</td>
-
     <th>55 mM</th>
+
     <td>55 mM</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th>CaCl2 · 2H2O</th>
+
     <td>CaCl2 · 2H2O</td>
-
     <th>2.20 g</th>
+
     <td>2.20 g</td>
-
     <th>15 mM</th>
+
     <td>15 mM</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th>KCl</th>
+
     <td>KCl</td>
-
     <th>18.65</th>
+
     <td>18.65</td>
-
     <th>250 mM</th>
+
     <td>250 mM</td>
   </tr>
   </tr>
 +
  </tbody>
   </table>
   </table>
  <li>Add 20 mL PIPES (.5 M, pH 6.7).</li>
  <li>Add 20 mL PIPES (.5 M, pH 6.7).</li>
Line 254: Line 784:
<!-- END COMPETENT CELLS -->
<!-- END COMPETENT CELLS -->
 +
 +
 +
 +
</div>
 +
<div class="whitebg box">
Line 259: Line 794:
<!-- TRANSFORMATION -->  
<!-- TRANSFORMATION -->  
-
<h3>Transformation Protocols</h3> <!-- name of protocol -->
+
<h3 id="transformation_protocol">Transformation Protocols</h3> <!-- name of protocol -->
-
<h4>NEB transformation protocol</h4> <!-- sub-part -->
+
<h4 id="NEB">NEB transformation protocol</h4> <!-- sub-part -->
<p>Materials</p>
<p>Materials</p>
-
<ul class="list-unstyled">
+
<ul>
  <li>DNA</li>
  <li>DNA</li>
  <li>Competent cells</li>
  <li>Competent cells</li>
Line 279: Line 814:
</ol>
</ol>
-
<p>You can find the original NEB Transformation Protocol <a href="http://www.neb.com/protocols/2012/05/21/transformation-protocol">here</a>.</p>
+
<p>You can find the original NEB Transformation Protocol <a target="_blank" href="http://www.neb.com/protocols/2012/05/21/transformation-protocol">here</a>.</p>
-
<h4>iGEM Transformation Protocol</h4> <!-- sub-part -->
+
<h4 id="igem">iGEM Transformation Protocol</h4> <!-- sub-part -->
<p>Materials</p>
<p>Materials</p>
-
<ul class="list-unstyled">
+
<ul>
  <li>DNA</li>
  <li>DNA</li>
  <li>Competent cells</li>
  <li>Competent cells</li>
Line 303: Line 838:
</ol>
</ol>
-
<p>You can find the original iGEM Transformation Protocol <a href="http://parts.igem.org/Help:Protocols/Transformation">here</a>.</p>
+
<p>You can find the original iGEM Transformation Protocol <a target="_blank" href="http://parts.igem.org/Help:Protocols/Transformation">here</a>.</p>
<!-- END TRANSFORMATION -->
<!-- END TRANSFORMATION -->
-
<h3></h3> <!-- name of protocol -->
+
 
-
<h4></h4> <!-- sub-part -->
+
</div>
 +
<div class="whitebg box">
 +
 
 +
 
 +
<!-- TRANSFORMATION yeast -->
 +
<h3  id="yeast_transformation_protocol">Yeast transformation and homolgous recombination procedure from Clontech Yeast Handbook</h3> <!-- name of protocol -->
 +
 
<p>Materials</p>
<p>Materials</p>
-
<ul class="list-unstyled">
+
<ul>
-
  <li></li>
+
<li>YPD or the appropriate SD liquid medium</li>
 +
<li>Sterile 1X TE/1X LiAc </li>
 +
<li>Sterile 1.5-ml microcentrifuge tubes for the transformation </li>
 +
  <li>Appropriate SD agar plates (100-mm diameter)</li>
 +
<li>Appropriate DNA template in solution (check amounts required)</li>
 +
<li>Appropriate yeast reporter strain for making competent cells</li>
 +
<li>Salmon sperm (carrier DNA)</li>
 +
<li>Sterile PEG/LiAc solution</li>
 +
<li>100% DMSO (Dimethyl sulfoxide; Sigma Cat No. D-8779)</li>
 +
<li>Sterile 1X TE buffer</li>
 +
<li>Sterile glass rod, bent Pasteur pipette, or 5-mm glass beads for spreading cells on plates</li>
 +
 +
 
</ul>
</ul>
<p>Procedure</p>
<p>Procedure</p>
<ol>
<ol>
-
  <li></li>
+
  <li>Inoculate 1 ml of YPD or SD with several colonies, 2–3 mm in diameter</li>
 +
<li>Vortex vigorously for 5 min to disperse any clumps</li>
 +
<li>Transfer this into a flask containing 50 ml of YPD or the appropriate SD medium</li>
 +
<li>Incubate at 30°C for 16–18 hr with shaking at 250 rpm to stationary phase (OD600>1.5)</li>
 +
<li>Transfer 30 ml of overnight culture to a flask containing 300 ml of YPD. Check the OD600 of
 +
the diluted culture and, if necessary, add more of the overnight culture to bring the OD600
 +
up to 0.2–0.3</li>
 +
<li> Incubate at 30°C for 3 hr with shaking (230 rpm). At this point, the OD600 should be
 +
0.4–0.6.</li>
 +
<li>Place cells in 50-ml tubes and centrifuge at 1,000 x g for 5 min at room temperature
 +
(20–21°C)</li>
 +
<li>Discard the supernatants and thoroughly resuspend the cell pellets in sterile TE. Pool the cells into one tube (final volume 25–50 ml)</li>
 +
<li>Centrifuge at 1,000 x g for 5 min at room temperature.</li>
 +
<li>Decant the supernatant</li>
 +
<li>Resuspend the cell pellet in 1.5 ml of freshly prepared, sterile 1X TE/1X LiAc</li>
 +
<li>Add at least 1 μg of linear DNA and 0.1 mg of salmon sperm DNA to a fresh 1.5-ml tube and mix</li>
 +
<li>Add 0.1 ml of yeast competent cells to each tube and mix well by vortexing</li>
 +
<li>Add 0.6 ml of sterile PEG/LiAc solution to each tube and vortex at high speed for 10 sec to
 +
mix</li>
 +
<li>Incubate at 30°C for 30 min with shaking at 200 rpm</li>
 +
<li> Add 70 μl of DMSO. Mix well by gentle inversion. Do not vortex !</li>
 +
<li>Heat shock for 15 min in a 42°C water bath</li>
 +
<li>Chill cells on ice for 1–2 min</li>
 +
<li>Centrifuge cells for 5 sec at 14,000 rpm at room temperature. Remove the
 +
supernatant</li>
 +
<li>Resuspend cells in 0.5 ml of sterile 1X TE buffer</li>
 +
<li>Plate 100 μl on each SD agar plate that will select for the desired transformants</li>
 +
 
 +
 
</ol>
</ol>
-
<p></p> <!-- protocol source -->
+
<p>You can download the Yeast Protocol Handbook (Clontech) containing the original procedure <a target="_blank" href="http://www.clontech.com/xxclt_ibcGetAttachment.jsp?cItemId=17602">here</a>.</p>
 +
 
 +
<!-- END TRANSFORMATION yeast-->
</div>
</div>
 +
<div class="whitebg box">
 +
 +
<!-- YPD MEDIUM-->
 +
<h3  id="YPD_medium_protocol">YPD Medium protocol</h3> <!-- name of protocol -->
 +
 +
<p></p>
 +
 +
<p>Procedure</p>
 +
<p>Prepare your YPD medium as follows</p>
 +
<li> 20 g/L Difco peptone </li>
 +
<li>10 g/L Yeast extract</li>
 +
<li> 20 g/L Agar (for plates only)</li>
 +
<li>Add H2O to 950 ml. Adjust the pH to 6.5 if necessary, then autoclave. Allow medium to cool
 +
to ~ 55°C and then add dextrose (glucose) to 2% (50 ml of a sterile 40% stock solution). Adjust
 +
the final volume to 1 L if necessary.
 +
s in 50-ml tubes and centrifuge at 1,000 x g for 5 min at room temperature
 +
(20–21°C)</li>
 +
<li>[Optional] For kanamycin-containing medium, prepare YPD or YPDA as above. After autoclaved
 +
medium has cooled to 55°C, add 0.2–0.3 ml of 50 mg/ml kanamycin (final concentration
 +
10–15 mg/L).</li>
 +
 +
 +
<p>You can download the Yeast Protocol Handbook (Clontech) containing the original procedure <a target="_blank" href="http://www.clontech.com/xxclt_ibcGetAttachment.jsp?cItemId=17602">here</a>.</p>
 +
 +
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 +
</div>
 +
 +
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<div class="col col-md-3">
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<nav id="affix-nav" class="sidebar hidden-sm hidden-xs">
 +
    <ul class="nav sidenav box" data-spy="affix" data-offset-top="200" data-offset-bottom="600">
 +
        <li class="active"><a href="#gel_protocol">Agarose Gel Preparation</a></li>
 +
        <li><a href="#amino_acid_solution">Amino acid solutions Protocol</a></li>
 +
        <li><a href="#colony_pcr">Colony PCR</a></li>
 +
        <li><a href="#gibson_protocol">Gibson Assembly Protocol</a></li>
 +
        <li><a href="#miniprep_protocol">Miniprep – with QlAprep Spin Miniprep kit</a></li>
 +
        <li><a href="#pcr_protocol">PCR Protocol</a>
 +
        <ul class="nav">
 +
          <li><a href="#taq">Taq PCR</a></li>
 +
        </ul>
 +
        </li>
 +
        <li><a href="#purification_protocol">PCR Product Purification Protocol</a></li>
 +
        <li><a href="#PEG_LiAc_solution">PEG/LiAc solution protocol</a></li>
 +
        <li><a href="#sdmedium_protocol">SD Medium</a></li>
 +
        <li><a href="#competent_protocol">Thermocompetent <i>E. coli</i> cells preparation</a>
 +
        <ul class="nav">
 +
          <li><a href="#inouebuffer">Inoue Transformation Buffer</a></li>
 +
        </ul>
 +
        </li>
 +
        <li><a href="#transformation_protocol">Transformation Protocols</a>
 +
      <ul class="nav">
 +
          <li><a href="#NEB">NEB transformation protocol</a></li>
 +
          <li><a href="#igem">iGEM Transformation Protocol</a></li>
 +
        </ul>
 +
        </li>
 +
        <li><a href="#yeast_transformation_protocol">Yeast transformation and homolgous recombination procedure from Clontech Yeast Handbook</a></li>
 +
        <li><a href="#YPD_medium_protocol">YPD Medium protocol</a></li>
 +
    </ul>
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</nav>
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Latest revision as of 15:17, 16 October 2014

Agarose Gel Preparation

Materials

  • TAE 1X
  • Agarose
  • GelRed

Procedure

  1. For a 1.2 % agarose gel (small fragments), put 0.6 grams of agarose into 50 mL of TAE 1X. For a 3 % agarose gel (big fragments), put 1.5 g of agarose into 50 mL of TAE 1X.
  2. Warm the solution in the microwave (max. Power) for 30 seconds, or until agarose has melted.
  3. Mix the solution.
  4. Add 1.3uL of Gel Red (1.5 for 3 % gel).
  5. Pour the solution into an agarose gel mold including the comb.
  6. Wait 20 min for the gel to solidify.
  7. Place the gel in TAE 1X and remove comb.
  8. Mix ~200ng of DNA with nuclease free water and loading buffer to a final 1X concentration (total volume of 12uL).
  9. Run the gel for 45 min at 100 Volts (more time if needed). For a 3 % gel, run for 2 hours at 80 Volts.
  10. Take a picture of the gel at the UV detector.

Amino acid solutions Protocol

Materials

  • Histidine-Hcl
  • Uracil
  • Leucine
  • Tryptophan

Procedure

Stock concentration Final concentration Total quantity for 50 mL
100 mM Histidine-Hcl(209g/mol) 20.9 g/l 0.418 g
20 mM Uracil (112 g/mol) 2.24 g/l 0.0448 g
100 mM Leucine (131 g/mol) 13.1 g/l 0.262 g
40 mM Tryptophan (204 g/mol) 8.16 g/l 0.1632g
  1. Filter and sterilize the solutions
  2. Add 8 mL per liter of selective medium or spread 500 µl on top of a selective plate

Colony PCR

Materials

  • Petri dish with transformed colonies
  • Taq Polymerase PCR material (see protocol for Taq polymerase)
  • Nuclease free water

Procedure

  1. Inoculate a single colony from the plate with a tip and agitate the tip into 10uL of nuclease free water into a PCR tube
  2. Heat shock the tubes at 95°C for 10 min.
  3. Transfer 1uL of the heatshocked solution into a new PCR tube and perform a Taq PCR according to the protocol for Taq polymerase (considering 1uL of DNA and for 25uL final product).

Gibson Assembly Protocol

Materials

  • Plasmids of interest (miniprep)
  • NEB Gibson assembly Kit (Gibson Assembly Master Mix (2X) and chemically competent cells)
  • Deionized H2O

Procedure

2-3 Fragments assembly* (X uL) 4-6 Fragments assembly* (X uL)
Total Amount of Fragments 0.02-0.5 pmols 0.2-1 pmols*
Gibson Assembly Master Mix (2X) 10 uL 10 uL
Deionized H2O 10-X uL 10-X uL
Total Volume 20 uL 20 uL
  1. Set up the following reaction on ice:
  2. *Optimized cloning efficiency is 50-100ng of vectors with 2-3 fold of excess inserts. Use 5 times more of inserts if size is less than 200 bps.

  3. Incubate samples in a thermocycler at 50C for 15 minutes when 2 or 3 fragments are being assembled or 60 minutes when 4-6 fragments are being assembled. Following incubation, store samples on ice or at -20°C for subsequent transformation.
  4. Transform 50 uL of competent cells (provided with the kit) with 2 μl of the assembly reaction, following the transformation protocol.

You can find the original NEB Gison Assembly Protocol here

Miniprep – with QlAprep Spin Miniprep kit

Materials

  • Ovenight liquid cell cultures (5-8 mL)
  • QlAprep Spin Miniprep kit

Procedure

  1. Pellet bacterial cells from overnight 5-8 mL culture (4000 rpm, 10 min) and discard the medium.
  2. Resuspend pelleted bacterial cells in 250 μL Buffer P1 (stored at 4°C). Ensure that RNase A has been added to Buffer P1. No cells clumps should be visible after resuspension of the pellet. Transfer the resuspended cells into a 1.5 microcentrifuge tube.
  3. Add 250 μL Buffer P2 and gently invert the tube 4-6 times to mix (do not vortex). If necessary, continue inverting the tube until the solution becomes viscous and slightly clear. Let stand for 2-4 minutes; never more than 5.
  4. Add 350 μL Buffer N3 and invert the tube immediately but gently 4-6 times. The solution should become cloudy.
  5. Centrifuge for 10 min at 13,000 rpm in a table-top microcentrifuge. A compact pellet will form.
  6. Apply the supernatant from step 5 to the QlAprep Spin Column by pipetting.
  7. Centrifuge for 1 min at 13,000 rpm. Discard the flow-through.
  8. Wash QlAprep Spin Column by adding 750 μL Buffer PE and centrifuge for 1 min at 13,000 rpm.
  9. Discard the flow-through, and centrifuge for an additional 1 min to remove residual wash buffer.
  10. Place the QlAprep column in a clean 1.5 ml microcentrifuge tube. To elute DNA, add 50 μL Buffer EP (10 mM Tris-Cl, pH 8.5) to the center of each QlAprep Spin Column, let stand for 1 min, and centrifuge for 1 min at 13,000 rpm.

You can find the original Qiagen Miniprep Protocol here.

PCR Protocol

Phusion PCR

Materials

  • Phusion® High-Fidelity DNA Polymerase PCR Kit
  • Nuclease-free Water
  • Primers
  • Template DNA

Procedure

  1. Setup the following reaction in a 0.5 mL PCR tube:
    Component 20 µL Reaction 50 µL Reaction Final Concentration
    5X Phusion HF or GC Buffer 4 µL 10 µL 1X
    10 mM dNTPs 0.4 µL 1 µL 200 µM
    10 µM Forward Primer 1 µL 2.5 µL 0.5 µM
    10 µM Reverse Primer 1 µL 2.5 µL 0.5 µM
    Template DNA variable variable <250 ng
    DMSO (optional) (0.6 µL) (1.5 µL) 3 %
    Phusion DNA Polymerase 0.2 µL 0.5 µL 1.0 units/50 µl PCR
    Nuclease-free Water To 20 µL To 50 µL
  2. Gently mix the reaction. Collect all liquid to the bottom of the tube by a quick spin if necessary. Overlay the sample with mineral oil if using a PCR machine without a heated lid.
  3. Transfer PCR tubes from ice to a PCR machine with the block preheated to 98°C and begin thermocycling:
    STEP TEMP TIME
    Initial Denaturation 98 °C 30 seconds
    25-35 Cycles 98°C 5-10 seconds
    45-72 °C Annealing Temp 20 seconds
    72 °C Elongation Temp 15-30 seconds per kb
    Final Extension 72 °C 5-10 minutes
    Hold 4-10 °C

You can find the original PCR Protocol for Phusion® High-Fidelity DNA Polymerase (M0530) here.

Taq PCR

Materials

  • ThermoPol Buffer 10X
  • dNTPs
  • Taq Polymerase
  • Template DNA
  • Primers
  • Nuclease-free water

Procedure

  1. Prepare the following reaction in a 0.5 mL PCR tube on ice:
    Component 25 µL Reaction 50 µL Reaction Final Concentration
    10X ThermoPol or Standard Taq Reaction Buffer 2.5 µL 5 μL 1X
    10 mM dNTPs 0.5 µL 1 µL 200 µM
    10 µM Forward Primer 0.5 µL 1 µL 0.2 µM
    10 µM Reverse Primer 0.5 µL 1 µL 0.2 µM
    Template DNA variable variable <1000 ng
    Taq DNA Polymerase 0.125 µL 0.25 µL 1.25 units/50 µL PCR
    Nuclease-free Water To 25 µL To 50 µL
    * Due to the difficulties in pipetting small volumes of enzyme, Taq DNA Polymerase can be diluted in 1X reaction buffer. For example, 1 µl of Taq DNA Polymerase is mixed with 4 µl of 1X reaction buffer and 1 µl of that mixture is added to the reaction. Enzyme diluted 1X reaction buffer should not be stored for future use.
  2. Gently mix the reaction and spin down in microcentrifuge. If the thermocycler does not have a heated cover, add one drop of mineral oil to the reaction tube to prevent evaporation.
  3. Cycling Conditions for a Routine PCR:
    STEP TEMP TIME CYCLES
    Initial Denaturation 95 °C 30 seconds 1
    Denaturation 95 °C 15-30 seconds 30
    Annealing 45-68 °C 15-60 seconds
    Extension 68 °C 1 minute per kb
    Final Extension 72 °C 5 minutes
    Hold 4-10°C

You can find the original NEB Taq PCR here.

PCR Product Purification Protocol

Materials

  • PCR products
  • Qiagen QlAquick PCR kit

Procedure

  1. Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
  2. To bind DNA, apply the sample to the QlAquick column and centrifuge for 1 min at 13,000 rpm.
  3. Discard the flow-through. Place the QlAquick column back into the same tube.
  4. To wash, add 750 uL Buffer PE to the QlAquick column and centrifuge for 1 min at 13,000 rpm.
  5. Discard flow-through and place the QlAquick column back in the same tube. Centrifuge the column for an additional 1 min.
  6. Place QlAquick column in a clean 1.5 mL microcentrifuge tube.
  7. To elute DNA, add 30 uL Buffer EP (10 mM Tris-Cl, pH 8.5) to the center of the QlAquick membrane, let the column stand for 1 min and then centrifuge for 1 min at 13,000 rpm.

You can find the original Qiagen PCR Product Purification Protocol here.

PEG/LiAc solution protocol

Prepare fresh just prior to use.

Materials

  • 50% PEG 3350 (Polyethylene glycol, avg. mol. wt. = 3,350; Sigma Cat No. P-3640) prepare with sterile deionized H2O; if necessary, warm solution to 50°C to help the PEG go into solution
  • 10X TE buffer: 0.1 M Tris-HCl, 10 mM EDTA, pH 7.5. Autoclaved.
  • 10X LiAc: 1 M lithium acetate (Sigma Cat No. L-6883) Adjust to pH 7.5 with dilute acetic acid and autoclaved.

Prepare the PEG/LiAc solution as follows:

Final Concentration Stock solution Concentration Volume to add to prepare 10mL of solution
PEG 4000 40% 50% PEG 8mL
TE buffer 1X 10X TE 1mL
LiAc 1X 10X LiAc 1mL

You can download the Yeast Protocol Handbook (Clontech) containing the original procedure here.

SD Medium

Materials

  • Amino Acid Power
  • yeast nitrogen base
  • ammonium sulphate
  • adenine sulphate
  • water
  • NaOH
  • agar
  • glucose

Procedure

  1. Place a stirrer bar in a 2 liters Erlenmeyers
  2. Add 2.6g amino acid powder, 3.4g yeast nitrogen base, 10g ammonium sulphate, adenine sulphate(+/- 1g) and 950mL water.
  3. adjust pH to 5.9 by adding a few drops of 10 M NaOH
  4. In a new erlenmeyer, add 35g agar and 900 ml water
  5. Autoclave the 2 flasks
  6. Transfer the bottle of medium to the agar bottle.
  7. Cool to 55°C
  8. Before pouring add 100ml 40% glucose (in 2l final)
  9. before pouring add 16ml* of the required amino acids (in 2L final)
  10. Pour plates

Thermocompetent E. coli cells preparation

Materials

  • Bacterial colony from plate (day 1)
  • LB medium (day 1)
  • DMSO (day 2)
  • Liquid nitrogen (day 2)
  • Sterile Inoue buffer (day 2) – for buffer preparation, see below

Note: the 250 mL of culture can be separated after growth into smaller tubes (for example, to facilitate centrifugation at 4 ºC). Make sure to respect the proportion of all added buffers and solutions.

Procedure

  1. Pick a single colony from a plate that has been incubated overnight at 37 ºC.
  2. Transfer the colony into 30 mL of LB in a 250 mL flask.
  3. Use this starter culture to inoculate three 1-liter flasks with 1 mL of starter culture, each containing 250 mL of LB (there’s no need to make triplicates, one flask is enough to get 100-120 x 200 µL tubes).
  4. Incubate flasks overnight (depends on growth, 8-17 hours) at 22 ºC (room temperature) with shaking at 180 rpm.
  5. Monitor the OD600 (every 45 min) until it reaches 0.55, and transfer the culture on ice for 10 min. It is important to stop growth at 0.55, can be longer than 10 min on ice.
  6. Centrifuge the cells at 2500 g for 10 min at 4 ºC (temperature is important, it’s better if you can do the rest of the protocol in a cold room).
  7. Pour off the medium and remove any remaining drop.
  8. Resuspend cells gently in 240 mL of ice-cold Inoue buffer (0 ºC).
  9. Repeat steps 6 to 8, using only 60 mL of ice-cold Inoue buffer for the resuspention.
  10. Add 4.5 mL of DMSO and store on ice for 10 min.
  11. Dispense 200 µL aliquots of the suspension into sterile microtubes.
  12. Put the tubes in a container and snap-freeze them by pouring liquid nitrogen on them. It is important to pour the liquid nitrogen on them, as they have to freeze very fast; the aliquots are best when small for the same reason.
  13. Store the tubes at -80 ºC until needed. Note: thaw on ice when used.

Inoue Transformation Buffer

Materials

  • MnCl2 · 4H2O
  • CaCl2 · 2H2O
  • KCl
  • Milli-Q water (or bidistilled)
  • Pre-rinsed .45 µm Nalgene filter - 1 or 2, depending on PIPES solution preparation

Procedure

  1. Make .5M PIPES (piperazine‐1,2‐bis[2‐ethanesulfonic acid]) at pH 6.7
    1. Dissolve 15.1 g of PIPES in 30 mL Milli-Q water.
    2. Adjust pH of solution to 6.7 (with KOH or HCl; you can easily add 30 mL of KOH to begin with).
    3. Add Milli-Q water to final volume of 100 mL.
    4. Optional: sterilize solution by vacuum filtration in pre-rinsed Nalgene filter of .45 µm pore size. Not necessary if used for Inoue Buffer.
  2. Dissolve solutes as follows in 800 mL of Milli-Q water.
  3. Reagent Qty/L Final Conc.
    MnCl2 · 4H2O 10.88 g 55 mM
    CaCl2 · 2H2O 2.20 g 15 mM
    KCl 18.65 250 mM
  4. Add 20 mL PIPES (.5 M, pH 6.7).
  5. Adjust total volume to 1 L with Milli-Q water.
  6. Sterilize Inoue Transformation Buffer through pre-rinsed .45 µm Nalgene filter.

Transformation Protocols

NEB transformation protocol

Materials

  • DNA
  • Competent cells
  • SOC medium (SOB + Glucose) - room temperature
  • Petri dish with antibiotic resistance - 37 ºC

Procedure

  1. Thaw competent cells on ice.
  2. Chill 5 ng of ligation mixture in a 1.5 ml microcentrifuge tube and then add 50 µL of competent cells. Do not vortex or mix.
  3. Place the mixture on ice for 30 min (do not mix).
  4. Heat-shock cells at 42 ºC for 30 s in a pre-heated water bath (works better than on a heating block) (do not mix).
  5. Place on ice and add 950 µL of room temperature SOC medium to the tube (make sure that it is not contaminated).
  6. Place tube at 37 ºC for 60 min. Shake or rotate (250 rpm). Warm selection plates to 37 ºC (not necessary, but increases efficiency).
  7. Spread 50-100 µL of samples on plates (dependent on efficiency of the competent cells); incubate overnight at 37 ºC.

You can find the original NEB Transformation Protocol here.

iGEM Transformation Protocol

Materials

  • DNA
  • Competent cells
  • SOC medium (SOB + Glucose)
  • Petri dish with antibiotic resistance

Procedure

  1. Thaw competent cells on ice.
  2. Add 50 µL of thawed competent cells into a pre-chilled 2 mL tube.
  3. Add 5 ng of resuspended DNA to the sample and pipet gently up and down a few times.
  4. Keep the sample on ice for 30 min.
  5. Heat-shock cells at 42 ºC for 60 s in a pre-heated water bath (works better than on a heating block).
  6. Place samples on ice for 5 min (can be more).
  7. Add 200 µL of SOC medium to the sample (make sure that it is not contaminated).
  8. Incubate cells at 37 ºC for 2 hours with shaking or rotating. 2 hours recovery time after incubation helps in transformation efficiency.
  9. Plate 20 µL and 200 µL of the sample on two plates and spread.
  10. Incubate the plates at 37 ºC for 12-14 hours (agar side of the plate has to be up). Note: Incubating for too long will increase the occurrence of satellite colonies (especially if resistant to Ampicillin).

You can find the original iGEM Transformation Protocol here.

Yeast transformation and homolgous recombination procedure from Clontech Yeast Handbook

Materials

  • YPD or the appropriate SD liquid medium
  • Sterile 1X TE/1X LiAc
  • Sterile 1.5-ml microcentrifuge tubes for the transformation
  • Appropriate SD agar plates (100-mm diameter)
  • Appropriate DNA template in solution (check amounts required)
  • Appropriate yeast reporter strain for making competent cells
  • Salmon sperm (carrier DNA)
  • Sterile PEG/LiAc solution
  • 100% DMSO (Dimethyl sulfoxide; Sigma Cat No. D-8779)
  • Sterile 1X TE buffer
  • Sterile glass rod, bent Pasteur pipette, or 5-mm glass beads for spreading cells on plates

Procedure

  1. Inoculate 1 ml of YPD or SD with several colonies, 2–3 mm in diameter
  2. Vortex vigorously for 5 min to disperse any clumps
  3. Transfer this into a flask containing 50 ml of YPD or the appropriate SD medium
  4. Incubate at 30°C for 16–18 hr with shaking at 250 rpm to stationary phase (OD600>1.5)
  5. Transfer 30 ml of overnight culture to a flask containing 300 ml of YPD. Check the OD600 of the diluted culture and, if necessary, add more of the overnight culture to bring the OD600 up to 0.2–0.3
  6. Incubate at 30°C for 3 hr with shaking (230 rpm). At this point, the OD600 should be 0.4–0.6.
  7. Place cells in 50-ml tubes and centrifuge at 1,000 x g for 5 min at room temperature (20–21°C)
  8. Discard the supernatants and thoroughly resuspend the cell pellets in sterile TE. Pool the cells into one tube (final volume 25–50 ml)
  9. Centrifuge at 1,000 x g for 5 min at room temperature.
  10. Decant the supernatant
  11. Resuspend the cell pellet in 1.5 ml of freshly prepared, sterile 1X TE/1X LiAc
  12. Add at least 1 μg of linear DNA and 0.1 mg of salmon sperm DNA to a fresh 1.5-ml tube and mix
  13. Add 0.1 ml of yeast competent cells to each tube and mix well by vortexing
  14. Add 0.6 ml of sterile PEG/LiAc solution to each tube and vortex at high speed for 10 sec to mix
  15. Incubate at 30°C for 30 min with shaking at 200 rpm
  16. Add 70 μl of DMSO. Mix well by gentle inversion. Do not vortex !
  17. Heat shock for 15 min in a 42°C water bath
  18. Chill cells on ice for 1–2 min
  19. Centrifuge cells for 5 sec at 14,000 rpm at room temperature. Remove the supernatant
  20. Resuspend cells in 0.5 ml of sterile 1X TE buffer
  21. Plate 100 μl on each SD agar plate that will select for the desired transformants

You can download the Yeast Protocol Handbook (Clontech) containing the original procedure here.

YPD Medium protocol

Procedure

Prepare your YPD medium as follows

  • 20 g/L Difco peptone
  • 10 g/L Yeast extract
  • 20 g/L Agar (for plates only)
  • Add H2O to 950 ml. Adjust the pH to 6.5 if necessary, then autoclave. Allow medium to cool to ~ 55°C and then add dextrose (glucose) to 2% (50 ml of a sterile 40% stock solution). Adjust the final volume to 1 L if necessary. s in 50-ml tubes and centrifuge at 1,000 x g for 5 min at room temperature (20–21°C)
  • [Optional] For kanamycin-containing medium, prepare YPD or YPDA as above. After autoclaved medium has cooled to 55°C, add 0.2–0.3 ml of 50 mg/ml kanamycin (final concentration 10–15 mg/L).
  • You can download the Yeast Protocol Handbook (Clontech) containing the original procedure here.

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