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Team:Bielefeld-CeBiTec/Notebook/Journal/rMFC/Aug
From 2014.igem.org
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<a href="https://static.igem.org/mediawiki/2014/3/33/Bielefeld_CeBiTec_2014-09-24_csoS1-4_cPCR_08_22.png" target="_blank"><img src="https://static.igem.org/mediawiki/2014/3/37/Bielefeld-CeBiTec_2014-10-14_PR6K_PCR_08_19.png" height="230px"></a><br><font size="1">Agarose gel from PCR amplification of pR6K. As a Ladder we used <a href="http://www.thermoscientificbio.com/nucleic-acid-electrophoresis/generuler-1-kb-dna-ladder-ready-to-use-250-to-10000-bp">GeneRuler™ 1 kb DNA Ladder from Thermo Scientific</a>. </font> | <a href="https://static.igem.org/mediawiki/2014/3/33/Bielefeld_CeBiTec_2014-09-24_csoS1-4_cPCR_08_22.png" target="_blank"><img src="https://static.igem.org/mediawiki/2014/3/37/Bielefeld-CeBiTec_2014-10-14_PR6K_PCR_08_19.png" height="230px"></a><br><font size="1">Agarose gel from PCR amplification of pR6K. As a Ladder we used <a href="http://www.thermoscientificbio.com/nucleic-acid-electrophoresis/generuler-1-kb-dna-ladder-ready-to-use-250-to-10000-bp">GeneRuler™ 1 kb DNA Ladder from Thermo Scientific</a>. </font> | ||
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<li>PCR product was <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#DNAPurificationbyCentrifugation" target="_blank">purified</a> out of the gel</li> | <li>PCR product was <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#DNAPurificationbyCentrifugation" target="_blank">purified</a> out of the gel</li> | ||
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| - | + | <div class="element" style="height:350px; width:120px; text-align:center"> | |
| + | <a href="https://static.igem.org/mediawiki/2014/3/33/Bielefeld_CeBiTec_2014-09-24_csoS1-4_cPCR_08_22.png" target="_blank"><img src="https://static.igem.org/mediawiki/2014/b/b3/Bielefeld-CeBiTec_2014-10-14_Knockout_deletion-cassette_PCR_08_09.png" height="230px"></a><br><font size="1">Agarose gel from PCR amplification of <i>pR6K</i> and <i>oprF</i>. As a Ladder we used <a href="http://www.thermoscientificbio.com/nucleic-acid-electrophoresis/generuler-1-kb-dna-ladder-ready-to-use-250-to-10000-bp">GeneRuler™ 1 kb DNA Ladder from Thermo Scientific</a>. </font> | ||
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</ul> | </ul> | ||
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Revision as of 21:47, 15 October 2014
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August |
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- Deletion of dcuB and integration of oprF into chromosome
- This week we amplified and purified the pR6K-cassette again in order to connect it to oprF
- pR6K
- PCR amplification of pR6K-cassette
- Plasmid isolation of pR6K-cassette and Purification out of the gel
Agarose gel from PCR amplification of pR6K. As a Ladder we used GeneRuler™ 1 kb DNA Ladder from Thermo Scientific.
- PCR amplification to connect the pR6K-cassette and oprF
- Bands as expected (~3300 bp)
- PCR product was purified out of the gel
Agarose gel from PCR amplification of pR6K and oprF. As a Ladder we used GeneRuler™ 1 kb DNA Ladder from Thermo Scientific.
- Fum A
- This week we amplified FumA and assembled it with the T7-Promotor as well als several Anderson-Promotor using Biobrick-Assembly
- PCR amplification of FumA (FumA_fwd, FumA_rev)
- Annealing temperature: 55°C
- Bands as expected (~1843 bp)
- Gibson Assembly with FumA and pSB1C3
- Transformation with electrocompotetent cells
- Plasmid isolation of Fum A
- BioBrick Assembly (Suffix)
- Transformation of pSB1C3_T7_Fum A with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~2130 bp)
- BioBrick Assembly (Suffix)
- Deletion of dcuB and integration of oprF into chromosome
- This week we checked our first colonies to verify the deletion of dcuB
- pR6K
- The pR6K-cassette for the dcuB deletion was purified out of the gel
- Transformation of pR6K-cassette for the deletion of dcuB with electrocompotetent cells
- pRedET
- Transformation of RedET plasmid with electrocompotetent cells
- dcuB
- Colony PCR to verify the deletion of dcuB (dcuB_del_kon1, dcuB_del_kon2)
- Annealing temperature: 55 °C
- Bands not as expected (~2390 bp)
- Fum A
- This week we assembled FumA with different promotor
- Transformation of
- BBa_J23101_FumA
- BBa_J23102_ Fum A
- BBa_J23104_FumA
- pSB1A2_T7 with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Band as expected (~2200 bp)
- Plasmid isolation of BBa_J23102_ Fum A
- Sequencing of
- BBa_J23101_FumA
- BBa_J23102_FumA
- BBa_J23104_FumA
- pSB1A2_T7_FumA showed different mutations
- Fum BCD
- This week wie amplified FumBCD and its backbone
- PCR amplification of Fum BCD-backbone (pSB1C3_pre_Fum_BCD , pSB1C3_pre_Fum_BCD)
- Annealing temperature: 55 °C
- Bands as expected (2070 bp)
- The Fum BCD backbone was purified out of the gel
- PCR amplification of Fum BCD (Fum_BCD_fwd , Fum_BCD_rev)
- Annealing temperature: 55 °C
- Bands not as expected (1579 bp)
- ccm
- This week we amplified the ccm-cassette and its backbone
- PCR amplification of the ccm-backbone (pSB1C3_suf_ccm, pSB1C3_pre_ccm)
- Annealing temperature: 65 °C
- Bands as expected (~2070 bp) but slightly visible because of inappropriate annealing temperature
- PCR amplification was repeated with an annealing temperature of 55 °C
- Both PCR products were purified out of the gel
- PCR amplification of ccm-cassette using a gradient (ccm_fwd, ccm_rev)
- Annealing temperature: 61 °C appeared as the optimum
- Bands as expected (~6281 bp)
- PCR amplification of ccm-cassette (ccm_fwd, ccm_rev)
- Annealing temperature: 61 °C
- Bands as expected (~6281 bp)
- PCR product was purified
- GSU 3274
- This week we amplified the GSU 3274 cytochrome and its backbone
- PCR amplification of GSU 3274-backbone (pSB1C3_pre_pccH, pSB1C3_suf_pccH)
- Annealing temperature: 65 °C
- Bands not as expected (~2070 bp) because of inappropriate annealing temperature
- PCR amplification was repeated with an annealing temperature of 55 °C
- Bands as expected (~2070 bp)
- PCR amplification of GSU 3274 using a gradient (pccH_fwd, pccH_rev)
- Annealing temperature: 55 °C appeared as the optimum
- Bands as expected (~453 bp)
- PCR amplification of GSU 3274 (pccH_fwd, pccH_rev)
- Annealing temperature: 55 °C
- Bands as expected (~453 bp)
- genomic DNA of G. sulfurreducens as well as the PCR product of the gradient-PCR was used as template
- PCR product was purified
Agarose gel from PCR amplification of ccm-cassette. As a Ladder we used GeneRuler™ 1 kb DNA Ladder from Thermo Scientific.
Agarose gel from PCR amplification of pccH. As a Ladder we used GeneRuler™ 1 kb DNA Ladder from Thermo Scientific.
- Deletion of dcuB and integration of oprF into chromosome
- This week we contninued to test colonies for the verification of the deletion if dcuB
- Connection of pR6K-cassette and oprF
- PCR amplification to connect the pR6K-cassette and oprF
- Bands as expected (~3300 bp)
- PCR product was purified out of the gel
- Colony PCR to verify the deletion of dcuB (dcuB_del_kon1, dcuB_del_kon2)
- Annealing temperature: 55 °C
- Bands not as expected (~4046 bp)
- PCR amplification to connect the pR6K-cassette and oprF
- Connection of pR6K-cassette and oprF
- Fum A
- This week wie tested some colonies for FumA
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (1843 bp)
- frd (E. coli)
- This week we amplified and transformed frd (E. coli)
- PCR amplification (T7_frd_Ec_fwd, T7_frd_Ec_rev)
- Annealing temperature: 55 °C
- Bands as expected (~3300 bp)
- Additionally there were undefined bands at ~1200 bp
- illiegal restriction sites were not removed yet
- Gibson Assembly with frd (E. coli) and pSB1C3
- Transformation with electrocompotetent cells of pSB1C3_frd
- Colony PCR of pSB1C3_frd (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands not as expected (~3600 bp)
- ccm
- This week we transformed the ccm-cassette and tested colonies for it
- DpnI-digest of ccm-backbone
- Gibson Assembly with ccm and pSB1C3
- Transformation with electrocompotetent cells of pSB1C3_ccm
- Colony PCR of pSB1C3_ccm (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands not as expected (~6611 bp) probably because it was not completely amplified because of its length
- To check whether one of the colonies is positiv a restriction digestion was done
- Restriction digestion with EcoRI and PstI
- Bands not as expected (~2070 bp and 6281 bp)
- GSU 3274
- This week we transformed the GSU 3274 and tested colonies for it
- DpnI-digest of GSU 3274-backbone
- Gibson Assembly with GSU 3274 and pSB1C3
- Transformation with electrocompotetent cells of pSB1C3_GSU 3274
- Colony PCR of pSB1C3_GSU 3274 (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~783 bp)
- Restriction digestion with EcoRI and PstI
- Bands not as expected (~2070 bp and 453 bp)
- Deletion of dcuB and integration of oprF into chromosome
- This week we tested the next colonies for the deletion of dcuB and performed the NPN-assay to verify the integration of oprF into chromosome
- oprF
- NPN-uptake assay for porine verification
- dcuB
- Colony PCR to verify the deletion of dcuB (dcuB_del_kon1, dcuB_del_kon2)
- Annealing temperature: 55°C
- Bands as expected (~4046 bp)
- another Colony PCR to verify the positive colony
- FumA
- This week we assembled FumA with different promotor
- BioBrick Assembly (Suffix)
- Backbone (digested with SpeI, PstI)
- BBa_J23101
- BBa_J23102
- BBa_J23104
- pSB1A2_T7
- Insert (digested with XbaI, PstI)
- FumA
- Transformation of all contrsucts with electrocompotetent cells
- Colony PCR with all contructs (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~2100 bp) for BBa_J23101_FumA and pSB1A2_T7_FumA
- frd (E. coli)
- This week we transformed frd and checked several colonies for it
- DpnI digest of Gibson-Assembly of frd (E. coli) to remove the template
- Transformation of Gibson-Assembly with electrocompotetent cells
- Colony PCR of pSB1C3_frd (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~3600 bp) but there were several other bands too
- Therefore another Transformation with electrocompotetent cells was done
- Colony PCR of pSB1C3_frd (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands not as expected (~ 3600 bp)
- PCR amplification of frd backbone (pSB1C3_frd_pre, pSB1C3_frd_suf)
- Annealing temperature: 55 °C
- Bands as expected (~ 2070 bp)
- frd backbone was purified out of the gel
- Gibson Assembly with frd and pSB1C3
- Transformation of pSB1C3_frd with chemocompetent cells
- Colony PCR of pSB1C3_frd (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~ 3600 bp)
- Restriction digestion with EcoRI and PstI
- Bands as expected (~2070 bp and 3300 bp)
- Plasmid isolation of pSB1C3_frd
- sequencing of pSB1C3_frd confirmed the correct construct
- next the illegal restriction sites had to be removed
- ccm
- This week we performed Eckhardt gels as a new method besides Colony PCR to identify positiv colonies
- Eckhardt gel of ccm was performed two times
- Bands not impeccable to identify (~6230 bp) and therefore a restriction digestion was done
- Bands not as expected (~2070 bp and ~6239 bp)
- GSU 3274
- This week we tested colonies for GSU 3274
- Colony PCR of GSU 3274 (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~783 bp)
- Plasmid isolation of GSU 3274
- Restriction digestion with PstI and EcoRI
- Bands as expected (~20170 bp and 453 bp)
