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

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         <h1 class="entry-title"><a href="https://www.camarts.cn/archives/4252.html" title="查看《火影忍者疾风传》中的全部作品" rel="bookmark">Week1(8/1/2016-8/7/2016)</a></h1>
 
         <h1 class="entry-title"><a href="https://www.camarts.cn/archives/4252.html" title="查看《火影忍者疾风传》中的全部作品" rel="bookmark">Week1(8/1/2016-8/7/2016)</a></h1>
 
<div class="entry-content">
 
<div class="entry-content">
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<b>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 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.
  
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<h1 class="entry-title"><a href="https://www.camarts.cn/archives/4252.html" title="查看《火影忍者疾风传》中的全部作品" rel="bookmark">Week4(9/5/2016-9/11/2016)</a></h1>
 
<h1 class="entry-title"><a href="https://www.camarts.cn/archives/4252.html" title="查看《火影忍者疾风传》中的全部作品" rel="bookmark">Week4(9/5/2016-9/11/2016)</a></h1>
 
<div class="entry-content">
 
<div class="entry-content">
 +
<b>Ⅱ. Expression of the plasmids constracted before<b>
 
<p>
 
<p>
 
<li>We choosed 4 tubes of plasmid to express in the cell-free system firstly.<br/>
 
<li>We choosed 4 tubes of plasmid to express in the cell-free system firstly.<br/>
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<h1 class="entry-title"><a href="https://www.camarts.cn/archives/4252.html" title="查看《火影忍者疾风传》中的全部作品" rel="bookmark">Week5(9/12/2016-9/18/2016)</a></h1>
 
<h1 class="entry-title"><a href="https://www.camarts.cn/archives/4252.html" title="查看《火影忍者疾风传》中的全部作品" rel="bookmark">Week5(9/12/2016-9/18/2016)</a></h1>
 
<div class="entry-content">
 
<div class="entry-content">
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<p>
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<b>Ⅲ.Detection of Enzyme Activity<b>
 +
<p>
  
−
<li>Plasmids pT-13-19-15 were handed in for sequencing, which confirmed its correctness.</li>
+
<li>Substrate: 1mM pNPA  Acetonitrile solution.<br/>
−
<b>The sequencing results for both of them were error.</b>
+
  10 times diluted Enzyme solution(unpurified) mixed with the equal volume substrate.<br/>
−
<li>Colonies containing Ni inducible promoter were used to inoculate overnight cultures.</li>
+
  This attempt of detection failed because our enzyme precipitated in acetonitrile.
−
<li>PCR was performed to check if the gene fragments were ligated correctly.</li>
+
</li>
−
    13_ fwd and 15_rev on pT-13-19-15<br/>
+
−
    Gel electrophoresis showed that it failed.<br/>
+
−
<li>Plasmids pCPC-3031-Ni were isolated using a miniprep kit.</li>
+
−
<li>Several PCRs were performed to check if the gene fragments were ligated correctly.</li>
+
−
1.13_fwd and 13_rev on pT-13-19-15<br/>
+
−
2.19_fwd and 19_rev on pT-13-19-15<br/>
+
−
3.15_fwd and 15_rev on pT-13-19-15<br/>
+
−
4.13_fwd and 19_rev on pT-13-19-15<br/>
+
−
5.19_fwd and 15_rev on pT-13-19-15<br/>
+
−
6.13_ wd and 15_rev on pT-13-19-15<br/>
+
−
    <b>The fourth and sixth ones were not successful.</b><br/>
+
−
<li><b>Repetition:</b>  Phosphorylated <i>13</i> was ligated into pT-19-15 and transformed into E.coli via heat shock.</li>
+
−
<li><b>Repetition:</b> Several PCRs were performed to check if the gene fragments were ligated correctly.</li>
+
−
1.13_fwd and 13_rev on pT-13-19-15<br/>
+
−
2.13_fwd and 19_rev on pT-13-19-15<br/>
+
−
<b>The second one was failed.</b>
+
  
 +
<li>Subsrtste: 1mM pNPA Tris-HCl buffer.<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.
 +
</li>
  
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<br/>
 
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−
 
−
 
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<a href="https://www.camarts.cn/archives/4252.html"><img class="aligncenter size-full wp-image-4256" src="http://static.camarts.cn/images/spinner-1600.gif"  alt="IMG_2956" width="800" height="533" srcset="images/img_1.jpg 800w, http://img.camarts.cn/2016/01/IMG_2956-150x100.jpg 150w, http://img.camarts.cn/2016/01/IMG_2956-300x200.jpg 300w, http://img.camarts.cn/2016/01/IMG_2956-768x512.jpg 768w, http://img.camarts.cn/2016/01/IMG_2956-450x300.jpg 450w" sizes="(max-width: 800px) 100vw, 800px" /><noscript><img class="aligncenter size-full wp-image-4256" src="http://img.camarts.cn/2016/01/IMG_2956.jpg?imageView/2/w/800/h/800/q/90" alt="IMG_2956" width="800" height="533" srcset="http://img.camarts.cn/2016/01/IMG_2956.jpg 800w, http://img.camarts.cn/2016/01/IMG_2956-150x100.jpg 150w, http://img.camarts.cn/2016/01/IMG_2956-300x200.jpg 300w, http://img.camarts.cn/2016/01/IMG_2956-768x512.jpg 768w, http://img.camarts.cn/2016/01/IMG_2956-450x300.jpg 450w" sizes="(max-width: 800px) 100vw, 800px" /></noscript></a></p>
 
−
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<footer class="entry-meta">
 
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<p>
 
<p>
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<li>Medium preparation :BG-11.</li>
+
<li>Substrate:0.2mM pNPA water solution.<br/>
−
<li>19_ fwd and 15_rev were used to amplify <i>19-15</i>.</li>
+
10 times diluted Enzyme solution(unpurified) mixed with the equal volume substrate.<br/>
−
Gel electrophoresis showed that amplification of fragments was successfull.</li>
+
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>Ligated <i>13</i> and <i>19-15</i> via overlap PCR.</li>
+
</li>
−
This PCR worked well and the products were extracted from the gel using a Agarose Gel DNA Extration Kit.</li>
+
<li>Substrate:PET.<br/>
−
<li>Restriction digest on pCPC-3031-Ni with Sac I.</li>
+
  PET was been put into 20 times diluted Enzyme solution(unpurified).<br/>
−
<li>The fragment <i>13-19-15</i> was ligated onto T vector and transformed into E.coli via heat shock.</li>
+
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.
−
<li>A colony PCR of pT-13-19-15 was performed with 12 colonies.</li>
+
</li>
−
Two of these colonies containing pT-13-19-15 were used to inoculate overnight cultures.</li>
+
−
<li><i>13-19-15</i> gene fragment was phosphorylated.</li>
+
−
<li>Phosphorylated <i>13-19-15</i> was ligated into pCPC-3031-Ni and transformed into E.coli via heat shock.</li>
+
  
−
<li>Plasmids pT-13-19-15 were isolated using a miniprep kit.</li>
+
<br />
−
<li>A colony PCR of pCPC-3031-Ni-13-19-15 was performed with 12 colonies.</li>
+
−
Three colonies were proved to be true. And two of them were used to inoculate overnight cultures.</li>
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<br />
 
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<a href="https://www.camarts.cn/archives/4252.html"><img class="aligncenter size-full wp-image-4256" src="http://static.camarts.cn/images/spinner-1600.gif"  alt="IMG_2956" width="800" height="533" srcset="images/img_1.jpg 800w, http://img.camarts.cn/2016/01/IMG_2956-150x100.jpg 150w, http://img.camarts.cn/2016/01/IMG_2956-300x200.jpg 300w, http://img.camarts.cn/2016/01/IMG_2956-768x512.jpg 768w, http://img.camarts.cn/2016/01/IMG_2956-450x300.jpg 450w" sizes="(max-width: 800px) 100vw, 800px" /><noscript><img class="aligncenter size-full wp-image-4256" src="http://img.camarts.cn/2016/01/IMG_2956.jpg?imageView/2/w/800/h/800/q/90" alt="IMG_2956" width="800" height="533" srcset="http://img.camarts.cn/2016/01/IMG_2956.jpg 800w, http://img.camarts.cn/2016/01/IMG_2956-150x100.jpg 150w, http://img.camarts.cn/2016/01/IMG_2956-300x200.jpg 300w, http://img.camarts.cn/2016/01/IMG_2956-768x512.jpg 768w, http://img.camarts.cn/2016/01/IMG_2956-450x300.jpg 450w" sizes="(max-width: 800px) 100vw, 800px" /></noscript></a></p>
 
 
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Revision as of 06:15, 30 September 2016

TEAM TIANJIN

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Team Tianjin-Attribution

Notes

Week1(8/1/2016-8/7/2016)

Ⅰ.Constraction of expression plasmid in CFPS(cell-free protein synthesis)
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.

  • 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.

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    Week2(8/15/2016-8/21/2016)

  • 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.

  • 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.
    T--Tianjin--cell-free_note-1

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    • Week3(8/29/2016-9/4/2016)

  • Our strategy is to exchange the site-directed mutation PETase-M154L for the other 21 mutations 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 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.)

  • Transformation
  • Plasmid isolation
  • Verification

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    Week4(9/5/2016-9/11/2016)

    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
    Show More 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.

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    Week5(9/12/2016-9/18/2016)

    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.
  • Subsrtste: 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.

    • Week6(9/19/2016-9/25/2016)

  • 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.
  • Substrate:PET.
    PET was been put into 20 times diluted Enzyme solution(unpurified).
    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.

    • 查看Team Tianjin全部实验 ›

    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