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Team:Bielefeld-CeBiTec/Notebook/Journal/CO2-fixation/Aug
From 2014.igem.org
(Difference between revisions)
| Line 402: | Line 402: | ||
<li><b>fbaA</b></li> | <li><b>fbaA</b></li> | ||
<ul> | <ul> | ||
| - | <li>This week we tried amplify | + | <li>This week we tried amplify second part of fbaA for purification.</li> |
<ul> | <ul> | ||
| - | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer# | + | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#fbaA_purify_rev" target="_blank">fbaA_purify_rev</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#fbaA_PstI_fw" target="_blank">fbaA_PstI_fw</a>)</li> |
<ul> | <ul> | ||
<li>Annealing temperature: ...</li> | <li>Annealing temperature: ...</li> | ||
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<li>This week we tried amplify both parts of tktA for purification.</li> | <li>This week we tried amplify both parts of tktA for purification.</li> | ||
<ul> | <ul> | ||
| - | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer# | + | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#tktA_purify_fw" target="_blank">tktA_purify_fw</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#tktA_PstI_rev" target="_blank">tktA_PstI_rev</a> and <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#tktA_purify_rev" target="_blank">tktA_purify_rev</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#tktA_PstI_fw" target="_blank">tktA_PstI_fw</a>)</li> |
<ul> | <ul> | ||
<li>Annealing temperature: ...</li> | <li>Annealing temperature: ...</li> | ||
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<li>This week we tried amplify both parts of gapA for purification.</li> | <li>This week we tried amplify both parts of gapA for purification.</li> | ||
<ul> | <ul> | ||
| - | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer# | + | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#PCR" target="_blank">PCR amplification</a> (<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#gapA_purify_fw" target="_blank">gapA_purify_fw</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#gapA_NotI_rev" target="_blank">gapA_NotI_rev</a> and <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#gapA_purify_rev" target="_blank">gapA_purify_rev</a>, <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Primer#gapA_NotI_fw" target="_blank">gapA_NotI_fw</a>)</li> |
<ul> | <ul> | ||
<li>Annealing temperature: ...</li> | <li>Annealing temperature: ...</li> | ||
Revision as of 12:42, 28 August 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.
- BioBrick Assembly (Suffix)
- Backbones (digested with SpeI, PstI)
- T7
- pTac
- pTet
- Inserts (digested with XbaI, PstI)
- prkA
- Hneap
- SELAN
- sRNA:pfkA
- Only the assembly with the pTac promotor was successful.
- Colony PCR and plasmid isolation of pTac_prkA, pTac_Hneap, pTac_SELAN and pTac_sRNA_pfkA
- Colony PCR of T7 promotor
- 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 T7 promotor from the 2013 distribution plate
- Bands as expected (~300 bp)
- csoS1-4
- We tried to [...]
- Colony PCR (VF-Primer, VR-Primer)
- Gibson Assembly
- Plasmid isolation
- Restriction digestion with SpeI and XbaI
- Bands as expected ()
- BioBrick Assembly (Suffix)
- Colony PCR of can_csoS1-4
- Bands as expected ()
- glpX
- We tried to [...]
- Gibson Assembly after DpnI digestion
- Colony PCR
- prkA
- We tried to [...]
- PCR amplification and purification for insertion in pHnCBcsoS1D
- Bands as expected ()
- Gibson Assembly with pHnCBcsoS1D
- RuBisCO
- We tried to...
- BioBrick Assembly (Suffix)
- Backbone (digested with SpeI, PstI)
- pTac_prkA
- Inserts (digested with XbaI, PstI)
- Hneap
- SELAN
- We assembled pTac_prkA with Hneap respectively SELAN
- Colony PCR
- pTac_prkA_Hneap
- Bands es expected ()
- pTac_prkA_SELAN
- Bands as expected ()
- Plasmid isolation of pTac_prkA_Hneap and pTac_prkA_SELAN
- Sequencing
- csoS1D
- Successful. We got the right sequence. The first part of the carboxysome is complete.
- can
- Five mutations. Another sequencing will follow.
- glpX
- Not successful. We got the CFP sequence instead of the glpX sequence, so we will try another backbone (pSB1C3_RFP).
- SBPase (glpX)
- This week we tried to amplify glpX
- PCR amplification (Primer1, Primer2) of pSB1C3-RFP backbone
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- PCR amplification (Primer1, Primer2) of glpX
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- Restriction digestion with DpnI
- Gibson Assembly with glpX_1 and glpX_2 on pSB1C3
- Bands (not) as expected (... bp)
- Another amplification and purification was tried.
- csoS1D
- This week we tried to do a BioBrick Assembly.
- BioBrick Assembly Suffix:
- Backbones (digested with EcoRI and XbaI)
- csoS1D
- Inserts (digested with digested with EcoRI and SpeI
- can_csoS1-4
- [...] was succesful
- csoS1-4
- This week we tried to isolate the plasmid.
- Plasmid isolation of csoS1-4
- Restriction digestion with PstI and EcoRI
- Bands (not) as expected (... bp)
- Sequencing
- Plasmid isolation of can, Selan, Hneap, can_csoS1-4
- can
- 4 to 5 mutations on the same positions. Maybe we got the wrong accession number
- csoS1D
- correct sequence
- csoS1-4
- not successful
- Selan
- not successful
- sRNA:pfkA
- not successful
- SBPase (glpX)
- This week we tried to amplify glpX
- PCR amplification (Primer1, Primer2) of pSB1C3-RFP backbone
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- PCR amplification (Primer1, Primer2) of glpX
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- Restriction digestion with DpnI
- Gibson Assembly with glpX_1 and glpX_2 on pSB1C3
- Bands (not) as expected (... bp)
- Another amplification and purification was tried.
- Colony PCR (Primer1, Primer2)
- Annealing temperature: ...
- Bands as expected (~1000 bp) but also additional bands
- Plasmid isolation of glpX
- Restriction digestion with PstI and EcoRI
- Bands not as expected
- Colony PCR (Primer1, Primer2)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- pHnCBcsoS1D, prkA
- This week we tried to combine the addgene plasmid with the prkA
- Transformation with electrocompotetent cells
- csoS1-4
- This week we tried again to amplify the shell proteins
- PCR amplification (Primer1, Primer2)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- Restriction digestion with DpnI
- Bands (not) as expected (... bp)
- Gibson Assembly with csoS1-4 on pSB1C3
- Colony PCR (Primer1, Primer2)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- prkA and RuBisCO
- This week we tried the pTet for prkA and RuBisCO
- BioBrick Assembly Suffix:
- Backbones (digested with [Enzyme])
- pTet
- Inserts (digested with [Enzyme])
- prkA and Hneap
- [...] was succesful
- Colony PCR (Primer1, Primer2)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- Only some colonies, TetR (repressor) not strong enough in the pTet_prkA construct
- GFP
- This week we tried isolate GFP from the parts distribution
- Plasmid isolation of [Construct]
- Purification vector
- This week we tried amplify the T7 promotor and RBS for the purification vector.
- PCR amplification (Primer1, Primer2)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- fbaA
- This week we tried amplify second part of fbaA for purification.
- PCR amplification (fbaA_purify_rev, fbaA_PstI_fw)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- tktA
- This week we tried amplify both parts of tktA for purification.
- PCR amplification (tktA_purify_fw, tktA_PstI_rev and tktA_purify_rev, tktA_PstI_fw)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- gapA
- This week we tried amplify both parts of gapA for purification.
- PCR amplification (gapA_purify_fw, gapA_NotI_rev and gapA_purify_rev, gapA_NotI_fw)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- IntCBD
- This week we tried amplify the intein tag for the purification vector.
- PCR amplification (Primer1, Primer2)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- Gibson Assembly with T7 RBS and IntCBD on pSB1C3
- T7 Promotor
- This week we tried the T7 promotor for prkA and Hneap
- BioBrick Assembly Suffix:
- [...] was succesful
- Colony PCR (Primer1, Primer2)
- Annealing temperature: ...
- Bands (not) as expected (... bp)
- Sequencing
- pSB1C3_glpX
- not successful. It was a sequence of a fluorescence protein (RFP backbone used)
- pSB1C3_csoS4ABcsoS1CAB
- not successful. It was another sequence. We think of a contamination.
- Selan
- too many insertion mutations
- sRNA:pfkA
- successful
