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| {{:Team:Peking/Headernotebook}} | | {{:Team:Peking/Headernotebook}} |
| {{:Team:Peking/boxes}} | | {{:Team:Peking/boxes}} |
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| [<html><a href="#top">TOP</a></html>] | | [<html><a href="#top">TOP</a></html>] |
| ===7.3=== | | ===7.3=== |
- | Antigen 43 PCR, 20ul system. T3 polymerase PCR.
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| | | |
- | Identify them by 1% agarose gel electrophoresis.
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| ===7.4=== | | ===7.4=== |
- | Antigen 43 PCR using different annealing temperature, with gradient 1 ℃.
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| | | |
- | Attend the group seminar.
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- |
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- | Retrieve the PCR product of T3 polymerase and digest it with EcoRI and PstI. Digest for the whole night.
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| ===7.5=== | | ===7.5=== |
- | Identify the product by agarose gel electrophoresis. Retrieve the PCR product of Antigen 43.
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- |
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- | Retrieve the digested T3 polymerase and ligated it to the plasmid PSB1A2.
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- |
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- | Transform the plasmid to Trans 5α strain.
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| | | |
- | PCR the antigen 43 with much larger annealing temperature gradient. Identify it with electrophoresis.
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| ===7.6=== | | ===7.6=== |
- | Design the primer of antigen 43 again by Primer Premier 5.0.
| + | |
| ===7.8=== | | ===7.8=== |
- | PCR antigen 43 using nest-PCR procedure. Using Taq DNA polymerase to do the first step nest PCR.
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| | | |
- | Identify it by electrophoresis. Retrieve the 3k band and do the second step of nest PCR by using the product of the
| |
- | first step as template.
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| ===7.9=== | | ===7.9=== |
- | Identify the second PCR product by electrophoresis. Retrieve the 3k band and digest it with EcoRI and SpeI to put it
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- | into plasmid. Digest it with PstI to test whether this is antigen 43.( antigen 43 have 6 PstI digestion sites.)
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| | | |
- | Design the six point mutation primer.
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| ===7.10=== | | ===7.10=== |
- | Do the transformation and ligation.
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- | ===7.12===
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- | Prepare plasmid DNA.
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| | | |
- | Digest the plasmid DNA with PstI to identify it.
| + | ===7.12=== |
| | | |
- | PCR the product using Easytaq DNA polymerase to identify the molecule weight of the product.
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| ===7.13=== | | ===7.13=== |
- | Learn to do the western blotting. Write the protocols.
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| | | |
- | Digest merT, merP and merC with Xbal and PstI. Meanwhile digest B0034(RBS) with SpeI and PstI.
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- |
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- | Connect the two digested product together.
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- |
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- | Transform the ligation product into Trans5αstrain.
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- |
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- | Pick the single clone from the plate.
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- |
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- | Send the PCR product of Antigen 43 for sequencing.
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| ===7.14=== | | ===7.14=== |
- | Prepare the plasmid DNA of rbs+merT, rbs+merP, rbs+merC.
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| | | |
- | Do the western blotting.
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| ===7.15=== | | ===7.15=== |
- | Digest the plasmid DNA by EcoRI and PstI to identify it.
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| | | |
- | Digest rbs+merT with Spel and Pstl and digest rbs+merP with Xbal and Pstl.
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- |
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- | Identify them using agarose gel electrophoresis.
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| ===7.16=== | | ===7.16=== |
- | Connect rbs with merT, merP and merC again.
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| | | |
- | Do the first point mutation. First PCR the antigen 43 gene with designed point mutation primers, then retrieve it by
| |
- | electrophoresis. Then do the blunting kination, finally do the ligation and put it into strains by transformation.
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| ===7.18=== | | ===7.18=== |
- | Prepare the plasmid DNA for rbs+merT, rbs+merP and rbs+merC, Antigen 43 mutant 1.
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| | | |
- | Identify them using electrophoresis.
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- |
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- | Connect rbs+merT with rbs+merP.
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- |
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- | Do the second step of point mutation for antigen 43. Do the PCR step. Identify it by electrophoresis.
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- | Blunting kination, ligation and transformation.
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- |
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- | Send the first point mutation product for sequencing.
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- |
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- | The rbs+merT,rbs+merP and rbs+merC sequenced correct.
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| ===7.19=== | | ===7.19=== |
- | Retrieve the product of digested rbs+merT and rbs+merP by electrophoresis. Connect the rbs+merT with rbs+merP,. Do the transformation.
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| | | |
- | Pick the single clone of antigen 43 second step point mutation strain.
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| ===7.20=== | | ===7.20=== |
- | Prepare the plasmid DNA of antigen 43 second point mutation strain. Send it for sequencing.
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| | | |
- | Do the third step point mutation.
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- |
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- | Identify the plasmid DNA by electrophoresis. Retrieve the third point mutation PCR product by electrophoresis.
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- |
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- | Digest rbs+merT+rbs+merP with Spel and Pstl, digest rbs+merC with Xbal and Pstl.
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| ===7.21=== | | ===7.21=== |
- | Identify the product of the digestion using electrophoresis.
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| | | |
- | Pick the single clone of the 3rd point mutation of antigen 43 strain on the plate.
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| ===7.22=== | | ===7.22=== |
- | Connect rbs+merT+rbs+merP with rbs+merC.
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| | | |
- | Using easyPFu to PCR antigen 43.The forward primer contains a rbs. Digest it with EcoRl and Spel to put it into PSB1A2 plasmid.
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- |
| |
- | Prepare the plasmid DNA of the product of the third point mutation of antigen 43.digest it with EcoRl and SpeI to identify it.
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- |
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- | Do the 4th point mutation PCR step.
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| ===7.23=== | | ===7.23=== |
- | Identify the plasmid using agarose gel electrophoresis.
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- |
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- | Send the plasmid DNA for sequencing.
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| | | |
- | Put the rbs+agn43 into plasmid by ligation.
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| ===7.29=== | | ===7.29=== |
- | Attend the group seminar.
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| | | |
- | Prepare the plasmid DNA for rbs+merT+rbs+merP+rbs+merC. Digest it with EcoRl and Pstl for identification. Digest it with Xbal and Pstl and digest the plasmid contains T7 promoter with Spel and Pstl.
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- |
| |
- | Do the 5th point mutation of antigen 43. Do the PCR step.
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- |
| |
- | Identify the product of the 4th point mutation and the rbs+merT+rbs+merP+rbs+merC by electrophoresis. Collect those correct ones and send them for sequencing.
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- |
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- | See the point mutation result in the sequence.
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- |
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- | Identify the T7+rbs+merT+rbs+merP+rbs+merC by electrophoresis.
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| ===7.30=== | | ===7.30=== |
- | Digest rbs+agn43 with EcoRl and Xbal. Digest phiR73+Po promoter with EcoRl and Spel.
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| | | |
- | Retrieve the digested T7+rbs+merT+rbs+merP+rbs+merC gel.
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- |
| |
- | Do the transformation.
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| ===7.31=== | | ===7.31=== |
- | Digest 2-2E constitutive promoter with EcoRl and Spel. Digest rbs+agn43 with EcoRl and Xbal.
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| | | |
- | Connect 2-2E promoter with rbs+agn43.
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| ==August== | | ==August== |
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| [<html><a href="#top">TOP</a></html>] | | [<html><a href="#top">TOP</a></html>] |
| ===8.1=== | | ===8.1=== |
- | Prepare the plasmid DNA of T7+rbs+merT+rbs+merP+rbs+merC and PhiR73+Po promoter+rbs+antigen 43.
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| | | |
- | Prepare the plasmid DNA of 2-2E promoter+rbs+antigen 43.
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- |
| |
- | Identify PhiR73+Po promoter+rbs+antigen 43 and 2-2E promoter+rbs+antigen 43 using electrophoresis.
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| ===8.2=== | | ===8.2=== |
- | Send the correct ones for sequencing.
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| | | |
- | Digest rbs+antigen 43 again.
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| ===8.4=== | | ===8.4=== |
- | Pick the clone of PhiR73+Po promoter+rbs+antigen 43 on the plate for autoaggregation assay.
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| | | |
- | Plan the assay.
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- |
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- | Design new primers for antigen 43 which contains different promoters in the forward primer.
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| ===8.5=== | | ===8.5=== |
- | Preliminary autoaggregation assay.
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| | | |
- | Send PhiR73+Po promoter+rbs+antigen 43 for sequencing.
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- |
| |
- | Transform PhiR73+Po promoter+rbs+antigen 43 into BL21 strains.
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| ===8.6=== | | ===8.6=== |
- | Pick the single clone.
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| | | |
- | Induce the antigen 43 gene’s expression by adding 10^-5 M IPTG for 4 hours.
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- |
| |
- | Do the auto-aggregation assay( for detail, see the inductive aggregation page or antigen 43 part.)
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- |
| |
- | PCR the rbs+agn43 using easyPFU.
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- |
| |
- | Identify it using electrophoresis.
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- |
| |
- | Digest the PCR product using EcoRl and Spel to put it into PSB1A2.
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- |
| |
- | Do the ligation and transformation.
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- |
| |
- | Send some of the PCR product for sequencing.
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| ===8.7=== | | ===8.7=== |
- | Digest merT+merC with Spel and Pstl, digest merP with Xbal and Pstl.
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- |
| |
- | Retrieve the gel. Do the ligation.
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| | | |
- | Pick three clones of rbs+merP.
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| ===8.8=== | | ===8.8=== |
- | Prepare the plasmid DNA for rbs+merP and merT+merC.
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| | | |
- | Pick single clones of merT+merP+merC. Do the colony PCR.
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- |
| |
- | Retrieve the rbs+agn43.
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- |
| |
- | Do the ligation and transformation.
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| ===8.9=== | | ===8.9=== |
- | PCR antigen 43.
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| | | |
- | Nest PCR using nest primers. Do the first step.identify it using electrophoresis.
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| ===8.10=== | | ===8.10=== |
- | PCR antigen 43 using nest primers. Using different template.
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| | | |
- | Using better template to run PCR.
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- |
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- | Do the transformation of antigen 43.
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| ===8.11=== | | ===8.11=== |
- | Retrieve the product of rbs+agn43. Digest it and do the ligation and transformation.
| + | |
| ===8.12=== | | ===8.12=== |
- | Pick the single clone of rbs+agn43.
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| | | |
- | Digest 1-23L with EcoRl and Xbal. Digest T7+merT+merP+merC with EcoRl and Spel.
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- |
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- | Digest pmerT+GFP with Spel and Pstl, digest TPC with Xbal and Pstl.
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- |
| |
- | Identify them using agarose gel electrophoresis.
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- |
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- | Do the ligation and transformation.
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| ===8.13=== | | ===8.13=== |
- | Identify rbs+agn using electrophoresis.
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- |
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- | Digest 1-23L with EcoRl and Xbal. Digest T7+merT+merP+merC with EcoRl and Spel.
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| | | |
- | Do the ligation and transformation.
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| ===8.14=== | | ===8.14=== |
- | Prepare the plasmid DNA.
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| | | |
- | Send the correct ones for sequencing.
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| ===8.15=== | | ===8.15=== |
- | See the sequencing result.
| + | |
| ===8.16=== | | ===8.16=== |
- | Digest PhiR73+Po promoter with EcoRl and Spel. Digest RBS with EcoRl and Xbal.
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- |
| |
- | Retract the whole genome of K12 strain.
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- |
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- | PCR antigen 43 using new template.
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| | | |
- | Pick single clones of antigen 43.
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| ===8.17=== | | ===8.17=== |
- | T7+TCP+Terminator done.
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| | | |
- | Transform it to BL21 strain.
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- |
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- | Send antigen 43 for sequencing.
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- |
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- | PCR antigen 43 using new template and better protocol.
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- |
| |
- | Do the colony PCR of PhiR73+Po promoter+rbs.
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- |
| |
- | Prepare the plasmid DNA and digest it for identification.
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- |
| |
- | Do the ligation and transformation.
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- |
| |
- | Digest pmerT+GFP with Spel and Pstl, digest TPC with Xbal and Pstl.
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- |
| |
- | Digest pPbrA with Spel and Pstl. Digest rbs+T3 pol with Xbal and Pstl.
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| ===8.18=== | | ===8.18=== |
- | Retrieve the digested product .
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| | | |
- | Identify them using electrophoresis.
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- |
| |
- | Pick the single clone of PCR of PhiR73+Po promoter+rbs, do the colony PCR.
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- |
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- | Prepare the plasmid DNA.
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- |
| |
- | Send the correct ones for sequencing.
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- |
| |
- | Connect pPbra with rbs+T3 pol. Connect PhiR73+Po promoter+rbs with antigen 43.
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- |
| |
- | Connect merp+GFP with TCP.
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- |
| |
- | Do the ligation and transformation.
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| ===8.19=== | | ===8.19=== |
- | Identify them using electrophoresis.
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- |
| |
- | Retrieve the gel.
| |
- |
| |
- | Do the ligation and transformation.
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| | | |
- | PCR antigen 43. Digest it using EcoRl and Spel.
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| ===8.20=== | | ===8.20=== |
- | Pick the colony of PhiR73+Po promoter+rbs+antigen 43.
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| | | |
- | Put rbs+antigen 43 into PSB1A2 plasmid. Do the ligation and transformation.
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- |
| |
- | Digest merp+GFP and T3 pol.
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| ===8.21=== | | ===8.21=== |
- | Identify the colony PCR product using electrophoresis.
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| | | |
- | Do the transformation.
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- |
| |
- | Digest rbs+agn43 with EcoRl and Xbal. Digest PhiR73+Po promoter using EcoRl and Spel.
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| ===8.22=== | | ===8.22=== |
- | Do the autoaggregation assay of antigen 43.
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| | | |
- | Induce its expression by adding IPTG.
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| ===8.23=== | | ===8.23=== |
- | Do the autoaggregation assay.
| + | |
| ===8.25=== | | ===8.25=== |
- | Prepare the plasmid DNA for TPC+Terminator.
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| | | |
- | Send the correct ones for sequencing.
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- |
| |
- | Construct pPbra using primers annealing.
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| ===8.26=== | | ===8.26=== |
- | Transform antigen 43.
| + | |
| ===8.27=== | | ===8.27=== |
- | Pick single clone of antigen 43.
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| | | |
- | Do the transformation of TPC+terminator.
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- |
| |
- | Do the transformation of pPbrA.
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- |
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- | Connect pBAD with rbs. Do the ligation and transformation.
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| ===8.30=== | | ===8.30=== |
- | Do the functional test of antigen 43.
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| | | |
- | Pick the clone of antigen 43.
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- |
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- | Pick the clone of merP+GFP+TCP.
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- |
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- | Do the ligation of pPbra+T3 pol again.
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- |
| |
- | Pick the single clone of Pbad+rbs.
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- |
| |
- | Do the transformation.
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| ===8.31=== | | ===8.31=== |
| Send the correct merp+GFP and Pbad+rbs for sequencing. | | Send the correct merp+GFP and Pbad+rbs for sequencing. |
Line 526: |
Line 307: |
| [<html><a href="#top">TOP</a></html>] | | [<html><a href="#top">TOP</a></html>] |
| ===9.1=== | | ===9.1=== |
- | Connect the antigen 43 into plasmid.
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| | | |
- | Send merP+GFP+TCP for sequencing.
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- |
| |
- | Connect pPbra+T3 pol using primers annealing.
| |
- |
| |
- | Do the ligation and transformation.
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| ===9.2=== | | ===9.2=== |
- | Prepare the plasmid DNA for rbs+agn43.
| |
- |
| |
- | See the sequencing result of merp+GFP+TCP.
| |
| | | |
- | Pick the clone of pPbra+T3 pol.
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| ===9.3=== | | ===9.3=== |
- | Send the rbs+agn43 for sequencing.
| |
| | | |
- | Digest rbs+agn43 with EcoRl and Xbal. Digest PhiR73+Po promoter with EcoRl and Spel.
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- |
| |
- | Pick the clone of pPbra+T3 pol. Prepare the plasmid DNA.
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| ===9.6=== | | ===9.6=== |
- | Do the PCR of antigen 43 using Hifi Taq DNA polymerase.
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| | | |
- | Digest merP+GFP+TCP with EcoRl and Spel. Put it into PSB3K3 backbone.
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- |
| |
- | Connect pPbra+T3 pol with 1-23L. pick the single clone. Prepare the plasmid DNA.
| |
- |
| |
- | Do the ligation and transformation.
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- |
| |
- | Pick the clone of Pbad+T3 pol.
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- |
| |
- | Make competent cell containing pc+merR+merp+rbs+T3pol. Transform T3 promoter into it.
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- |
| |
- | Induce the expression using different concentration of IPTG.
| |
- |
| |
- | Re-suspend the cell. Measure the GFP intensity by a microplate reader.
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| ===9.7=== | | ===9.7=== |
- | Digest merP+GFP+TCP with EcoRl and Pstl to put it into PSB3K3.
| |
| | | |
- | Send pbra+T3 pol+terminator for sequencing.
| |
- |
| |
- | Identify the pBAD+T3 pol using electrophoresis.
| |
- |
| |
- | Make competent cells of pc+merR+merp+rbs+T3pol.
| |
- |
| |
- | Transform T3 promoter into it.
| |
| ===9.8=== | | ===9.8=== |
- | Re-suspend the cell.
| |
| | | |
- | Measure the GFP intensity using microplate reader.
| |
- |
| |
- | PCR antigen 43 using hifi Taq DNA polymerase.
| |
| ===9.9=== | | ===9.9=== |
- | PCR Rbs+agn 43 using agn for/rev primer to identify it.
| |
| | | |
- | Digest the correct ones using EcoRl and Spel.
| |
- |
| |
- | Send the correct ones for sequencing.
| |
- |
| |
- | Transform T3 promoter into cells containing pc+merR+merp+rbs+T3pol.
| |
- |
| |
- | Send pBAD+T3 pol for sequencing.
| |
- |
| |
- | pPbra+T3pol+terminator done.
| |
- |
| |
- | Measure the GFP intensity using a microplate reader.
| |
| ===9.12=== | | ===9.12=== |
- | Digest rbs+agn43 with EcoRl and Xbal. Digest PhiR73+Po promoter with EcoRl and Spel.
| |
| | | |
- | Identify them using electrophoresis.
| |
- |
| |
- | Retrieve the gel.
| |
- |
| |
- | Do the ligation and transformation.
| |
- |
| |
- | Pick the clone.
| |
| ===9.13===. | | ===9.13===. |
- | Digest Antigen 43 with EcoRl and Xbal. Digest PhiR73+Po promoter+rbs with EcoRl and Spel.
| |
| | | |
- | Identify them using electrophoresis.
| |
| ===9.14=== | | ===9.14=== |
- | PCR antigen 43.
| |
- |
| |
- | Get the candidate of rbs+agn43.
| |
| | | |
- | Send the correct ones for sequencing.
| |
| ===9.15=== | | ===9.15=== |
- | Put antigen 43 into PSB1A2.
| |
| | | |
- | Do the ligation and transformation.
| |
| ===9.16=== | | ===9.16=== |
- | Digest PSB1A2 and PSB1A3.
| + | |
| ===9.17=== | | ===9.17=== |
- | Digest PSB1C3 with EcoRI and Spel.
| |
| | | |
- | Digest antigen 43 with EcoRl and Spel.
| |
- |
| |
- | Do the ligation and transformation.
| |
| ===9.21=== | | ===9.21=== |
- | Retract the whole genome of K12 strain.
| + | |
| ===9.22=== | | ===9.22=== |
- | Nest PCR of antigen 43 using new template and new primers.
| |
| | | |
- | Put antigen 43 into PSB1C3.
| |
- |
| |
- | Pick the single clone of antigen 43.
| |
| ===9.23=== | | ===9.23=== |
- | Prepare the plasmid DNA for antigen43.
| |
| | | |
- | Digest the plasmid DNA using EcoRl and Spel.
| |
- |
| |
- | Identify them using electrophoresis.
| |
- |
| |
- | Make the competent cell contains PBAD+ T3 pol. Transform T3 promoter+GFP into it.
| |
- |
| |
- | Pick the clone of PMERT+T3 pol.
| |
- |
| |
- | Digest PSB3C5 using EcoRl and Pstl.
| |
| ===9.24=== | | ===9.24=== |
- | PSB3K5: EcoRl and Pstl.
| |
| | | |
- | T7+TPC+Ter: Xbal and Pstl.
| |
- |
| |
- | MerP+GFP:EcoRl and Spel.
| |
- |
| |
- | Do the ligation and transformation.
| |
| ===9.25=== | | ===9.25=== |
- | Retrieve the digested merp+GFP.
| |
- |
| |
- | Induce the expression of PBAD+T3 pol using 10^-5 M arabinose.
| |
- |
| |
- | Do the antigen 43 PCR using touchdown PCR.
| |
| | | |
- | Do the ligation and transformation.
| |
| ===9.26=== | | ===9.26=== |
- | Make the competent cell contains T3 promoter+GFP. Transform pmert+T3pol and 1-18i+merR.
| |
| | | |
- | Do the colony PCR to identify it.
| |
| ===9.27=== | | ===9.27=== |
- | Attend the seminar.
| + | |
| ===9.28=== | | ===9.28=== |
- | Connect T7+PhiR73+Po promoter+rbs+antigen 43.
| |
| | | |
- | Do the ligation and transformation.
| |
- |
| |
- | PCR the T3 promoter+PhiR73+Po promoter.
| |
| ===9.29=== | | ===9.29=== |
- | Retrieve the PCR product.
| |
| | | |
- | Digest the product using EcoRl and Spel.
| |
- |
| |
- | Digest TCP with Xbal and Pstl. Identify it using electrophoresis.
| |
- |
| |
- | Digest merp+GFP using Spel and Pstl.
| |
- |
| |
- | Do the transformation.
| |
| ===9.30=== | | ===9.30=== |
- | Do the ligation and transformation.
| |
| | | |
- | Prepare the plasmid DNA and identify it using PCR.
| |
| | | |
| ==October== | | ==October== |
Line 740: |
Line 407: |
| [<html><a href="#top">TOP</a></html>] | | [<html><a href="#top">TOP</a></html>] |
| ===10.1=== | | ===10.1=== |
- | Digest pTET+T7 pol using EcoRl and Spel.
| |
| | | |
- | Retrieve the gel.
| |
- |
| |
- | Connect T3 promoter+PhiR73+Po promoter+ antigen 43.
| |
- |
| |
- | Do the ligation and transformation.
| |
| ===10.3=== | | ===10.3=== |
- | Connect pTET+T7 pol and T7 promoter+PhiR73+Po promoter+ antigen 43.
| |
| | | |
- | Do the ligation and transformation.
| |
| ===10.4=== | | ===10.4=== |
- | Do the auto-aggregation assay of antigen 43.
| + | |
| ===10.5=== | | ===10.5=== |
- | Do the auto-aggregation assay.
| + | |
| ===10.7=== | | ===10.7=== |
- | Digest merp+GFP using Spel and Pstl.
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- | Digest TCP using Xbal and Pstl.
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- | Do the ligation and transformation.
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| ===10.8=== | | ===10.8=== |
- | Identify the digested product using electrophoresis.
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- | Do the ligation and transformation.
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| ===10.9=== | | ===10.9=== |
- | Prepare the plasmid DNA.
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- | Identify them using PCR.
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- | Send the correct ones for sequencing.
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| ===10.10=== | | ===10.10=== |
- | Antigen 43 clone step done.
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- | Connect ptet+T7 pol with T7 promoter+PhiR73+Po promoter+ antigen 43.
| + | ===10.11=== |
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- | Do the ligation and transformation.
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- | ===10.11===
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- | Do the auto-aggregation assay.
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| ===10.12=== | | ===10.12=== |
- | Do the auto-aggregation assay.
| + | |
| ===10.13=== | | ===10.13=== |
- | Measure the result.
| + | |
| ===10.15=== | | ===10.15=== |
- | Attend group seminar.
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- | Do the auto-aggregation assay.
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| ===10.16-10.21=== | | ===10.16-10.21=== |
- | Connect merp+GFP with TCP.
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- | Connect pc+merR with terminator.
| + | ===10.21-10.25=== |
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- | Transform these two plasmid into one single strain.
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- | Antigen 43 auto-aggregation assay. Analyse the result.
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- | ===10.21-10.25===
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- | Upload and edit parts of our group.
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| [<html><a href="#top">TOP</a></html>] | | [<html><a href="#top">TOP</a></html>] |
| <html> | | <html> |
| </div> | | </div> |
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- | <div id="project description bottom">
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- | <div id="bottomgreen">
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- | <br>
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- | <a href="https://2010.igem.org/Team:Peking/Team/MJing"><font color=#000000>==go to his page==</font></a>
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- | </div>
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- | </html>
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