Difference between revisions of "Team:NEFU China/Protocol"

 
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<link href="https://2018.igem.org/wiki/index.php?title=Template:NEFU_China/CSS-notebook-2018-05&amp;action=raw&amp;ctype=text/css"  rel="stylesheet" type="text/css">
 
<link href="https://2018.igem.org/wiki/index.php?title=Template:NEFU_China/CSS-notebook-2018-05&amp;action=raw&amp;ctype=text/css"  rel="stylesheet" type="text/css">
 
<style>
 
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#top_title, #sideMenu{
 
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<div id="menu" style="background-color:rgba(0,0,0,0.6)!important">
 
<div id="menu" style="background-color:rgba(0,0,0,0.6)!important">
 
<li id="nav" style="left: 8%!important; width: 100%!important;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;
 
<li id="nav" style="left: 8%!important; width: 100%!important;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;
<!--<a class="menu1" href="#" style="text-align: right;">☰</a>-->
+
 
<ul class="firstmenu" style="float: left">
 
<ul class="firstmenu" style="float: left">
 
 
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<ul id="sub_02">
 
<ul id="sub_02">
 
<li><a href="https://2018.igem.org/Team:NEFU_China/Background" target="_self">BACKGROUND</a></li>
 
<li><a href="https://2018.igem.org/Team:NEFU_China/Background" target="_self">BACKGROUND</a></li>
<li><a href="https://2018.igem.org/Team:NEFU_China/Description" target="_self">DESCRIPTION</a></li>
+
<li><a href="https://2018.igem.org/Team:NEFU_China/Description" target="_self">DESCRIPTION &amp; DESIGN</a></li>
<li><a href="https://2018.igem.org/Team:NEFU_China/Design" target="_self">DESIGN</a></li>
+
<li><a href="https://2018.igem.org/Team:NEFU_China/Coding book" target="_self">CODE BOOK</a></li>
<li><a href="https://2018.igem.org/Team:NEFU_China/Coding book" target="_self">CODING BOOK</a></li>
+
 
  </ul>
 
  </ul>
 
  </li>
 
  </li>
 
 
 
<li class="mainlevel" id="mainlevel_03">
 
<li class="mainlevel" id="mainlevel_03">
  <a href="https://2018.igem.org/Team:NEFU_China/Experiment"><img id="parts" src="https://static.igem.org/mediawiki/2018/6/62/T--NEFU_China--_RESULTS.png">EXPERIMENT</a>
+
  <a href="https://2018.igem.org/Team:NEFU_China/Demonstrate"><img id="parts" src="https://static.igem.org/mediawiki/2018/6/62/T--NEFU_China--_RESULTS.png">EXPERIMENTS</a>
 
  <ul id="sub_03">
 
  <ul id="sub_03">
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Lock_Key" target="_self">LOCK &amp; KEY</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Lock_Key" target="_self">LOCK &amp; KEY</a></li>
  <li><a href="https://2018.igem.org/Team:NEFU_China/Suicide" target="_self">SUICIDE</a></li>
+
  <li><a href="https://2018.igem.org/Team:NEFU_China/Suicide" target="_self">INFORMATION DESTRUCTION</a></li>
  <li><a href="https://2018.igem.org/Team:NEFU_China/Splicing" target="_self">SPLICING</a></li>
+
  <li><a href="https://2018.igem.org/Team:NEFU_China/Splicing" target="_self">Pre-RNA SPLICING</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Demonstrate" target="_self">DEMONSTRATE</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Demonstrate" target="_self">DEMONSTRATE</a></li>
 
  <hr>
 
  <hr>
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  <ul id="sub_05">
 
  <ul id="sub_05">
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model" target="_self">OVERVIEW</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model" target="_self">OVERVIEW</a></li>
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model1" target="_self">MODEL1</a></li>
+
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model1" target="_self">CORRESPONDING COEFFICIENT</a></li>
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model2" target="_self">MODEL2</a></li>
+
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model2" target="_self">KILLING MODEL</a></li>
 
  </ul>
 
  </ul>
 
  </li>
 
  </li>
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Attributions" target="_self">ATTRIBUTIONS</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Attributions" target="_self">ATTRIBUTIONS</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Members" target="_self">MEMBERS</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Members" target="_self">MEMBERS</a></li>
 
  <!-- <li><a href="https://2018.igem.org/Team:NEFU_China/Sponsoring" target="_self">SPONSORING</a></li>-->
 
 
  </ul>
 
  </ul>
 
  </li>
 
  </li>
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  <a href="https://2018.igem.org/Team:NEFU_China/Human_Practices"><img id="humanpractice" src="https://static.igem.org/mediawiki/2018/9/91/T--NEFU_China--_HUMANPRACTICE.png">HUMAN PRACTICE</a>
 
  <a href="https://2018.igem.org/Team:NEFU_China/Human_Practices"><img id="humanpractice" src="https://static.igem.org/mediawiki/2018/9/91/T--NEFU_China--_HUMANPRACTICE.png">HUMAN PRACTICE</a>
 
  <ul id="sub_08">
 
  <ul id="sub_08">
 +
  <li><a href="https://2018.igem.org/Team:NEFU_China/Human_Practices" target="_self">OVERVIEW</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Gold_integrated" target="_self">GOLD INTEGRATED</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Gold_integrated" target="_self">GOLD INTEGRATED</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Silver" target="_self">SILVER</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Silver" target="_self">SILVER</a></li>
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</div>
 
</div>
 
<div>
 
<div>
<img alt="Notebook" src="https://static.igem.org/mediawiki/2018/0/02/T--NEFU_China--Notebook.png" style="width:100%">
+
<img alt="Protocol" src="https://static.igem.org/mediawiki/2018/0/09/T--NEFU_China--protocol.png" style="width:100%">
 
</div>
 
</div>
 
<div id="content">
 
<div id="content">
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</h1>
 
</h1>
 
<div class="widget">
 
<div class="widget">
<div class="widget-content">
+
<div class="widget-content" style="
 +
    font-size: 26px!important;
 +
">
 
 
<h1>KEY: Saccharomyces cerevisiae YPH499</h1><br>
+
<h1>KEY: <I>Saccharomyces cerevisiae</I> YPH499</h1><br>
1. Transformation culture conditions: incubator of 30℃, plates with SD/-Leu-agar solid medium.<br>
+
<ol>
2. Inoculation culture conditions: a 30℃ constant temperature shaker with 220 rpm in SD/-Leu liquid medium.<br><br>
+
<li>
 
+
Transformation culture conditions: incubator of 30℃, plates with SD/-Leu-agar solid medium.
 
+
</li>
<h1>Lock and Information:  Saccharomyces cerevisiae YPH499</h1><br>
+
<li>
1. Transformation culture conditions: incubator of 30℃, plates with SD/-Ura-agar solid medium.<br>
+
Inoculation culture conditions: a 30℃ constant temperature shaker with 220 rpm in SD/-Leu liquid medium.
2. Inoculation culture conditions: a 30℃ constant temperature shaker with 220 rpm in SD/-Ura liquid medium<br><br>
+
</li>
 
+
</ol>
<h1>Fig2c-Bax:Saccharomyces cerevisiae YPH499</h1><br>
+
1. Transformation culture conditions: incubator of 30℃, plates with SD/-Ura-agar solid medium.<br>
+
<br>
2. Inoculation culture conditions: a 30℃ constant temperature shaker with 220 rpm in SD/-Ura liquid medium.<br>
+
3. Inducible expression conditions: a 30℃ constant temperation shaker with 220 rpm in SD/-Ura liquid medium.<br>
+
<h1>Lock and Information:  <I>Saccharomyces cerevisiae</I> YPH499</h1><br>
contaning different concentrations of alpha factor.<br><br>
+
<ol>
 +
<li>
 +
Transformation culture conditions: incubator of 30℃, plates with SD/-Ura-agar solid medium.<br>
 +
</li>
 +
<li>
 +
Inoculation culture conditions: a 30℃ constant temperature shaker with 220 rpm in SD/-Ura liquid medium.<br>
 +
</li>
 +
 +
</ol>
 +
 +
                        <br>
 +
<h1>pFig2c-Bax: <I>Saccharomyces cerevisiae</I> YPH499</h1><br>
 +
<ol>
 +
<li>
 +
Transformation culture conditions: incubator of 30℃, plates with SD/-Ura-agar solid medium.<br>
 +
</li>
 +
<li>
 +
Inoculation culture conditions: a 30℃ constant temperature shaker with 220 rpm in SD/-Ura liquid medium.<br>
 +
</li>
 +
<li>
 +
Inducible expression conditions: a 30℃ constant temperation shaker with 220 rpm in SD/-Ura liquid medium contaning different concentrations of alpha factor.<br>
 +
</li>
 +
</ol>
 
</div>  
 
</div>  
 
</div>
 
</div>
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<h1>Vector construction of Lock and Information:</h1><br>
 
<h1>Vector construction of Lock and Information:</h1><br>
                        1  CYC promoter, CYC1 terminator were amplified from genomic DNA of Saccharomyces cerevisiae YPH499 with corresponding primers respectively. And the DNA of the lock and information fragment was synthesized by company with restriction enzyme cutting sites HindIII, EcoRI and EcoRI, NheI.<br>
+
<ol>
                        2 Modified CYC1 promoter and CYC1 terminator by adding the HA1 or HA2 by using PCR.<br>
+
<li>
3 Four fragments of HA1-CYC promoter, Stem loop(the lock),  Information and  Cyc1 terminator-HA2 the were double-digested with SacI-HindIIIHindIII-EcoRI, EcoRI-NheI, and NheI-BamHI, respectively.<br>
+
CYC promoter, CYC1 terminator were amplified from genomic DNA of <I>Saccharomyces cerevisiae</I> YPH499 with corresponding primers respectively. And the DNA of the lock and information fragment was synthesized by company with restriction enzyme cutting sites <i>Hind</i>III, <i>EcoR</i>I and <i>EcoR</i>I, <i>Nhe</i>I.
4 Ligated them into an expression vector pesc-Ura by T4 ligase.<br>
+
</li>
5 To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br><br>
+
<li>
 +
Modified CYC1 promoter and CYC1 terminator by adding the HA1 or HA2 by using PCR.<br>
 +
</li>
 +
<li>
 +
Four fragments of HA1-CYC promoter, Stem loop (the lock),  Information and  Cyc1 terminator-HA2 the were double-digested with <i>Sac</i>I-<i>Hind</i>III<i>Hind</i>III-<i>EcoR</i>I, <i>EcoR</i>I-<i>Nhe</i>I, and <i>Nhe</i>I-<i>BamH</i>I, respectively.<br>
 +
</li>
 +
<li>
 +
Ligated them into an expression vector pesc-Ura by T4 ligase.<br>
 +
</li>
 +
<li>
 +
To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br>
 +
</li>
 +
    </ol>
 +
                       
 +
<br>
 +
 
<h1>Vector construction of Lock and EGFP:</h1><br>
 
<h1>Vector construction of Lock and EGFP:</h1><br>
                        1  CYC promoter, CYC1 terminator were amplified from genomic DNA of Saccharomyces cerevisiae YPH499 with corresponding primers respectively. And the DNA of the lock  was synthesized by company with restriction enzyme cutting sites HindIII, EcoRI . The EGFP gene was amplified from palsmid pEGFP-N2, and modified it by adding EcoRI and NheI respectively.<br>
+
<ol>
2 Modified CYC1 promoter and CYC1 terminator by adding the HA1 or HA2 by using PCR.<br>
+
<li>
3 Four fragments of HA1-CYC promoter, Stem loop(the lock),  EGFP and  Cyc1 terminator-HA2 the were double-digested with SacI-HindIIIHindIII-EcoRI, EcoRI-NheI, and NheI-BamHI, respectively.<br>
+
CYC promoter, CYC1 terminator were amplified from genomic DNA of <I>Saccharomyces cerevisiae</I> YPH499 with corresponding primers respectively. And the DNA of the lock  was synthesized by company with restriction enzyme cutting sites <i>Hind</i>III, <i>EcoR</i>I. The EGFP gene was amplified from palsmid pEGFP-N2, and modified it by adding <i>EcoR</i>I and <i>Nhe</i>I respectively.<br>
4 Ligated them into an expression vector pesc-Ura by T4 ligase.<br>
+
</li>
5 To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br><br>
+
<li>
 +
Modified CYC1 promoter and CYC1 terminator by adding the HA1 or HA2 by using PCR.<br>
 +
</li>
 +
<li>
 +
Four fragments of HA1-CYC promoter, Stem loop (the lock),  EGFP and  Cyc1 terminator-HA2 the were double-digested with <i>Sac</i>I-<i>Hind</i>III<i>Hind</i>III-<i>EcoR</i>I, <i>EcoR</i>I-<i>Nhe</i>I, and <i>Nhe</i>I-<i>BamH</i>I, respectively.<br>
 +
</li>
 +
<li>
 +
Ligated them into an expression vector pesc-Ura by T4 ligase.<br>
 +
</li>
 +
<li>
 +
To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br>
 +
</li>
 +
    </ol>
 +
                       
 +
<br>
 +
 
<h1>Vector construction of Lock and Gluc:</h1><br>
 
<h1>Vector construction of Lock and Gluc:</h1><br>
                        1  CYC promoter, CYC1 terminator were amplified from genomic DNA of Saccharomyces cerevisiae YPH499 with corresponding primers respectively. And the DNA of the lock  was synthesized by company with restriction enzyme cutting sites HindIII, EcoRI . The Gluc gene was amplified from palsmid pGluc-Basic2, and modified it by adding EcoRI and NheI respectively.<br>
+
<ol>
2 Modified CYC1 promoter and CYC1 terminator by adding the HA1 or HA2 by using PCR.<br>
+
<li>
3 Four fragments of HA1-CYC promoter, Stem loop(the lock),  Gluc and  Cyc1 terminator-HA2 the were double-digested with SacI-HindIIIHindIII-EcoRI, EcoRI-NheI, and NheI-BamHI, respectively.<br>
+
CYC promoter, CYC1 terminator were amplified from genomic DNA of <I>Saccharomyces cerevisiae</I> YPH499 with corresponding primers respectively. And the DNA of the lock  was synthesized by company with restriction enzyme cutting sites <i>HindIII</i>, EcoRI</i>. The Gluc gene was amplified from palsmid pGluc-Basic2, and modified it by adding <i>EcoR</i>I and <i>Nhe</i>I respectively.<br>
4 Ligated them into an expression vector pesc-Ura by T4 ligase.<br>
+
</li>
5 To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br><br>
+
<li>
 +
Modified CYC1 promoter and CYC1 terminator by adding the HA1 or HA2 by using PCR.<br>
 +
</li>
 +
<li>
 +
Four fragments of HA1-CYC promoter, Stem loop (the lock),  Gluc and  Cyc1 terminator-HA2 the were double-digested with <i>Sac</i>I-<i>Hind</i>III<i>Hind</i>III-<i>EcoR</i>I, <i>EcoR</i>I-<i>Nhe</i>I, and <i>Nhe</i>I-<i>BamH</i>I, respectively.<br>
 +
</li>
 +
<li>
 +
Ligated them into an expression vector pesc-Ura by T4 ligase.<br>
 +
</li>
 +
<li>
 +
To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br>
 +
</li>
 +
    </ol>
 +
                       
 +
<br>
 +
 
<h1>Vector construction of Key:</h1><br>
 
<h1>Vector construction of Key:</h1><br>
                        1  RPR1 promoter was amplified from plasmid named  
+
<ol>
 +
<li>
 +
RPR1 promoter was amplified from plasmid named  
 
pRPR1_gRNA_handle_RPR1t. <br>
 
pRPR1_gRNA_handle_RPR1t. <br>
Modified RPR1 promoter by adding the Key sequence and SpeI, XhoI by using PCR.<br>
+
</li>
The fragment of pRPR1-Key was  double-digested with SpeI and XhoI respectively.<br>
+
<li>
4 Ligated it into an expression vector pRPR1_gRNA_handle_RPR1t by T4 ligase.<br>
+
Modified RPR1 promoter by adding the Key sequence and <i>Spe</i>I, <i>Xho</i>I by using PCR.<br>
5 To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br><br>
+
</li>
 +
<li>
 +
The fragment of pRPR1-Key was  double-digested with <i>Spe</i>I and <i>Xho</i>I respectively.<br>
 +
</li>
 +
<li>
 +
Ligated it into an expression vector pRPR1_gRNA_handle_RPR1t by T4 ligase.<br>
 +
</li>
 +
<li>
 +
To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br>
 +
</li>
 +
    </ol>
 +
                       
 +
<br>
  
 
<h1>Vector construction of suicide switch:</h1><br>
 
<h1>Vector construction of suicide switch:</h1><br>
1 Bax(alpha) Gene was amplified from genomic DNA of 293T cell  with corresponding primers respectively.<br> Fig2C promoter fragment was from iGEM parts registry.<br>
+
<ol>
2 Modified Bax fragment by adding SpeI and HindIII by using PCR.<br>
+
<li>
3 Two fragments of Fig2C promoter,  Bax gene were double-digested with EcoRI-SpeI, and SpeI-HindIII, respectively.<br>
+
Bax (alpha) Gene was amplified from genomic DNA of 293T cell  with corresponding primers respectively.<br> Fig2C promoter fragment was from iGEM parts registry.<br>
4 Ligated the fragments into an expression vector pesc-Ura by T4 ligase.<br>
+
</li>
5 To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br><br>
+
<li>
 +
Modified Bax fragment by adding <i>Spe</i>I and <i>Hind</i>III by using PCR.<br>
 +
</li>
 +
<li>
 +
Two fragments of Fig2C promoter,  Bax gene were double-digested with <i>EcoR</i>I-<i>Spe</i>I, and <i>Spe</i>I-<i>Hind</i>III, respectively.<br>
 +
</li>
 +
<li>
 +
Ligated the fragments into an expression vector pesc-Ura by T4 ligase.<br>
 +
</li>
 +
<li>
 +
To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br>
 +
</li>
 +
</ol>
 +
 +
<br>
 
 
 
 
 
<h1>Vector construction of pFig2C-EGFP</h1><br>
 
<h1>Vector construction of pFig2C-EGFP</h1><br>
Fig2C promoter fragment was from iGEM parts registry. The EGFP gene was amplified from palsmid pEGFP-N2, and modified it by adding SpeI and HindIII respectively.<br>
+
<ol>
2 Two fragments of Fig2C promoter,  EGFP gene were double-digested with EcoRI-SpeI, and SpeI-HindIII, respectively.<br>
+
<li>
3 Ligated the fragments into an expression vector pesc-Ura by T4 ligase.<br>
+
Fig2C promoter fragment was from iGEM parts registry. The EGFP gene was amplified from palsmid pEGFP-N2, and modified it by adding <i>Spe</i>I and <i>Hind</i>III respectively.<br>
4 To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br><br>
+
</li>
 +
<li>
 +
Two fragments of Fig2C promoter,  EGFP gene were double-digested with <i>EcoR</i>I-</i>Spe</i>I, and <i>Spe</i>I-</i>Hind</i>III, respectively.<br>
 +
</li>
 +
<li>
 +
Ligated the fragments into an expression vector pesc-Ura by T4 ligase.<br>
 +
</li>
 +
<li>
 +
To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.<br>
 +
</li>
 +
    </ol>
 +
 +
<br>
 
</div>  
 
</div>  
 
</div>  
 
</div>  
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<h1>Qualitative verification using EGFP</h1><br>
 
<h1>Qualitative verification using EGFP</h1><br>
1.Transform expression plasmid pRPR1-Key and pCYC-Lock-EGFP<br>
+
<ol>
into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30 ° C for 36 hours.<br>
+
<li>
2.Resupend a single colony in 10ml SD/-Ura liquid medium <br>
+
Transform expression plasmid pRPR1-Key and pCYC-Lock-EGFP<br>
3.Shake at 30 ° C to OD600 = 0.6<br>
+
into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.<br>
4.500 ul of the bacterial solution was taken out, a picture was prepared, and the expression of EGFP was observed with a fluorescence microscope.<br><br>
+
</li>
 
+
<li>
 +
Resupend a single colony in 10ml SD/-Ura liquid medium <br>
 +
</li>
 +
<li>
 +
Shake at 30℃ to OD600nm = 0.6<br>
 +
</li>
 +
<li>
 +
500ul of the bacterial solution was taken out, a picture was prepared, and the expression of EGFP was observed with a fluorescence microscope.<br>
 +
</li>
 +
    </ol>
 +
 +
                        <br>
 +
 
<h1>Quantitative verification using Gluc</h1><br>
 
<h1>Quantitative verification using Gluc</h1><br>
1.Transform expression plasmid pRPR1-Key and pCYC-Lock-Gluc<br>
+
    <ol>
into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30 ° C for 36 hours.<br>
+
<li>
2.Resupend a single colony in 10ml SD/-Ura liquid medium<br>  
+
Transform expression plasmid pRPR1-Key and pCYC-Lock-Gluc
3.Shake at 30 ° C to OD600 = 0.6<br>
+
into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.<br>
4.500 ul of bacterial solution was taken for ultrasonic cell disruption, and luciferase substrate CTZ was added to detect the expression of luciferase Gluc.<br><br>
+
</li>
 +
<li>
 +
Resupend a single colony in 10ml SD/-Ura liquid medium<br>  
 +
</li>
 +
<li>
 +
Shake at 30℃ to OD600nm = 0.6<br>
 +
</li>
 +
<li>
 +
500ul of bacterial solution was taken for ultrasonic cell disruption, and luciferase substrate Coelenterazine was added to detect the expression of luciferase Gluc.<br>
 +
</li>
 +
    </ol>
 +
<br>
 
</div>  
 
</div>  
 
</div>
 
</div>
Line 316: Line 452:
 
 
 
<h1>Qualitative verification</h1><br>
 
<h1>Qualitative verification</h1><br>
 
+
                        <ol>
1.Transform expression plasmid pFig2C-EGFP into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30 ° C for 36 hours.<br>
+
<li>
2.Resupend a single colony in 10ml SD/-Ura liquid medium <br>
+
Transform expression plasmid pFig2C-EGFP into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.<br>
3.Shake at 30 ° C to OD600 = 0.6<br>
+
</li>
4.500 ul of the bacterial solution was taken out, a picture was prepared, and the expression of EGFP was observed with a fluorescence microscope.<br><br>
+
<li>
 +
Resupend a single colony in 10ml SD/-Ura liquid medium <br>
 +
</li>
 +
<li>
 +
Shake at 30℃ to OD600nm = 0.6<br>
 +
</li>
 +
<li>
 +
500ul of the bacterial solution was taken out, a picture was prepared, and the expression of EGFP was observed with a fluorescence microscope.<br>
 +
</li>
 +
    </ol>
 +
<br>
  
 
<h1>Quantitative verification by q-PCR</h1><br>
 
<h1>Quantitative verification by q-PCR</h1><br>
 
+
                        <ol>
1.Transform expression plasmid pFig2C-EGFP into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30 ° C for 36 hours.<br>
+
<li>
2.Resupend a single colony in 10ml SD/-Ura liquid medium <br>
+
Transform expression plasmid pFig2C-EGFP into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.<br>
3.Shake at 30 ° C to OD600 = 0.6<br>
+
</li>
4.Take 1ml of bacterial solution to extract RNA, perform reverse transcription.<br>
+
<li>
5.Perform quantitative PCR using reverse transcription products as templates.<br><br>
+
Resupend a single colony in 10ml SD/-Ura liquid medium <br>
 +
</li>
 +
<li>
 +
Shake at 30℃ to OD600nm = 0.6<br>
 +
</li>
 +
<li>
 +
Take 1ml of bacterial solution to extract RNA, perform reverse transcription.<br>
 +
</li>
 +
<li>
 +
Perform quantitative PCR using reverse transcription products as templates.<br>
 +
</li>
 +
    </ol>
 +
 +
<br>
 
</div>  
 
</div>  
 
</div>
 
</div>
Line 340: Line 499:
 
 
 
<h1>Qualitative verification using EGFP</h1><br>
 
<h1>Qualitative verification using EGFP</h1><br>
1.The constructed plasmid pCYC-Lock-EGFP was subjected to PCR to obtain a HA1-pCYC-Lock-EGFP-tCYC-HA2 fragment. 10 ul of PCR product was taken, purified and transformed. Plate on SD/-Leu-Ura selection plates and incubate at 30 ° C for 36 hours.<br>
+
<ol>
2.Resupend a single colony in 10ml SD/-Ura liquid medium <br>
+
<li>
3.Shake at 30 ° C to OD600 = 0.6<br>
+
The constructed plasmid pCYC-Lock-EGFP was subjected to PCR to obtain a HA1-pCYC-Lock-EGFP-tCYC-HA2 fragment. 10ul of PCR product was taken, purified and transformed. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.<br>
4.500 ul of the bacterial solution was taken out, a picture was prepared, and the expression of EGFP was observed with a fluorescence microscope.<br><br>
+
</li>
 +
<li>
 +
Resupend a single colony in 10ml SD/-Ura liquid medium <br>
 +
</li>
 +
<li>
 +
Shake at 30℃ to OD600nm = 0.6<br>
 +
</li>
 +
<li>
 +
500ul of the bacterial solution was taken out, a picture was prepared, and the expression of EGFP was observed with a fluorescence microscope.<br>
 +
</li>
 +
    </ol>
 +
<br>
  
 
<h1>PCR verification</h1><br>
 
<h1>PCR verification</h1><br>
 
+
                        <ol>
1.The constructed plasmid pCYC-Lock-EGFP was subjected to PCR to obtain a HA1-pCYC-Lock-EGFP-tCYC-HA2 fragment. 10 ul of PCR product was taken, purified and transformed. Plate on SD/-Leu-Ura selection plates and incubate at 30 ° C for 36 hours.<br>
+
    <li>
2.Resupend a single colony in 10ml SD/-Ura liquid medium <br>
+
The constructed plasmid pCYC-Lock-EGFP was subjected to PCR to obtain a HA1-pCYC-Lock-EGFP-tCYC-HA2 fragment. 10ul of PCR product was taken, purified and transformed. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.<br>
3.Shake at 30 ° C to OD600 = 0.6<br>
+
</li>
4.1 ml of the bacterial solution was taken for DNA extraction.<br>
+
<li>
5.The obtained genomic DNA was subjected to PCR using a specific primer to verify whether the homologous recombination was successful.<br><br>
+
Resupend a single colony in 10ml SD/-Ura liquid medium <br>
 +
</li>
 +
<li>
 +
Shake at 30℃ to OD600nm = 0.6<br>
 +
</li>
 +
<li>
 +
1 ml of the bacterial solution was taken for DNA extraction.<br>
 +
</li>
 +
<li>
 +
The obtained genomic DNA was subjected to PCR using a specific primer to verify whether the homologous recombination was successful.<br>
 +
</li>
 +
 +
    </ol>
 +
 
 
 
 
 
</div>  
 
</div>  
Line 361: Line 544:
 
</h1>
 
</h1>
 
<div class="widget">
 
<div class="widget">
<div class="widget-content">
+
<div class="widget-content">
1.The constructed plasmid pCYC-Lock-EGFP was subjected to PCR to obtain a HA1-pCYC-Lock-EGFP-tCYC-HA2 fragment. 10 ul of PCR product was taken, purified and transformed. Plate on SD/-Leu-Ura selection plates and incubate at 30 ° C for 36 hours.<br>
+
<ol>
2.Resupend a single colony in 10ml SD/-Ura liquid medium <br>
+
<li>
3.Shake at 30 ° C to OD600 = 0.6<br>
+
The constructed plasmid pCYC-Lock-EGFP was subjected to PCR to obtain a HA1-pCYC-Lock-EGFP-tCYC-HA2 fragment. 10ul of PCR product was taken, purified and transformed. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.<br>
4.1 ml of the bacterial solution was taken for DNA extraction.<br>
+
</li>
5.The obtained genomic DNA was subjected to PCR using a specific primer to verify whether the homologous recombination was successful.<br>
+
<li>
6.Take 1ml of bacterial solution to extract RNA, perform reverse transcription to obtain the cDNA.<br>
+
Resupend a single colony in 10ml SD/-Ura liquid medium <br>
7.The cDNA was subjected to PCR using specific primers, and the product was purified and submitted to the company for sequencing.<br>
+
</li>
 +
<li>
 +
Shake at 30℃ to OD600nm = 0.6<br>
 +
</li>
 +
<li>
 +
1 ml of the bacterial solution was taken for DNA extraction.<br>
 +
</li>
 +
<li>
 +
The obtained genomic DNA was subjected to PCR using a specific primer to verify whether the homologous recombination was successful.<br>
 +
</li>
 +
<li>
 +
Take 1ml of bacterial solution to extract RNA, perform reverse transcription to obtain the cDNA.<br>
 +
</li>
 +
<li>
 +
The cDNA was subjected to PCR using specific primers, and the product was purified and submitted to the company for sequencing.<br>
 +
</li>
 +
</ol>
 +
 
 
 
 
 
</div>  
 
</div>  

Latest revision as of 22:23, 17 October 2018

Notebook-2018

Protocol

Cultural Conditions

KEY: Saccharomyces cerevisiae YPH499


  1. Transformation culture conditions: incubator of 30℃, plates with SD/-Leu-agar solid medium.
  2. Inoculation culture conditions: a 30℃ constant temperature shaker with 220 rpm in SD/-Leu liquid medium.

Lock and Information: Saccharomyces cerevisiae YPH499


  1. Transformation culture conditions: incubator of 30℃, plates with SD/-Ura-agar solid medium.
  2. Inoculation culture conditions: a 30℃ constant temperature shaker with 220 rpm in SD/-Ura liquid medium.

pFig2c-Bax: Saccharomyces cerevisiae YPH499


  1. Transformation culture conditions: incubator of 30℃, plates with SD/-Ura-agar solid medium.
  2. Inoculation culture conditions: a 30℃ constant temperature shaker with 220 rpm in SD/-Ura liquid medium.
  3. Inducible expression conditions: a 30℃ constant temperation shaker with 220 rpm in SD/-Ura liquid medium contaning different concentrations of alpha factor.

Vector Construction

Vector construction of Lock and Information:


  1. CYC promoter, CYC1 terminator were amplified from genomic DNA of Saccharomyces cerevisiae YPH499 with corresponding primers respectively. And the DNA of the lock and information fragment was synthesized by company with restriction enzyme cutting sites HindIII, EcoRI and EcoRI, NheI.
  2. Modified CYC1 promoter and CYC1 terminator by adding the HA1 or HA2 by using PCR.
  3. Four fragments of HA1-CYC promoter, Stem loop (the lock), Information and Cyc1 terminator-HA2 the were double-digested with SacI-HindIII, HindIII-EcoRI, EcoRI-NheI, and NheI-BamHI, respectively.
  4. Ligated them into an expression vector pesc-Ura by T4 ligase.
  5. To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.

Vector construction of Lock and EGFP:


  1. CYC promoter, CYC1 terminator were amplified from genomic DNA of Saccharomyces cerevisiae YPH499 with corresponding primers respectively. And the DNA of the lock was synthesized by company with restriction enzyme cutting sites HindIII, EcoRI. The EGFP gene was amplified from palsmid pEGFP-N2, and modified it by adding EcoRI and NheI respectively.
  2. Modified CYC1 promoter and CYC1 terminator by adding the HA1 or HA2 by using PCR.
  3. Four fragments of HA1-CYC promoter, Stem loop (the lock), EGFP and Cyc1 terminator-HA2 the were double-digested with SacI-HindIII, HindIII-EcoRI, EcoRI-NheI, and NheI-BamHI, respectively.
  4. Ligated them into an expression vector pesc-Ura by T4 ligase.
  5. To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.

Vector construction of Lock and Gluc:


  1. CYC promoter, CYC1 terminator were amplified from genomic DNA of Saccharomyces cerevisiae YPH499 with corresponding primers respectively. And the DNA of the lock was synthesized by company with restriction enzyme cutting sites HindIII, EcoRI. The Gluc gene was amplified from palsmid pGluc-Basic2, and modified it by adding EcoRI and NheI respectively.
  2. Modified CYC1 promoter and CYC1 terminator by adding the HA1 or HA2 by using PCR.
  3. Four fragments of HA1-CYC promoter, Stem loop (the lock), Gluc and Cyc1 terminator-HA2 the were double-digested with SacI-HindIII, HindIII-EcoRI, EcoRI-NheI, and NheI-BamHI, respectively.
  4. Ligated them into an expression vector pesc-Ura by T4 ligase.
  5. To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.

Vector construction of Key:


  1. RPR1 promoter was amplified from plasmid named pRPR1_gRNA_handle_RPR1t.
  2. Modified RPR1 promoter by adding the Key sequence and SpeI, XhoI by using PCR.
  3. The fragment of pRPR1-Key was double-digested with SpeI and XhoI respectively.
  4. Ligated it into an expression vector pRPR1_gRNA_handle_RPR1t by T4 ligase.
  5. To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.

Vector construction of suicide switch:


  1. Bax (alpha) Gene was amplified from genomic DNA of 293T cell with corresponding primers respectively.
    Fig2C promoter fragment was from iGEM parts registry.
  2. Modified Bax fragment by adding SpeI and HindIII by using PCR.
  3. Two fragments of Fig2C promoter, Bax gene were double-digested with EcoRI-SpeI, and SpeI-HindIII, respectively.
  4. Ligated the fragments into an expression vector pesc-Ura by T4 ligase.
  5. To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.

 

Vector construction of pFig2C-EGFP


  1. Fig2C promoter fragment was from iGEM parts registry. The EGFP gene was amplified from palsmid pEGFP-N2, and modified it by adding SpeI and HindIII respectively.
  2. Two fragments of Fig2C promoter, EGFP gene were double-digested with EcoRI-SpeI, and SpeI-HindIII, respectively.
  3. Ligated the fragments into an expression vector pesc-Ura by T4 ligase.
  4. To detemine whether the vector is constructed successfully, conoly PCR and sequencing were done.

Lock and key interaction verification

Qualitative verification using EGFP


  1. Transform expression plasmid pRPR1-Key and pCYC-Lock-EGFP
    into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.
  2. Resupend a single colony in 10ml SD/-Ura liquid medium
  3. Shake at 30℃ to OD600nm = 0.6
  4. 500ul of the bacterial solution was taken out, a picture was prepared, and the expression of EGFP was observed with a fluorescence microscope.

Quantitative verification using Gluc


  1. Transform expression plasmid pRPR1-Key and pCYC-Lock-Gluc into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.
  2. Resupend a single colony in 10ml SD/-Ura liquid medium
  3. Shake at 30℃ to OD600nm = 0.6
  4. 500ul of bacterial solution was taken for ultrasonic cell disruption, and luciferase substrate Coelenterazine was added to detect the expression of luciferase Gluc.

Fig2C promoter verification of α-factor response

Qualitative verification


  1. Transform expression plasmid pFig2C-EGFP into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.
  2. Resupend a single colony in 10ml SD/-Ura liquid medium
  3. Shake at 30℃ to OD600nm = 0.6
  4. 500ul of the bacterial solution was taken out, a picture was prepared, and the expression of EGFP was observed with a fluorescence microscope.

Quantitative verification by q-PCR


  1. Transform expression plasmid pFig2C-EGFP into YPH499. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.
  2. Resupend a single colony in 10ml SD/-Ura liquid medium
  3. Shake at 30℃ to OD600nm = 0.6
  4. Take 1ml of bacterial solution to extract RNA, perform reverse transcription.
  5. Perform quantitative PCR using reverse transcription products as templates.

Verification of homologous recombination

Qualitative verification using EGFP


  1. The constructed plasmid pCYC-Lock-EGFP was subjected to PCR to obtain a HA1-pCYC-Lock-EGFP-tCYC-HA2 fragment. 10ul of PCR product was taken, purified and transformed. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.
  2. Resupend a single colony in 10ml SD/-Ura liquid medium
  3. Shake at 30℃ to OD600nm = 0.6
  4. 500ul of the bacterial solution was taken out, a picture was prepared, and the expression of EGFP was observed with a fluorescence microscope.

PCR verification


  1. The constructed plasmid pCYC-Lock-EGFP was subjected to PCR to obtain a HA1-pCYC-Lock-EGFP-tCYC-HA2 fragment. 10ul of PCR product was taken, purified and transformed. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.
  2. Resupend a single colony in 10ml SD/-Ura liquid medium
  3. Shake at 30℃ to OD600nm = 0.6
  4. 1 ml of the bacterial solution was taken for DNA extraction.
  5. The obtained genomic DNA was subjected to PCR using a specific primer to verify whether the homologous recombination was successful.
 

Information expression verification

  1. The constructed plasmid pCYC-Lock-EGFP was subjected to PCR to obtain a HA1-pCYC-Lock-EGFP-tCYC-HA2 fragment. 10ul of PCR product was taken, purified and transformed. Plate on SD/-Leu-Ura selection plates and incubate at 30℃ for 36 hours.
  2. Resupend a single colony in 10ml SD/-Ura liquid medium
  3. Shake at 30℃ to OD600nm = 0.6
  4. 1 ml of the bacterial solution was taken for DNA extraction.
  5. The obtained genomic DNA was subjected to PCR using a specific primer to verify whether the homologous recombination was successful.
  6. Take 1ml of bacterial solution to extract RNA, perform reverse transcription to obtain the cDNA.
  7. The cDNA was subjected to PCR using specific primers, and the product was purified and submitted to the company for sequencing.