"
Team:Bielefeld-CeBiTec/Notebook/Journal/Isobutanol/Aug
From 2014.igem.org
(Difference between revisions)
| Line 57: | Line 57: | ||
<ul> | <ul> | ||
<li>Annealing temperature: 65 °C</li> | <li>Annealing temperature: 65 °C</li> | ||
| - | <li>Bands not as expected ( | + | <li>Bands not as expected (~ 3450 bp) </li> |
</ul> | </ul> | ||
</ul> | </ul> | ||
| Line 68: | Line 68: | ||
<ul> | <ul> | ||
<li>Annealing temperature: 65 °C</li> | <li>Annealing temperature: 65 °C</li> | ||
| - | <li>Bands not as expected ( | + | <li>Bands not as expected (3450 bp) </li> |
</ul> | </ul> | ||
<ul> | <ul> | ||
| Line 97: | Line 97: | ||
<ul> | <ul> | ||
<li>We used pSB1C3-RFP instead of pSB1C3-CFP as template for backbone amplification</li> | <li>We used pSB1C3-RFP instead of pSB1C3-CFP as template for backbone amplification</li> | ||
| - | <li> | + | <li>Annealing temperature: 54 °C</li> |
| - | <li>Bands as expected ( | + | <li>Bands as expected (~ 2200 bp)</li> |
</ul> | </ul> | ||
<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#RestrictionDigestion" target="_blank">Restriction digestion</a> with <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/KitsAndEnzymes" target="_blank"><i>DpnI</i></a></li> | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#RestrictionDigestion" target="_blank">Restriction digestion</a> with <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/KitsAndEnzymes" target="_blank"><i>DpnI</i></a></li> | ||
| Line 106: | Line 106: | ||
<ul> | <ul> | ||
<li>Annealing temperature: 65 °C</li> | <li>Annealing temperature: 65 °C</li> | ||
| - | <li>Bands not as expected ( | + | <li>Bands not as expected (3450 bp)</li> |
</ul> | </ul> | ||
</ul> | </ul> | ||
| Line 138: | Line 138: | ||
<li>pSB1K3-RFP was used as template for backbone amplification</li> | <li>pSB1K3-RFP was used as template for backbone amplification</li> | ||
<li>Annealing temperature: 53 °C</li> | <li>Annealing temperature: 53 °C</li> | ||
| - | <li>Bands as expected for <br><i>alsS</i>: about | + | <li>Bands as expected for <br><i>alsS</i>: about 1800 bp, <br><i>ilvC</i>: about 1550 bp, <br><i>ilvD</i>: about 1950 bp, <br><i>kivD</i>: about 1700 bp, <br>but not for pSB1K3-RFP</li> |
</ul> | </ul> | ||
<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a></li> with Q5 for pSB1K3-RFP | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a></li> with Q5 for pSB1K3-RFP | ||
| Line 144: | Line 144: | ||
<li>Primer were used as described before</li> | <li>Primer were used as described before</li> | ||
<li>Annealing temperature: 53 °C</li> | <li>Annealing temperature: 53 °C</li> | ||
| - | <li>Bands as expected ( | + | <li>Bands as expected (~ 2200 bp)</li> |
</ul> | </ul> | ||
| Line 157: | Line 157: | ||
<ul> | <ul> | ||
<li>Annealing temperature: 65 °C</li> | <li>Annealing temperature: 65 °C</li> | ||
| - | <li>Bands as expected ( | + | <li>Bands as expected (3600 bp)</li> |
</ul> | </ul> | ||
<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#ColonyPCR" target="_blank">Colony PCR</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#fw_alsS_ilvC" target="_blank">fw_alsS_ilvC</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#rv_ilvD_ilvC" target="_blank">rv_ilvD_ilvC</a>)</li> | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#ColonyPCR" target="_blank">Colony PCR</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#fw_alsS_ilvC" target="_blank">fw_alsS_ilvC</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#rv_ilvD_ilvC" target="_blank">rv_ilvD_ilvC</a>)</li> | ||
<ul> | <ul> | ||
<li>Annealing temperature: 65 °C</li> | <li>Annealing temperature: 65 °C</li> | ||
| - | <li>Bands as expected ( | + | <li>Bands as expected (3300 bp)</li> |
</ul> | </ul> | ||
<li>Liquid cultures for a restriction digest were prepared.</li> | <li>Liquid cultures for a restriction digest were prepared.</li> | ||
| Line 168: | Line 168: | ||
<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#RestrictionDigestion" target="_blank">Restriction digestion</a> with <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/KitsAndEnzymes#RestrictionDigestion" target="_blank"><i>NotI</i></a></li> | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#RestrictionDigestion" target="_blank">Restriction digestion</a> with <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/KitsAndEnzymes#RestrictionDigestion" target="_blank"><i>NotI</i></a></li> | ||
<ul> | <ul> | ||
| - | <li>Bands as expected (backbone: | + | <li>Bands as expected (backbone:~ 2200 bp and insert: 7000 bp)</li> |
</ul> | </ul> | ||
</ul> | </ul> | ||
| Line 200: | Line 200: | ||
<ul> | <ul> | ||
<li>Annealing temperature: 54 °C</li> | <li>Annealing temperature: 54 °C</li> | ||
| - | <li>Bands as expected (~ | + | <li>Bands as expected (~1200 bp for the <i>adhA</i> and 2200 bp for the Backbone)</li> |
</ul> | </ul> | ||
| Line 226: | Line 226: | ||
<ul> | <ul> | ||
<li>Annealing temperature: 65°C</li> | <li>Annealing temperature: 65°C</li> | ||
| - | <li>Bands as expected (~ | + | <li>Bands as expected (~ 1200 bp)</li> |
</ul> | </ul> | ||
</ul> | </ul> | ||
| Line 263: | Line 263: | ||
<ul> | <ul> | ||
<li>Annealing temperature: 65 °C</li> | <li>Annealing temperature: 65 °C</li> | ||
| - | <li>Bands as expected (~ | + | <li>Bands as expected (~ 1800 bp)</li> |
</ul> | </ul> | ||
</ul> | </ul> | ||
Revision as of 16:37, 16 October 2014
 |
August |
 |
- psB1C3-alsS-ilvC-ilvD
- This week we wanted to identify positive colonies.
- Colony PCR (fw_alsS_ilvC, rv_kivD_ilvD)
- Annealing temperature: 65 °C
- Bands not as expected (~ 3450 bp)
- New try of the combination of the four CDS's with the pSB1C3 backbone.
- Gibson Assembly with kivD, alsS, ilvC and ilvD and pSB1C3
- Restriction digestion with DpnI
- Transformation with electrocompetent and chemocompetent cells
- Colony PCR (fw_alsS_ilvC, rv_kivD_ilvD)
- Annealing temperature: 65 °C
- Bands not as expected (3450 bp)
- alsS, ilvC, ilvD, kivD and backbone of pSB1C3
- We started again back by zero to solve our problems.
- PCR amplification (as described before)
- We used pSB1C3-RFP instead of pSB1C3-CFP as template for backbone amplification
- Annealing temperature: 54 °C
- Bands as expected (~ 2200 bp)
- Restriction digestion with DpnI
- Gibson Assembly with alsS, ilvC, ilvD and kivD on pSB1C3
- Transformation with electrocompotetent cells
- Colony PCR (fw_alsS_ilvC, rv_kivD_ilvD)
- Annealing temperature: 65 °C
- Bands not as expected (3450 bp)
- alsS, ilvC, ilvD, kivD and backbone pSB1K3
- This week we tried to begin from zero again with optimized conditions and new competent cells.
Therefor we prepared new plasmids from alsS, ilvC, ilvD, kivD and the backbone pSB1K3-RFP - PCR amplification
- Primer were used as described before
- pSB1K3-RFP was used as template for backbone amplification
- Annealing temperature: 53 °C
- Bands as expected for
alsS: about 1800 bp,
ilvC: about 1550 bp,
ilvD: about 1950 bp,
kivD: about 1700 bp,
but not for pSB1K3-RFP - PCR amplification with Q5 for pSB1K3-RFP
- Primer were used as described before
- Annealing temperature: 53 °C
- Bands as expected (~ 2200 bp)
- PCR products were purified
- Gibson Assembly with kivD, alsS, ilvC and ilvD on pSB1K3
- Restriction digestion with DpnI
- Aberation from protocol: Incubation for about 10 hours.
- Transformation with electrocompotetent cells
- Colony PCR (fw_ilvC_ilvD, rv_pSB1C3_kivD)
- Annealing temperature: 65 °C
- Bands as expected (3600 bp)
- Colony PCR (fw_alsS_ilvC, rv_ilvD_ilvC)
- Annealing temperature: 65 °C
- Bands as expected (3300 bp)
- Liquid cultures for a restriction digest were prepared.
- Plasmid isolation of pSB1K3-alsS-ilvC-ilvD-kivD
- Restriction digestion with NotI
- Bands as expected (backbone:~ 2200 bp and insert: 7000 bp)
- adhA
- This week the Lactococcus lactis arrived. We tried to amplify it's adhA.
- PCR amplification of the adhA (rev-pBS1C3-adhA, fw-pSB1C3_adhA) and the Backbone out of psB1K3-RFP (rev-adhA_pSB1C3, fw-adhA-pSB1C3)
- Annealing temperature: 54 °C
- Bands as expected (~1200 bp for the adhA and 2200 bp for the Backbone)
- PCR products were extracted out of the gel and purified.
- Gibson Assembly with adhA and pSB1K3
- Transformation with chemocompetent cells
- Colony PCR (rev-pBS1C3-adhArev-pBS1C3-adhA, fw-pSB1C3_adhA)
- Annealing temperature: 65°C
- Bands as expected (~ 1200 bp)
-
PCR:
- BioBrick Assembly:
- BioBrick Assembly (Suffix)
- Transformation with electrocompotetent cells
- Colony PCR (fw-pSB1C3-alsS, rv-ilvC-alsS)
- Annealing temperature: 65 °C
- Bands as expected (~ 1800 bp)
- Liquid cultures for a restriction digest were prepared.
