Difference between revisions of "Team:Tianjin/Note/CFPS"

 
(28 intermediate revisions by 3 users not shown)
Line 5: Line 5:
  
 
<html lang="en">
 
<html lang="en">
 +
<style>
 +
#Notes{
 +
  color: inherit;
 +
  background-color: rgba(255, 255, 255, 0.1);
 +
}
 +
</style>
 +
 
<head>
 
<head>
 
<meta charset="utf-8" />  
 
<meta charset="utf-8" />  
Line 14: Line 21:
  
 
<!------------------------------------------- This part should be dismissed in WIKI u
 
<!------------------------------------------- This part should be dismissed in WIKI u
 +
 +
 +
 
 
 
     <style type="text/css">
 
     <style type="text/css">
Line 51: Line 61:
 
      
 
      
 
     <header id="main-header" role="banner">
 
     <header id="main-header" role="banner">
−
      
+
     <style>
 +
.note-content,.note-content2,.note-content3,.note-content4,.note-content5,.note-content6,.note-content li,.note-content2 li,.note-content3 li,.note-content4 li,.note-content5 li,.note-content6 li{
 +
font-family:Arial;
 +
font-size:18px;
 +
text-align:justify;
 +
}
 +
</style>
 
    
 
    
 
        
 
        
Line 71: Line 87:
 
 
 
     <b>Ⅰ.Constraction of expression plasmid in CFPS(cell-free protein synthesis)</b><br/>
 
     <b>Ⅰ.Constraction of expression plasmid in CFPS(cell-free protein synthesis)</b><br/>
−
The mutations of PETase gene had been contracted by over-lap PCR and Restriction Enzyme cutting sites(SacⅠ&EcoRⅠ) had been added to it’s ends (5’&3’) separately.
+
The mutants of PETase gene had been contracted by over-lap PCR and Restriction Enzyme cutting sites(SacⅠ&EcoRⅠ) had been added to it’s ends (5’&3’) separately.
  
 
 
Line 118: Line 134:
 
Verification : Colony PCR with fast taq Polymerase, primers: PETase-S/PETase -A, template: Colony of  E.coli  with plasmid pRset_CFP-1-M154L. Bands as expected(about 760bp) in agarose gel.
 
Verification : Colony PCR with fast taq Polymerase, primers: PETase-S/PETase -A, template: Colony of  E.coli  with plasmid pRset_CFP-1-M154L. Bands as expected(about 760bp) in agarose gel.
 
</li><br />
 
</li><br />
−
<li>Cultivation the E.coli cells transformed yesterday in several 5mL liquid LB culture mediums with Amp at 37℃ for 12 hours.<br/>
+
 
−
<li>Plasmid isolation of pRset_CFP-1-M154L.<br/>
+
 
<img class="aligncenter size-full wp-image-4256" src="https://static.igem.org/mediawiki/2016/5/55/T--Tianjin--cell-free_note-1.png"  alt="T--Tianjin--cell-free_note-1" width="800" height="533">
 
<img class="aligncenter size-full wp-image-4256" src="https://static.igem.org/mediawiki/2016/5/55/T--Tianjin--cell-free_note-1.png"  alt="T--Tianjin--cell-free_note-1" width="800" height="533">
 +
 +
<li>Cultivation the E.coli cells transformed yesterday in several 5mL liquid LB culture mediums with Amp at 37℃ for 12 hours.</li><br/>
 +
<li>Plasmid isolation of pRset_CFP-1-M154L.</li><br/>
  
 
</p>
 
</p>
Line 150: Line 168:
  
  
−
<p><li>Our strategy is to exchange the site-directed mutation PETase-M154L for the other 21 mutations and 1 wild type, separately.<br/>
+
<p><li>Our strategy is to exchange the site-directed mutant PETase-M154L for the other 21 mutants and 1 wild type, separately.<br/>
 
XbaⅠ&EcoRⅠdouble restriction endonuclease digestion in pRset_CFP-1-M154L<br/>
 
XbaⅠ&EcoRⅠdouble restriction endonuclease digestion in pRset_CFP-1-M154L<br/>
 
No expected bands(3600bp&750bp) in agarose gel. We don’t find the reason why the plasmid constuced can’t be cut into the two expected bands, so we decided to change the initial strategy.  
 
No expected bands(3600bp&750bp) in agarose gel. We don’t find the reason why the plasmid constuced can’t be cut into the two expected bands, so we decided to change the initial strategy.  
 
</li><br/>
 
</li><br/>
−
<li>Ligaion of digested pRset_CFP-1, digested <i>CFP</i> gene and the rest 22 digested gene interested (including  21 PETase site-directed mutations geneand 1 wild type ) separately in accordance with the 1:5:5 molecular ratio. The newly constructed plasmid is called pRset_CFP-1-R90I (R90T, R90A, S92A, Q119A, M154A, W159H, W159M, N205L, N205V, S207T, S207A, I208V, S238F, S238V,A240P, S242I.)</li><br/>
+
<li>Ligaion of digested pRset_CFP-1, digested <i>CFP</i> gene and the rest 22 digested gene interested (including  21 PETase site-directed mutants geneand 1 wild type ) separately in accordance with the 1:5:5 molecular ratio. The newly constructed plasmid is called pRset_CFP-1-R90I (R90T, R90A, S92A, Q119A, M154A, W159H, W159M, N205L, N205V, S207T, S207A, I208V, S238F, S238V,A240P, S242I.)</li><br/>
 
<li>Transformation</li>
 
<li>Transformation</li>
 
<li> Plasmid isolation</li>
 
<li> Plasmid isolation</li>
Line 190: Line 208:
 
<div class="note-content4">
 
<div class="note-content4">
  
−
          hebo
+
<b>Ⅱ. Expression of the plasmids constracted before</b>
 +
 
 +
<li>We choosed 4 tubes of plasmid to express in the cell-free system firstly.<br/>
 +
The protocol of the cell-free protein synthesis system(50 µL) we used :<br/>
 +
MQ H2O&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;7.9µL<br/>
 +
Feeding buffer&nbsp;&nbsp;&nbsp;&nbsp;25µL<br/>
 +
Mg2+ solution&nbsp;&nbsp;&nbsp;&nbsp;1.1µL<br/>
 +
Gene( plasmid as template)&nbsp;&nbsp;1µL<br/>
 +
Lysate&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;15µL<br/>
 +
(PS: The details of the system are not available.)<br/>
 +
</li>
 +
 
 +
<b>Systems were expressed in 96-well plates and put the 96-well plates into the ELIASA (microplate reader) at 30℃ for 12 hours.</b><br/>
 +
<img class="aligncenter size-full wp-image-4256" src="https://static.igem.org/mediawiki/2016/3/3d/T--Tianjin--cell-free_note-2.png"  alt="T--Tianjin--cell-free_note-2" width="800" height="533">
 +
 
 +
<li><b>Parallel experiments for expression in CFPS system</b></li><br/>
 +
 
 +
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/9/97/T--Tianjin--cf-blank.png"  alt="T--Tianjin--cf-blank" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/d/d0/T--Tianjin--cf-m1.png"  alt="T--Tianjin--cf-m1" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/4/44/T--Tianjin--cf-m2.png"  alt="T--Tianjin--cf-m2" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/3/34/T--Tianjin--cf-m3.png"  alt="T--Tianjin--cf-m3" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/7/75/T--Tianjin--cf-m4.png"  alt="T--Tianjin--cf-m4" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/b/be/T--Tianjin--cf-m5.png"  alt="T--Tianjin--cf-m5" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/4/4e/T--Tianjin--cf-m6.png"  alt="T--Tianjin--cf-m6" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/4/4e/T--Tianjin--cf-m7.png"  alt="T--Tianjin--cf-m7" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/9/97/T--Tianjin--cf-m8.png"  alt="T--Tianjin--cf-m8" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/d/d1/T--Tianjin--cf-m9.png"  alt="T--Tianjin--cf-m9" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/6/61/T--Tianjin--cf-m10.png"  alt="T--Tianjin--cf-m10" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/c/c9/T--Tianjin--cf-m11.png"  alt="T--Tianjin--cf-m11" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/3/36/T--Tianjin--cf-m12.png"  alt="T--Tianjin--cf-m12"height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/d/d2/T--Tianjin--cf-m13.png"  alt="T--Tianjin--cf-m13" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/3/35/T--Tianjin--cf-m14.png"  alt="T--Tianjin--cf-m14" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/b/b3/T--Tianjin--cf-m15.png"  alt="T--Tianjin--cf-m15" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/2/2c/T--Tianjin--cf-m16.png"  alt="T--Tianjin--cf-m16" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/9/91/T--Tianjin--cf-m17.png"  alt="T--Tianjin--cf-m17" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/3/3f/T--Tianjin--cf-m18.png"  alt="T--Tianjin--cf-m18" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/a/ad/T--Tianjin--cf-m19.png"  alt="T--Tianjin--cf-m19" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/0/03/T--Tianjin--cf-m20.png"  alt="T--Tianjin--cf-m20" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/b/b9/T--Tianjin--cf-m21.png"  alt="T--Tianjin--cf-m21" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/3/3d/T--Tianjin--cf-m22.png"  alt="T--Tianjin--cf-m22" height="250px">
 +
<img class="col-md-4" src="https://static.igem.org/mediawiki/2016/3/3e/T--Tianjin--cf-m-no.png"  alt="T--Tianjin--cf-m-no"height="250px">
 +
 
 +
<br/>
 +
 
 +
<p>
 +
<b>The figures above show that the plasmids can express in the CFPS system, although the results of the parallel experimennts indicate that the CFPS system is unstable.</b> 
 +
</p>
 +
 
 +
       
 
          
 
          
  
Line 219: Line 286:
 
<div class="note-content5">
 
<div class="note-content5">
  
−
<b>Ⅲ.Detection of Enzyme Activity<b>
+
<b>Ⅲ.Detection of Enzyme Activity</b>
 
<p>
 
<p>
  
Line 227: Line 294:
 
</li>
 
</li>
  
−
<li>Subsrtste: 1mM pNPA Tris-HCl buffer.<br/>  
+
<li>Subsrtrate: 1mM pNPA Tris-HCl buffer.<br/>  
 
10 times diluted Enzyme solution(unpurified) mixed with the equal volume substrate.<br/>
 
10 times diluted Enzyme solution(unpurified) mixed with the equal volume substrate.<br/>
 
This attempt of detection failed, too. Because we found that Tris can react with pNPA , and pNPA would be transfered to pNP, too.  
 
This attempt of detection failed, too. Because we found that Tris can react with pNPA , and pNPA would be transfered to pNP, too.  
Line 269: Line 336:
 
After static reaction at 39℃ for 8 hours, we detected the characteristic adsorption peak of the product ,pNP, which has no other characteristic adsorption peak except in 400nm.
 
After static reaction at 39℃ for 8 hours, we detected the characteristic adsorption peak of the product ,pNP, which has no other characteristic adsorption peak except in 400nm.
 
</li>
 
</li>
 +
 +
<img class="aligncenter size-full wp-image-4256" src="https://static.igem.org/mediawiki/2016/f/f4/T--Tianjin--cell-free_note-3.png"  alt="T--Tianjin--cf-m-no" width="800" height="533">
 +
 +
<b>The control group in the image above indicate that something else in the CFPS system can cause characteristic adsorption peak except in 400nm with the sunstrate.</b><br/><br/><br/>
 +
 
<li>Substrate:PET.<br/>
 
<li>Substrate:PET.<br/>
 
   PET was been put into 20 times diluted Enzyme solution(unpurified).<br/>
 
   PET was been put into 20 times diluted Enzyme solution(unpurified).<br/>
−
After static reaction at 39℃ for 48 hours, we detected the characteristic adsorption peak of the product ,MHET, which has no other characteristic adsorption peak except in 260nm. Besides, we also deteected the system by Multispectral Scanning.
+
After static reaction at 39℃ for 5 days, we detected the characteristic adsorption peak of the product ,MHET, which has no other characteristic adsorption peak except in 260nm. Besides, we also deteected the product by Multispectral Scanning.
 
</li></p>
 
</li></p>
 +
 +
Please visit our Result part for more detailed result.
  
 
        
 
        
Line 300: Line 374:
  
  
−
</div>
+
</div><!--
 
<div class="side-nav">
 
<div class="side-nav">
 
<ul>
 
<ul>
Line 312: Line 386:
 
<li><a class="topLink" href="#Week7" style="color:#5555FF">Week7</a></li>
 
<li><a class="topLink" href="#Week7" style="color:#5555FF">Week7</a></li>
 
</ul>
 
</ul>
−
</div>   
+
</div>  -->
  
  

Latest revision as of 14:07, 19 October 2016

TEAM TIANJIN

LOGO


Team Tianjin-Attribution

Notes For CFPS system

Week1(8/24/2016-8/30/2016)

Ⅰ.Constraction of expression plasmid in CFPS(cell-free protein synthesis)
The mutants of PETase gene had been contracted by over-lap PCR and Restriction Enzyme cutting sites(SacⅠ&EcoRⅠ) had been added to it’s ends (5’&3’) separately.

  • Transformation of E.coli (Trans-T1 Phage Resistant Chemically Competent Cell) with pRset_CFP-1(with AmpR) and plating on solid LB culture medium with Amp.
  • Cultivation the E.coli cells transformed yesterday in several 5mL liquid LB culture mediums with Amp at 37℃ for 12 hours.
  • Plasmid isolation of pRset_CFP-1.
  • Primers were designed for the target (CFP gene) within the plasmid pRset_CFP-1.
  • PCR with Q5-Polymerase to amplify CFP gene out of plasmid pRset_CFP-1 and add Restriction Enzyme cutting sites(XbaⅠ&SacⅠ) to it’s ends(5’&3’) separately.
    Bands as expected(about 760bp) in agarose gel , gel purification of the PCR products.

    • Show More

    Week2(8/31/2016-9/6/2016)

  • XbaⅠ&SacⅠdouble restriction endonuclease digestion in CFP gene.

  • XbaⅠ&EcoRⅠdouble restriction endonuclease digestion in pRset_CFP-1
    Bands as expected(760bp&3000bp) in agarose gel , gel purification of the digested products(3000bp).

  • Ligaion of digested pRset_CFP-1, digested CFP gene and digested PETase(M154L) gene in accordance with the 1:5:5 molecular ratio. The newly constructed plasmid is called pRset_CFP-1-M154L.
    Transformation of E.coli (Trans-T1 Phage Resistant Chemically Competent Cell) with pRset_CFP-1-M154L(with AmpR) and plating on solid LB culture medium with Amp.
    Verification : Colony PCR with fast taq Polymerase, primers: PETase-S/PETase -A, template: Colony of E.coli with plasmid pRset_CFP-1-M154L. Bands as expected(about 760bp) in agarose gel.

    • T--Tianjin--cell-free_note-1
  • Cultivation the E.coli cells transformed yesterday in several 5mL liquid LB culture mediums with Amp at 37℃ for 12 hours.

  • Plasmid isolation of pRset_CFP-1-M154L.

    • Show More

    Week3(9/7/2016-9/13/2016)

  • Our strategy is to exchange the site-directed mutant PETase-M154L for the other 21 mutants and 1 wild type, separately.
    XbaⅠ&EcoRⅠdouble restriction endonuclease digestion in pRset_CFP-1-M154L
    No expected bands(3600bp&750bp) in agarose gel. We don’t find the reason why the plasmid constuced can’t be cut into the two expected bands, so we decided to change the initial strategy.

  • Ligaion of digested pRset_CFP-1, digested CFP gene and the rest 22 digested gene interested (including 21 PETase site-directed mutants geneand 1 wild type ) separately in accordance with the 1:5:5 molecular ratio. The newly constructed plasmid is called pRset_CFP-1-R90I (R90T, R90A, S92A, Q119A, M154A, W159H, W159M, N205L, N205V, S207T, S207A, I208V, S238F, S238V,A240P, S242I.)

  • Transformation
  • Plasmid isolation
  • Verification

    • Show More

    Week4(9/14/2016-9/20/2016)

    Ⅱ. Expression of the plasmids constracted before
  • We choosed 4 tubes of plasmid to express in the cell-free system firstly.
    The protocol of the cell-free protein synthesis system(50 µL) we used :
    MQ H2O     7.9µL
    Feeding buffer    25µL
    Mg2+ solution    1.1µL
    Gene( plasmid as template)  1µL
    Lysate     15µL
    (PS: The details of the system are not available.)
    • Systems were expressed in 96-well plates and put the 96-well plates into the ELIASA (microplate reader) at 30℃ for 12 hours.
    T--Tianjin--cell-free_note-2
  • Parallel experiments for expression in CFPS system

    • T--Tianjin--cf-blank T--Tianjin--cf-m1 T--Tianjin--cf-m2 T--Tianjin--cf-m3 T--Tianjin--cf-m4 T--Tianjin--cf-m5 T--Tianjin--cf-m6 T--Tianjin--cf-m7 T--Tianjin--cf-m8 T--Tianjin--cf-m9 T--Tianjin--cf-m10 T--Tianjin--cf-m11 T--Tianjin--cf-m12 T--Tianjin--cf-m13 T--Tianjin--cf-m14 T--Tianjin--cf-m15 T--Tianjin--cf-m16 T--Tianjin--cf-m17 T--Tianjin--cf-m18 T--Tianjin--cf-m19 T--Tianjin--cf-m20 T--Tianjin--cf-m21 T--Tianjin--cf-m22 T--Tianjin--cf-m-no

    The figures above show that the plasmids can express in the CFPS system, although the results of the parallel experimennts indicate that the CFPS system is unstable.

    Show More

    Week5(9/21/2016-9/27/2016)

    Ⅲ.Detection of Enzyme Activity

  • Substrate: 1mM pNPA Acetonitrile solution.
    10 times diluted Enzyme solution(unpurified) mixed with the equal volume substrate.
    This attempt of detection failed because our enzyme precipitated in acetonitrile.
  • Subsrtrate: 1mM pNPA Tris-HCl buffer.
    10 times diluted Enzyme solution(unpurified) mixed with the equal volume substrate.
    This attempt of detection failed, too. Because we found that Tris can react with pNPA , and pNPA would be transfered to pNP, too.

    • Show More

    Week6(9/28/2016-10/2/2016)

  • Substrate:0.2mM pNPA water solution.
    10 times diluted Enzyme solution(unpurified) mixed with the equal volume substrate.
    After static reaction at 39℃ for 8 hours, we detected the characteristic adsorption peak of the product ,pNP, which has no other characteristic adsorption peak except in 400nm.
    • T--Tianjin--cf-m-no The control group in the image above indicate that something else in the CFPS system can cause characteristic adsorption peak except in 400nm with the sunstrate.


  • Substrate:PET.
    PET was been put into 20 times diluted Enzyme solution(unpurified).
    After static reaction at 39℃ for 5 days, we detected the characteristic adsorption peak of the product ,MHET, which has no other characteristic adsorption peak except in 260nm. Besides, we also deteected the product by Multispectral Scanning.

    • Please visit our Result part for more detailed result.
    Show More
    info_outline
    Notice: This page is currently under construction. Contents in this page are temporaory and will be modified several times before the final release.     — 2016 iGEM Team Tianjin

    Team Tianjin Sponsor Alltech
    Team Tianjin Sponsor GenScript
    Team Tianjin Sponsor SynbioTech