Team:INSA Toulouse/contenu/lab practice/notebook/calendar/logic gates

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   <h1 class="title1">Calendar</h1>
   <h1 class="title1">Calendar</h1>
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   <h2 class="title2">Logic Gates Characterization</h2>
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   <h2 class="title2">Logic Gates </h2>
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  <img src="https://static.igem.org/mediawiki/2013/d/dc/AND1-notebook.png" class="imgcontent" />
 
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   <div class="infos">
   <div class="infos">
   <ul class="circlearrow">
   <ul class="circlearrow">
 +
  <li><span class="spantitle2">Week 4 (1-7 July)</span><br>
 +
04/07<br>
 +
Summary of all the work we have to do for the logic gates.  These are the necessary genes we needed to cloned into the logic gates.<br>
 +
Fro And1: rbs-luxI and rbs-Ci-ter<br>
 +
For Xor1: rbs FimE ter<br>
 +
For And2: reversed rbs luxI<br>
 +
For Xor2: reversed rbs-RFP-ter<br><br>
 +
</li>
 +
   <li><span class="spantitle2">Week 6 (15-21 July)</span><br>
   <li><span class="spantitle2">Week 6 (15-21 July)</span><br>
-
15/07<br>
+
Amplification of fimE recombinase (rbs+fimE) from the Michigan Team.<br>
-
PCR to invert RFP and rbs.LuxI with the restriction site ClaI BamHI<br><br>
+
Minipreps, and electrophoresis checking-> good amplification.<br><br>
-
16/07<br>
+
-
Purification of the PCR and verification by gel.<br><br>
+
-
19/07<br>
+
-
Assembling of  rbs.LuxI and cI for the final system with the AND1 gate.<br>
+
-
Arrival of the synthesis.<br><br>
+
-
20/07<br>
+
-
Verification of the clonage.<br>
+
-
Assembling the synthesis parts (the 4 gates) into pSB1C3.<br><br>
+
</li>
</li>
-
  <li><span class="spantitle2">Week 7 (22-28 July)</span><br>
+
 
-
22/07<br>
+
<li><span class="spantitle2">Week 7 (22-28 July)</span><br>
-
Assembling XOR1 with FimE, LuxI with cI <br>
+
Problem with AND1, the synthesis is not correct. We cannot go on with this gate. We planned order a new synthesis.<br>
 +
Amplification of a new rbs-luxI (BBa_K516011). We realized that the first rbs –luxI we amplified was not the good one (wrong size).<br>
 +
Cloning of rbs+fimE with a terminator, wrong electrophoresis profile.<br>
 +
Cloning of rbs-luxI with rbs-CI-ter. This cloning step was successful.<br>
 +
Transfer of xor2 synthesis from puc54 to pSB1C3. We did not get xor2 inside pSB1C3, but only the backbone vector.<br>
 +
Insertion of reversed RFP inside AND2 (with cla1/bamH1). Electrophoresis profiles were not correct, so the insertion was not successful. It was probably a problem of restriction time.
 +
<br><br>
</li>
</li>
-
  </ul></li>
 
   </ul>
   </ul>
-
</li>
 
   </div>
   </div>
</div>
</div>
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   <div class="infos">
   <div class="infos">
   <ul class="circlearrow">
   <ul class="circlearrow">
-
   <li><a href="">Week Z</a></li>
+
   <li><a href="">Week 8 (29-04 August)</a><br>
-
  <li><a href="">Week Y</a></li>
+
Cloning of rbs+fimE with a terminator. This time we succeeded.<br>
-
  </ul>
+
Amplification of the fragment rbs luxI-rbs-CI-ter for the AND1 gate.<br>
 +
Insertion of rbs-FImE-ter inside the Xor1 gate. We made restriction controls with different enzymes (stu1,hindIII), but the results were not fruitful.<br>
 +
We tried again to introduce RFP inside AND2, still not working.<br>
 +
We succeeded to transfer Xor2 inside pSB1C3.<br>
</li>
</li>
-
   </div>
+
  <li><a href="">Week 9 (05-11 August)</a><br>
 +
Still lot of problems to insert reversed RFP inside AND2. The transformation does not work.  We needed to find a solution (strataclone? Infusion?...).<br>
 +
Insertion of reversed rbs luxi inside AND2. Same problem as for AND2-RFP.<br>
 +
Cloning of rbs-fimE-ter  into Xor1. It did not work because of a ligation problem.<br>
 +
Insertion of reversed RFP into XOR2, no insertion, only the backbone vector was present.<br>
 +
</li>
 +
<li><a href="">Week 10 (12-18 August)</a><br>
 +
As we faced lot of issues with the reversed RFP and reversed rbs-luxI, we decided to order new oligonucleotide in order to create new reversed fragments as we did during the week 6
 +
PCR to invert RFP and rbs.LuxI with the restriction site ClaI BamHI, and purification.<br>
 +
We tested a wide range of elongation temperatures (60°C-75°C). We got the right fragments for the two biobricks with good size. But on the electrophoresis revelations we got one parasite fragment around 5kb.
 +
<br>
 +
</li>
 +
<li><a href="">Week 11 (19-25 August)</a><br>
 +
We amplified the reversed fragment RFP and rbs luxI with the new oligos. We did not find the solution to avoid the parasite fragment so we used PCR clean-up & gel purification.<br>
 +
Insertion of these fragments into the gate (rbs-luxI into AND2 and RFP into XOR2 and AND2).<br> We did not get better results even with these new fragments.<br><br>
 +
We realized in fact we have a problem with the XOR2 gate. Instead of having only one site cla1 inside the XOR2, we had two. The problem was therefore the restriction with cla1!<br><br>
 +
Extraction And 1 gate from And gate part of Bonnet construction by PCR.<br>
 +
Cloning: (Digestion, Ligation, Transformation , Pre-culture, Miniprep )<br>
 +
Insertion of  And 1 gate extracted by PCR into the plasmid backbone pSB1K3<br>
 +
Assembly of And 1 gate extracted by PCR and rbs RFP term part<br>
 +
Assembly of Xor 1 gate and rbs RFP term parts<br>
 +
<br>
 +
</li>
 +
<li><a href="">Week 12 (26-31 August)</a><br><br>
 +
Creation of another reversed RFP fragment but with bamH1 restriction site on each side of this DNA fragment. With this, we were able to overcome the problem of two cla1 restriction site inside XOR2. We cloned this fragment into XOR2. But it didn’t work.<br>
 +
It seemed that RFP was well inserted into AND2, but after DNA sequencing analysis, we didn’t get the right fragment at the right place.<br>
 +
First verification of cloning parts size by digestion by EcoRI and PstI enzymes:<br>
 +
<br>
 +
o And 1 – pSB1K3 <br>
 +
- pSB1K3 linearized: about 2200 bp.<br>
 +
- And 1 fragments: about 500 bp.<br>
 +
o Xor 1 - rbs RFP term – pSB1K3<br>
 +
- pSB1K3 linearized: about 2200 bp.<br>
 +
- Xor 1 - rbs RFP term fragments: about 1200 bp.<br>
 +
o And 1 - rbs RFP term – pSB1C3<br>
 +
- pSB1C3 linearized: about 2000 bp.<br>
 +
- And 1 - rbs RFP term fragments: about 1200 bp.<br>
 +
<br>
 +
   <img src="https://static.igem.org/mediawiki/2013/6/62/Red_sensor2.png" class="imgcontent" /><br><br>
 +
  <img src="https://static.igem.org/mediawiki/2013/9/99/Red_sensor3.png" class="imgcontent" /><br><br>
 +
=> Cloning parts size is confirmed.<br><br>
 +
• Second verification of cloning parts by digestion:<br>
 +
o Xor  1 -  rbs RFP term digested by EcoRI and BstXI  => 2 fragments: about 1007 bp and 2370 bp .<br>
 +
o And 1 – rbs RFP term digested by EcoRI and BstXI => 2 fragments: about 1012 bp and 2350 bp.<br>
 +
o And 1 – pSB1K3 digested by EcoRI and PsiI => 2 fragments: about 266 bp and 2440 bp.<br><br>
 +
<img src="https://static.igem.org/mediawiki/2013/3/31/Red_sensor4.png" class="imgcontent" /><br><br>
 +
<img src="https://static.igem.org/mediawiki/2013/5/5f/Red_sensor5.png" class="imgcontent" /><br><br>
 +
=>  Cloning parts  are confirmed.<br>
 +
• Third  verification of cloning parts by  sequencing<br>
 +
=>  And 1 – pSB1K3, Xor  1 -  rbs RFP term, And 1 – rbs RFP term constructions are confirmed<br></li>
 +
</ul>
</div>
</div>
 +
</div>
 +
 +
 +
 +
<div class="accordeon">
<div class="accordeon">
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   <div class="infos">
   <div class="infos">
   <ul class="circlearrow">
   <ul class="circlearrow">
-
   <li><a href="">Week 1 (02-08 Sept)</a></li></span><br>
+
   <li><a href="">Week 13 (01-08 Sept)</a></li></span><br>
-
06/09<br>
+
PCR to amplified reversed RFP (BamH1/cla1) et RFP (BamH1/BamH1)<br>
-
Cloning AND2 and XOR2 with RFPinv<br><br>
+
Cloning of reversed RFP inside AND2 and XOR2. The transformation worked well, but on the electrophoresis profile we got only the backbone plasmid with no insert.<br>
-
08/09<br>
+
• Change antibiotic marker of part Xor 1 – rbs RFP term part from Kanamycin to Chloramphenicol<br>
-
Verfication of the cloning, AND2.RFPinv ok<br><br>
+
• Change antibiotic marker of part And 1 part from Kanamycin to Chloramphenicol<br><br>
</li>
</li>
-
  <li><a href="">Week 1 (09-15 Sept)</a></li></span><br>
+
 
-
10/09<br>
+
  <li><a href="">Week 14 (09-15 Sept)</a></li></span><br>
Cloning AND2.RFPinv with PolT7 and XOR2 with RFPinv<br><br>
Cloning AND2.RFPinv with PolT7 and XOR2 with RFPinv<br><br>
-
11/09<br>
 
In fusion to have XOR2 with RFPinv because cloning is not working<br><br>
In fusion to have XOR2 with RFPinv because cloning is not working<br><br>
-
13/09<br>
 
XOR2.RFPinv with in fusion OK<br><br>
XOR2.RFPinv with in fusion OK<br><br>
-
14/09<br>
 
Cloning XOR2.RFPinv and AND2.RFPinv with the good PolT7 (with promoter)<br><br>
Cloning XOR2.RFPinv and AND2.RFPinv with the good PolT7 (with promoter)<br><br>
-
15/09<br>
+
XOR2.RFPinv and AND2.RFPinv with PolT7 ok for characterisation.<br>
-
XOR2.RFPinv and AND2.RFPinv with PolT7 ok for characterisation  
+
In vitro characterization: Xor 1 gate with Bxb1 recombinase expressed from our construction part.<br>
</li>
</li>
-
 
+
 
-
  </div>
+
<li><a href="">Week 15 (16-22 Sept)</a></li></span><br>
 +
In vitro characterization:<br><br>
 +
o Xor 1 and And 1 gates with Bxb1 recombinase expressed from our construction part.<br>
 +
o Xor 2 and And 2 gates with FimE recombinase expressed from our construction part.<br>
 +
<br>
 +
</li>
 +
 
 +
<li><a href="">Week 16 (23-29 Sept)</a></li></span><br>
 +
In vitro characterization:<br>
 +
o Xor 1 and And 1 gates:<br>
 +
With our Bxb1 recombinase expressed from our our construction part.<br>
 +
With Tp901 recombinase expressed from Dual Controller plasmid of Bonnet (KC529324)<br>
 +
With Tp901 and Bxb1 recombinases expressed from Dual Controller plasmid of Bonnet (KC529324)<br>
 +
o      Xor 1 and And 1 gates switched by Bxb 1 :<br>
 +
With Tp901 recombinase expressed from Dual Controller plasmid of Bonnet (KC529324)<br>
 +
o      Xor 2 and And 2 gates:<br>
 +
With FimE recombinase expressed from our construction part.<br>
 +
With FimE recombinase expressed from our construction part and PhiC31 recombinase expressed from Suiti construction part.<br>
 +
o Xor 2 gate switched by FimE:<br>
 +
With PhiC31 recombinase expressed from Suiti construction part.<br>
 +
</li>
 +
</ul>
</div>
</div>
 +
</div>
 +
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<p class="texte">  
<p class="texte">  
<img src="https://static.igem.org/mediawiki/2013/3/3a/Back_arrow_-_14px.png"class="imgcontent2" /><a href="https://2013.igem.org/Team:INSA_Toulouse/contenu/lab_practice/notebook/calendar/wet_lab">Back to Wet Lab</a></p>
<img src="https://static.igem.org/mediawiki/2013/3/3a/Back_arrow_-_14px.png"class="imgcontent2" /><a href="https://2013.igem.org/Team:INSA_Toulouse/contenu/lab_practice/notebook/calendar/wet_lab">Back to Wet Lab</a></p>
 +
 +
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 +
</div>
</div>

Latest revision as of 02:19, 5 October 2013

logo


Calendar

Logic Gates

July 2013

  • Week 4 (1-7 July)
    04/07
    Summary of all the work we have to do for the logic gates. These are the necessary genes we needed to cloned into the logic gates.
    Fro And1: rbs-luxI and rbs-Ci-ter
    For Xor1: rbs FimE ter
    For And2: reversed rbs luxI
    For Xor2: reversed rbs-RFP-ter

  • Week 6 (15-21 July)
    Amplification of fimE recombinase (rbs+fimE) from the Michigan Team.
    Minipreps, and electrophoresis checking-> good amplification.

  • Week 7 (22-28 July)
    Problem with AND1, the synthesis is not correct. We cannot go on with this gate. We planned order a new synthesis.
    Amplification of a new rbs-luxI (BBa_K516011). We realized that the first rbs –luxI we amplified was not the good one (wrong size).
    Cloning of rbs+fimE with a terminator, wrong electrophoresis profile.
    Cloning of rbs-luxI with rbs-CI-ter. This cloning step was successful.
    Transfer of xor2 synthesis from puc54 to pSB1C3. We did not get xor2 inside pSB1C3, but only the backbone vector.
    Insertion of reversed RFP inside AND2 (with cla1/bamH1). Electrophoresis profiles were not correct, so the insertion was not successful. It was probably a problem of restriction time.

August 2013

  • Week 8 (29-04 August)
    Cloning of rbs+fimE with a terminator. This time we succeeded.
    Amplification of the fragment rbs luxI-rbs-CI-ter for the AND1 gate.
    Insertion of rbs-FImE-ter inside the Xor1 gate. We made restriction controls with different enzymes (stu1,hindIII), but the results were not fruitful.
    We tried again to introduce RFP inside AND2, still not working.
    We succeeded to transfer Xor2 inside pSB1C3.
  • Week 9 (05-11 August)
    Still lot of problems to insert reversed RFP inside AND2. The transformation does not work. We needed to find a solution (strataclone? Infusion?...).
    Insertion of reversed rbs luxi inside AND2. Same problem as for AND2-RFP.
    Cloning of rbs-fimE-ter into Xor1. It did not work because of a ligation problem.
    Insertion of reversed RFP into XOR2, no insertion, only the backbone vector was present.
  • Week 10 (12-18 August)
    As we faced lot of issues with the reversed RFP and reversed rbs-luxI, we decided to order new oligonucleotide in order to create new reversed fragments as we did during the week 6 PCR to invert RFP and rbs.LuxI with the restriction site ClaI BamHI, and purification.
    We tested a wide range of elongation temperatures (60°C-75°C). We got the right fragments for the two biobricks with good size. But on the electrophoresis revelations we got one parasite fragment around 5kb.
  • Week 11 (19-25 August)
    We amplified the reversed fragment RFP and rbs luxI with the new oligos. We did not find the solution to avoid the parasite fragment so we used PCR clean-up & gel purification.
    Insertion of these fragments into the gate (rbs-luxI into AND2 and RFP into XOR2 and AND2).
    We did not get better results even with these new fragments.

    We realized in fact we have a problem with the XOR2 gate. Instead of having only one site cla1 inside the XOR2, we had two. The problem was therefore the restriction with cla1!

    Extraction And 1 gate from And gate part of Bonnet construction by PCR.
    Cloning: (Digestion, Ligation, Transformation , Pre-culture, Miniprep )
    Insertion of And 1 gate extracted by PCR into the plasmid backbone pSB1K3
    Assembly of And 1 gate extracted by PCR and rbs RFP term part
    Assembly of Xor 1 gate and rbs RFP term parts

  • Week 12 (26-31 August)

    Creation of another reversed RFP fragment but with bamH1 restriction site on each side of this DNA fragment. With this, we were able to overcome the problem of two cla1 restriction site inside XOR2. We cloned this fragment into XOR2. But it didn’t work.
    It seemed that RFP was well inserted into AND2, but after DNA sequencing analysis, we didn’t get the right fragment at the right place.
    First verification of cloning parts size by digestion by EcoRI and PstI enzymes:

    o And 1 – pSB1K3
    - pSB1K3 linearized: about 2200 bp.
    - And 1 fragments: about 500 bp.
    o Xor 1 - rbs RFP term – pSB1K3
    - pSB1K3 linearized: about 2200 bp.
    - Xor 1 - rbs RFP term fragments: about 1200 bp.
    o And 1 - rbs RFP term – pSB1C3
    - pSB1C3 linearized: about 2000 bp.
    - And 1 - rbs RFP term fragments: about 1200 bp.





    => Cloning parts size is confirmed.

    • Second verification of cloning parts by digestion:
    o Xor 1 - rbs RFP term digested by EcoRI and BstXI => 2 fragments: about 1007 bp and 2370 bp .
    o And 1 – rbs RFP term digested by EcoRI and BstXI => 2 fragments: about 1012 bp and 2350 bp.
    o And 1 – pSB1K3 digested by EcoRI and PsiI => 2 fragments: about 266 bp and 2440 bp.





    => Cloning parts are confirmed.
    • Third verification of cloning parts by sequencing
    => And 1 – pSB1K3, Xor 1 - rbs RFP term, And 1 – rbs RFP term constructions are confirmed

September 2013

  • Week 13 (01-08 Sept)

    • PCR to amplified reversed RFP (BamH1/cla1) et RFP (BamH1/BamH1)
    Cloning of reversed RFP inside AND2 and XOR2. The transformation worked well, but on the electrophoresis profile we got only the backbone plasmid with no insert.
    • Change antibiotic marker of part Xor 1 – rbs RFP term part from Kanamycin to Chloramphenicol
    • Change antibiotic marker of part And 1 part from Kanamycin to Chloramphenicol

  • Week 14 (09-15 Sept)

    • Cloning AND2.RFPinv with PolT7 and XOR2 with RFPinv

    In fusion to have XOR2 with RFPinv because cloning is not working

    XOR2.RFPinv with in fusion OK

    Cloning XOR2.RFPinv and AND2.RFPinv with the good PolT7 (with promoter)

    XOR2.RFPinv and AND2.RFPinv with PolT7 ok for characterisation.
    In vitro characterization: Xor 1 gate with Bxb1 recombinase expressed from our construction part.
  • Week 15 (16-22 Sept)

    • In vitro characterization:

    o Xor 1 and And 1 gates with Bxb1 recombinase expressed from our construction part.
    o Xor 2 and And 2 gates with FimE recombinase expressed from our construction part.

  • Week 16 (23-29 Sept)

    • In vitro characterization:
    o Xor 1 and And 1 gates:
    With our Bxb1 recombinase expressed from our our construction part.
    With Tp901 recombinase expressed from Dual Controller plasmid of Bonnet (KC529324)
    With Tp901 and Bxb1 recombinases expressed from Dual Controller plasmid of Bonnet (KC529324)
    o Xor 1 and And 1 gates switched by Bxb 1 :
    With Tp901 recombinase expressed from Dual Controller plasmid of Bonnet (KC529324)
    o Xor 2 and And 2 gates:
    With FimE recombinase expressed from our construction part.
    With FimE recombinase expressed from our construction part and PhiC31 recombinase expressed from Suiti construction part.
    o Xor 2 gate switched by FimE:
    With PhiC31 recombinase expressed from Suiti construction part.

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