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Team:Bielefeld-CeBiTec/Notebook/Journal/CO2-fixation/Aug
From 2014.igem.org
(Difference between revisions)
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</ul> | </ul> | ||
| + | → Sequencing of the construct was not successful. We got the wrong sequence so it will be done again. | ||
</ul> <!-- /csoS1-4 --> | </ul> <!-- /csoS1-4 --> | ||
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<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PurificationPromega" target="_blank">Plasmid isolation</a> of pSB1C3_can_csoS1-4</li> | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PurificationPromega" target="_blank">Plasmid isolation</a> of pSB1C3_can_csoS1-4</li> | ||
</ul> | </ul> | ||
| + | → After we got the sequencing results of pSB1C3_can we found out that we have some mutations so this construct has to be made again with the right sequence of <i>can</i>. | ||
</ul> <!-- /csoS1-4 and can --> | </ul> <!-- /csoS1-4 and can --> | ||
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<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PurificationPromega" target="_blank">Plasmid isolation</a> of <i>glpX</i></li> | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PurificationPromega" target="_blank">Plasmid isolation</a> of <i>glpX</i></li> | ||
</ul> | </ul> | ||
| + | → Sequencing of the construct was not successful. All samples showed the sequence of CFP from the backbone. We will start again, this time with pSB1C3_RFP for the backbone. | ||
</ul> <!-- /glpX --> | </ul> <!-- /glpX --> | ||
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<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PurificationPromega" target="_blank">Plasmid isolation</a> of p<sub>tac</sub>_prkA_Hneap and p<sub>tac</sub>_prkA_SELAN</li> | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PurificationPromega" target="_blank">Plasmid isolation</a> of p<sub>tac</sub>_prkA_Hneap and p<sub>tac</sub>_prkA_SELAN</li> | ||
</ul> | </ul> | ||
| + | → Because of the mutations in <i>Selan</i> we cannot use this construct. Also the restriction digestion of pSB1C3_p<sub>tac</sub>_prkA_Hneap was not successful. | ||
</ul> <!-- /RuBisCO --> | </ul> <!-- /RuBisCO --> | ||
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</ul> | </ul> | ||
</ul> | </ul> | ||
| + | → After we got the sequencing results of pSB1C3_can we found out that we have some mutations so this construct has to be made again with the right sequence of can. | ||
</ul><!-- can_csoS1-4 and csoS1D --> | </ul><!-- can_csoS1-4 and csoS1D --> | ||
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</ul> <!-- gesamte Liste --> | </ul> <!-- gesamte Liste --> | ||
</div> | </div> | ||
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<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#Gibson" target="_blank">Gibson Assembly</a> with <i>glpX_1, glpX_2</i> and pSB1C3</li> | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#Gibson" target="_blank">Gibson Assembly</a> with <i>glpX_1, glpX_2</i> and pSB1C3</li> | ||
<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#Transformationviaelectroporation" target="_blank">Transformation</a> with electrocompotetent cells</li> | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#Transformationviaelectroporation" target="_blank">Transformation</a> with electrocompotetent cells</li> | ||
| - | + | <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#VF-Primer" target="_blank">VF-Primer</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#VR-Primer" target="_blank">VR-Primer</a>) | ||
| + | </li> | ||
| + | <ul> | ||
| + | <li>Annealing temperature: 55 °C</li> | ||
| + | <li>Bands as expected (~1300 bp)</li> | ||
| + | </ul> | ||
| + | </ul> | ||
| + | <ul> | ||
| + | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PurificationPromega" target="_blank">Plasmid isolation</a> of pSB1C3_glpX</li> | ||
| + | </ul> | ||
| + | |||
</ul> | </ul> | ||
| + | → Sequencing not successful. It was a sequence of RFP. We will start again, this time with pSB1K3_RFP with an ampicillin resistance for the backbone. | ||
</ul> | </ul> | ||
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</ul> | </ul> | ||
</ul> | </ul> | ||
| + | → Sequencing not successful again. | ||
</ul> | </ul> | ||
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| - | < | + | <br> |
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| - | + | <ul> | |
| - | + | <li><b><i>can</i> <a href="http://parts.igem.org/Part:BBa_K1465205" target="_blank">(BBa_K1465205)</a></b></li> | |
| - | + | <ul> | |
| - | + | → We made another sequencing but got these five mutations again at the same positions as before. Maybe we got the wrong accession number, so we will further work with our <i>can</i> construct. | |
| - | + | </ul> | |
| - | + | </ul> | |
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<br> | <br> | ||
| - | <li><b><i>csoS1-4</i></b></li> | + | <li><b><i>csoS1-4</i> <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1465206" target="_blank">(BBa_K1465206)</a></b></li> |
<ul> | <ul> | ||
<li>We tried to find correct colonies of the psB1C3_csoS1-4 construct so another part of the carboxysome is complete.</li> | <li>We tried to find correct colonies of the psB1C3_csoS1-4 construct so another part of the carboxysome is complete.</li> | ||
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<br> | <br> | ||
| - | <li><b><i>sRNA:pfkA</i> and T7</b></li> | + | <li><b><i>sRNA:pfkA</i> and T7 <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1465227" target="_blank">(BBa_K1465227)</a></b></li> |
<ul> | <ul> | ||
<li>We tried to assemble the <i>sRNA:pfkA</i> construct and pSB1A2_T7</li> | <li>We tried to assemble the <i>sRNA:pfkA</i> construct and pSB1A2_T7</li> | ||
Revision as of 14:53, 15 October 2014
 |
August |
 |
- Promotors T7, ptac and pTet
- We tried to assemble some inserts with three different promotors to test which one is the best choice.
- Plasmid isolation of ptac, ptac, T7, prkA, Hneap, SELAN, sRNA:pfkA and can
- BioBrick Assembly (Suffix)
- Backbones (digested with SpeI, PstI)
- pSB1A2_T7
- pSB1C3_ptac
- pSB1K3_pTet
- Inserts (digested with XbaI, PstI)
- prkA
- Hneap
- SELAN
- sRNA:pfkA
- Transformation of all constructs with electrocompotetent cells
- Colony PCR of pSB1C3_ptac_prkA, pSB1C3_ptac_Hneap, pSB1C3_ptac_SELAN and pSB1C3_ptac_sRNA:pfkA (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~2500 bp (ptac_prkA), ~3200 bp (ptac_Hneap) ~3200 bp (ptac_SELAN) ~1700 bp (ptac_sRNA:pfkA))
- Colony PCR of pSB1A2_T7_prkA, pSB1A2_T7_Hneap, pSB1A2_T7_SELAN and pSB1A2_T7_sRNA:pfkA (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands not as expected → Showed in all cases a band 400 bp over the expected value. We tried to extract and transform the promotor from another distribution plate (2013)
- Colony PCR of pSB1K3_pTet_prkA, pSB1K3_Tet_Hneap, pSB1K3_Tet_SELAN and pSB1K3_Tet_sRNA:pfkA (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands not as expected → We tried it again.
- Colony PCR of pSB1A2_T7 from the 2013 distribution plate (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~300 bp)
- Plasmid isolation of pSB1C3_ptac_prkA, pSB1C3_ptac_Hneap, pSB1C3_ptac_SELAN, pSB1C3_ptac_sRNA_pfkA and pSB1A2_T7
- csoS1-4 (shell proteins csoS4AB and csoS1CAB)
- We used the amplified products to assemble and transform them to get the shell protein construct.
- Restriction digestion with DpnI
- Gibson Assembly with csoS1-4 and pSB1C3
- Transformation with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~2100 bp)
- Plasmid isolation
- Restriction digestion with SpeI and XbaI
- Bands as expected (~1800 bp and ~2200 bp)
- can and csoS1-4
- We tried to assemble the shell proteins and the carbonic anhydrase for the carboxysome.
- BioBrick Assembly (Suffix)
- Transformation with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~3600 bp)
- Plasmid isolation of pSB1C3_can_csoS1-4
- glpX
- We tried to assemble and transform the glpX parts again.
- Restriction digestion with DpnI
- Gibson Assembly with glpX_1, glpX_2 and pSB1K3
- Transformation with electrocompotetent cells
- Colony PCR on one part of the fragment (fw-pSB1C3-BBa_B0034-SBPase, rv-SBPase-Schnittstelle)
- Annealing temperature: 55 °C
- Bands as expected (~500 bp)
- Plasmid isolation of glpX
- prkA and pHnCBscoS1D
- We tried to amplify prkA again and to assemble it with the plasmid pHnCBcsoS1D.
- Plasmid isolation of DH5α prkA
- PCR amplification on the isolated prkA (prkA_pHn_fwd, prkA_pHn_rev)
- Annealing temperature: 55 °C
- Bands as expected (~1000 bp)
- PCR products were purified out of the gel
- Gibson Assembly with prkA and pHnCBcsoS1D
- RuBisCO
- We tried to assemble both RuBisCO with pSB1C3_ptac_prkA
- BioBrick Assembly (Suffix)
- Backbone (digested with SpeI, PstI)
- ptac_prkA
- Inserts (digested with XbaI, PstI)
- Hneap
- SELAN
- We assembled pSB1C3_ptac_prkA with Hneap respectively SELAN
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- pSB1C3_ptac_prkA_Hneap
- Bands not as expected (too short). → We will try to ligate pSB1C3_ptac_prkA and Hneap again.
- pSB1C3_ptac_prkA_SELAN
- Bands as expected (~4200 bp)
- Plasmid isolation of ptac_prkA_Hneap and ptac_prkA_SELAN
- can_csoS1-4 and csoS1D
- We tried to assemble pSB1C3_can_csoS1-4 and csoS1D and transform the construct.
- BioBrick Assembly Suffix:
- Transformation with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~4300 bp)
Agarose gel from the restriction digestion with SpeI and XbaI. As a Ladder we used GeneRuler™ 1 kb DNA Ladder from Thermo Scientific.
- glpX
- This week we tried to amplify the backbone pSB1C3 for glpX again. We took the pSB1C3_RFP as a template.
- PCR amplification of the pSB1C3_RFP backbone (fw_SBPase_pSB1C3, rv_SBPase_pSB1)
- Annealing temperature: 54 °C
- Bands as expected (~2100 bp)
- PCR products were purified
- Restriction digestion with DpnI
- Gibson Assembly with glpX_1, glpX_2 and pSB1C3
- Transformation with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~1300 bp)
- Plasmid isolation of pSB1C3_glpX
- csoS1-4
- We tried to isolate the right plasmid again.
- Plasmid isolation of pSB1C3_csoS1-4
- Restriction digestion with PstI and EcoRI as a control
- Bands as expected (~2100 bp (backbone) and ~1700 bp (insert))
- can (BBa_K1465205)
-
→ We made another sequencing but got these five mutations again at the same positions as before. Maybe we got the wrong accession number, so we will further work with our can construct.
- pHnCBcsoS1D_prkA
- This week we tried to transform the pHnCBcsoS1D_prkA construct.
- Transformation with electrocompotetent cells
- Colony PCR (Primer1, Primer2)
- Annealing temperature: ...
- Bands (not) as expected (~... bp)
- csoS1-4
- This week we tried to amplify and transform the shell proteins again.
- PCR amplification (fw_pSB1C3_csoS4A, rv_csoS4A_PstI)
- Annealing temperature: 55 °C
- Bands as expected (~180 bp)
- PCR amplification (fw_PstI_csoS4A, rv_SpeI_Intergen)
- Annealing temperature: 55 °C
- Bands as expected (~1200 bp)
- PCR amplification (fw_SpeI_Intergen, rv_csoS1_pSB1C3)
- Annealing temperature: 55 °C
- Bands as expected (~350 bp)
- PCR amplification of the backbone (fw_csoS1_pSB1C3, rv_pSB1C3_csoS4A)
- Annealing temperature: 55 °C
- Bands as expected (~2070 bp)
- All PCR products were purified
- Restriction digestion with DpnI
- Gibson Assembly with csoS1-4 and pSB1C3
- Transformation with electrocompotetent cells
- prkA and pTet
- This week we tried to assemble the pTet promotor with the prkA.
- BioBrick Assembly (Suffix)
- Transformation with electrocompotetent cells → Only a few colonies did grow. Maybe the TetR (repressor) is not strong enough so the prkA is too toxic.
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~2200 bp)
- Hneap and pTet
- This week we tried to assemble the pTet promotor with the Hneap.
- BioBrick Assembly (Suffix)
- Transformation with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~3000 bp)
- sap_2
- This week we tried to bring the synthesized sap_2 construct in the pJet vector with blunt end cloning. We also amplified the backbonefor an assembly.
- Blunt-End cloning of sap_2 in the pJet vector
- Colony PCR (Primer1, Primer2)
- Annealing temperature: ... °C
- Bands as expected (~1500 bp)
- PCR amplification of the backbone (pSB1C3) (pSB1C3_pre_sap_1, pSB1C3_suf_sap2)
- Annealing temperature: 55 °C
- Bands as expected (~2100 bp)
- GFP BioBrick (BBa_E0040)
- This week we tried isolate the green fluorescent protein GFP (pSB1A2_GFP) of the parts distribution 2014.
- Plasmid isolation of pSB1A2_GFP
- Purification vector
- This week we tried to amplify the T7_RBS promotor for the purification vector.
- PCR amplification (Primer1, Primer2)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- sap_2
- We tried to isolate pJet_sap_2 for further experiments.
- Plasmid isolation of pJet_sap_2
- glpX
- We tried to amplify the pSB1K3 backbone for an assembly with glpX.
- PCR amplification of the pSB1C3_RFP backbone (fw_SBPase_pSB1C3, rv_SBPase_pSB1)
- Annealing temperature: 54 °C
- Bands as expected (~2100 bp)
- PCR products were purified
- Restriction digestion with DpnI
- Gibson Assembly with glpX_1, glpX_2 and pSB1K3
- Transformation with electrocompotetent cells
- csoS1-4 (BBa_K1465206)
- We tried to find correct colonies of the psB1C3_csoS1-4 construct so another part of the carboxysome is complete.
- Colony PCR (fw_pSB1C3_csoS4A, rv_csoS1_pSB1C3)
- Annealing temperature: 65 °C
- Bands (not) as expected (~1600 bp)
- Plasmid isolation of pSB1C3_csoS1-4
- Restriction digestion with EcoRI and PstI
- Bands as expected (~2000 bp backbone, ~1800 bp insert)
- sRNA:pfkA and ptac
- We tried to assemble the sRNA:pfkA construct and pSB1C3_ptac
- BioBrick Assembly (Suffix)
- Backbone (digested with SpeI, PstI)
- pSB1C3_ptac
- Insert (digested with XbaI, PstI)
- sRNA:pfkA
- Transformation with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~1700 bp)
- sRNA:pfkA and T7 (BBa_K1465227)
- We tried to assemble the sRNA:pfkA construct and pSB1A2_T7
- BioBrick Assembly (Suffix)
- Backbone (digested with SpeI, PstI)
- pSB1A2_T7
- Insert (digested with XbaI, PstI)
- sRNA:pfkA
- Transformation with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~900 bp)
- Plasmid isolation of pSB1A2_T7_sRNA:pfkA
- GFP
- We tried to amplify GFP for a fusion with the shell proteins.
- PCR amplification (fw-csoS1A-GFP, rv-csoS1B-GFP)
- Annealing temperature: 54 °C
- Bands as expected (~750 bp)
- PCR products were purified out of the gel
- can and csoS1-4
- We tried to assemble can and csoS1-4 for the carboxysome.
- BioBrick Assembly (Prefix)
- Transformation with electrocompotetent cells
