Difference between revisions of "Team:Paris Bettencourt/Notebook/VitaminB2"

Line 270: Line 270:
 
   <tr>
 
   <tr>
 
     <td><i>From left to right:<br/>
 
     <td><i>From left to right:<br/>
−
<i>1kb Ladder, RibA, D, E, T25 and T48 amplified at 52°C <br/>
+
      <i>1kb Ladder, RibA, D, E, T25 and T48 amplified at 52°C <br/>
−
and Rib A, D, E, T25 and T48 amplified at 64°C<i>
+
      and Rib A, D, E, T25 and T48 amplified at 64°C<i>
 
     </td>
 
     </td>
 
   </tr>
 
   </tr>
 
</table>
 
</table>
 +
 +
<br/>
 +
The bands are not really specific and seems to be smeared over the gel.<br/>
 +
However, we can see that the extremity of each band correspond approximatively <br/>
 +
to the expected size of our parts, except RibD amplified at 64°C for which no band has been detected.
 +
 +
We purified our PCR product according to the previously used protocol,<br/>
 +
and then measure the DNA concentration using a Nanodrop.
 +
 +
<table style="width:25%">
 +
  <tr>
 +
    <td><b>Part Name </b></td>
 +
    <td><b>PCR product amplified at 52°C concentration (ng/μL)</b></td>
 +
    <td><b>PCR product amplified at 64°C concentration (ng/μL) </b></td>
 +
  </tr>
 +
 +
  <tr>
 +
    <td>RibA</td>
 +
    <td>54.3</td>
 +
    <td>132.7</td>
 +
  </tr>
 +
 +
  <tr>
 +
    <td>RibD</td>
 +
    <td>50.5</td>
 +
    <td>140.2</td>
 +
  </tr>
 +
 +
  <tr>
 +
    <td>RibE</td>
 +
    <td>67.1</td>
 +
    <td>78.2</td>
 +
  </tr>
 +
 +
  <tr>
 +
    <td>RibT25</td>
 +
    <td>63.6</td>
 +
    <td>136.0</td>
 +
  </tr>
 +
 +
  <tr>
 +
    <td>RibT48</td>
 +
    <td>61.2</td>
 +
    <td>143.1</td>
 +
  </tr>
 +
</table>
 +
 +
<br/><b>16/07</b><br/>
 +
Annealing of o15.011 (TCGACCATGCTTGTCTTCGAAGACTTGGGGGAT) and o15.012 (CTAGATCCCCCAAGTCTTCGAAGACAAGCATGG) using the following protocol:
 +
<br/>
 +
<table>
 +
  <tr>
 +
    <td>Annealing Protocol
 +
<ul>
 +
 +
<li>Phosphorylation of the oligos
 +
<ul>
 +
  <li>        5.6μL DNAse/RNAse free water
 +
  <li> 6.0μL  o15.011 (10µM)
 +
  <li> 6.0μL  o15.012 (10µM)
 +
  <li> 2.0μL  10X T4 DNA ligase buffer
 +
  <li> 0.4μL  T4 PolyNucleotide Kinase
 +
Total:  20μL
 +
 +
</ul>
 +
<br/>
 +
 +
  <li>incube 30min at 37°C
 +
  <li>add 1μL of 1M NaCl
 +
  <li>incube 5min at 95°C
 +
  <li>let the mix cool down
 +
  <li>use 2μL of the mix as a 10X solution
 +
</ul>
 +
    </tr>
 +
  </td>
 +
</table>
 +
 +
<br/>
 +
Inoculate LB + erythromycin (150ng/μL) with g15.21 containing pKV6.<br/>
 +
Inoculate M17 + erythromycin (10ng/μL) with g15.13 containing pSIP411.

Revision as of 16:07, 10 August 2015

13/07
  • Received gBlocks RibA, RibD, RibE, RibT25 and RibT48 and amplification oligos from IDT.
    • Dilution in water and PCR amplification, using the following protocol:
    • 1 μL gBlock (0.1 to 1ng)
    • 1 μL forward primer (10 μM)
    • 1 μL reverse primer (10 μM)
    • 22 μL DNAse/RNAse free water
    • 25 μL LifeTech MasterMix (2X)

    RibA + o15.001 (GCGCCCGAAGACTTATGCAG) + o15.002(GGCCCCGCGCATATGAAG)
    RibD + o15.003(CGCTATAGAAGACTTGAGAAGATCTG) + o15.004(GCGCGGCACCACATATGAAG)
    RibE + o15.005(CGGCTATAGAAGACTTGCGC) + o15.006(CGCGCCGGCATATGAAGA)
    RibT25 + o15.007(CCGCGTATAGAAGACTGCTAGA) + o15.008(CAGCAGCATATGAAGACAACCC)
    RibT48 + o15.009(GCGGTATAGAAGACTGCTAGAGA) + o15.010(CAGCAGCATATGAAGACAACCC)

    For each PCR reaction, a negative control without matrix DNA was prepared.


    12 cycles amplification, using the following parameters:
    time (min) temperature (°C) function
    3:00 98 melting
    0:30 98 melting
    0:30 52 annealing
    1:00 72 extension
    10:00 72 extension
    forever 12 storage
    PCR purification using QIAGEN kit
      PCR purification protocol
    • Add 5 volumes of resuspension buffer to 1 volume of PCR product in an 1.5mL microcentrifuge tube, mix by pipetting up and down
    • Transfer in a centrifugation column
    • Centrifuge 1 min at 14000 rpm
    • Throw the filtration product
    • Add 700μL of washing solution
    • Centrifuge 1 min at 14000 rpm
    • Throw the filtration product
    • Add 500μL of washing solution
    • Centrifuge 1 min at 14000 rpm
    • Throw the filtration product
    • Centrifuge 1 min at 14000 rpm
    • Throw the filtration product
    • Put the column in a sterile 1.5mL microcentrifuge tube
    • Add 45μL of DNAse/RNAse free water on the membrane
    • Wait 2 minutes
    • Centrifuge 2min at 10000rpm
    • Discard the column, DNA is saved in water

Concentrations measured with a Nanodrop:
[PCR product with gBlock] (ng/μL) [PCR product without gBlock] (ng/μL)
RibA 3.5 3.4
RibD 6.4 3.3
RibE 5.0 3.7
RibT25 3.5 3.8
RibT48 8.7 3.3
Almost no difference between the PCR and their corresponding negative control.
It could be the fallout of the limited number of cycles. (We only used 12 cycles, as advised by IDT)
NEB Tm calculator gave really different Tm for the PCR primers than Geneious and IDT.
We decided to launch two PCR, both with 35 cycles, but with two different annealing
temperature: 52 and 64°C.

14/07
Launched the two different PCR with different Tm.

PCR with high annealing temperature, 35 cycles:
time (min) temperature (°C) function
3:00 98 melting
0:30 98 melting
0:30 64 annealing
1:00 72 extension
10:00 72 extension
forever 12 storage

PCR with low annealing temperature, 35 cycles:
time (min) temperature (°C) function
3:00 98 melting
0:30 98 melting
0:30 64 annealing
1:00 72 extension
10:00 72 extension
forever 12 storage

After PCR, we ran the PCR products on a TAE - 1% agarose gel (100V, 20min) to check
if the amplification product correspond to the expected size of the gBlocks.
From left to right:
1kb Ladder, RibA, D, E, T25 and T48 amplified at 52°C
and Rib A, D, E, T25 and T48 amplified at 64°C

The bands are not really specific and seems to be smeared over the gel.
However, we can see that the extremity of each band correspond approximatively
to the expected size of our parts, except RibD amplified at 64°C for which no band has been detected. We purified our PCR product according to the previously used protocol,
and then measure the DNA concentration using a Nanodrop.
Part Name PCR product amplified at 52°C concentration (ng/μL) PCR product amplified at 64°C concentration (ng/μL)
RibA 54.3 132.7
RibD 50.5 140.2
RibE 67.1 78.2
RibT25 63.6 136.0
RibT48 61.2 143.1

16/07
Annealing of o15.011 (TCGACCATGCTTGTCTTCGAAGACTTGGGGGAT) and o15.012 (CTAGATCCCCCAAGTCTTCGAAGACAAGCATGG) using the following protocol:
Annealing Protocol
  • Phosphorylation of the oligos
    • 5.6μL DNAse/RNAse free water
    • 6.0μL o15.011 (10µM)
    • 6.0μL o15.012 (10µM)
    • 2.0μL 10X T4 DNA ligase buffer
    • 0.4μL T4 PolyNucleotide Kinase Total: 20μL

  • incube 30min at 37°C
  • add 1μL of 1M NaCl
  • incube 5min at 95°C
  • let the mix cool down
  • use 2μL of the mix as a 10X solution

Inoculate LB + erythromycin (150ng/μL) with g15.21 containing pKV6.
Inoculate M17 + erythromycin (10ng/μL) with g15.13 containing pSIP411.