Team:Peking/Notebook/ZRLiu

From 2010.igem.org

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===7.5===
===7.5===
Purification of digested PCR product: merP, merT, and merC
Purification of digested PCR product: merP, merT, and merC
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To get the plasmid: pbrR_MBP_COM (pET21a)
To get the plasmid: pbrR_MBP_COM (pET21a)
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==August==
==August==
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===8.3===
===8.3===
Design the DsbA-MBP Construction
Design the DsbA-MBP Construction
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===9.1===
===9.1===
-
Connect the antigen 43 into plasmid.
 
-
Send merP+GFP+TCP for sequencing.
+
Digestion (20μL):
 +
 
 +
pSB1C3: 5μL
 +
 
 +
EcoRI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (EcoRI Buffer): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel Extraction
 +
 
 +
Digestion (20μL):
 +
 
 +
pbrR_MBP_STD (pSB1A2): 5μL
 +
 
 +
EcoRI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (EcoRI Buffer): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel Extraction
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (PbrR_MBP_STD digested with EcoRI and SpeI): 6μL
 +
 
 +
Vector (pSB1C3 backbone digested with EcoRI and SpeI): 2μL
 +
 
 +
Transformation: OmniMAX
 +
 
-
Connect pPbra+T3 pol using primers annealing.
 
-
Do the ligation and transformation.
 
===9.2===
===9.2===
-
Prepare the plasmid DNA for rbs+agn43.
 
-
See the sequencing result of merp+GFP+TCP.
+
Mini-Prep
 +
 
 +
Verification: Digestion (20μL):
 +
 
 +
Plasmid: 5μL
 +
 
 +
EcoRI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (EcoRI Buffer): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis to verify
 +
 
 +
There should be one band, which is about 500bp
 +
 
 +
DNA Sequencing
 +
 
 +
To get the plasmid: pbrR-MBP (pSB1C3)
 +
 
 +
 
-
Pick the clone of pPbra+T3 pol.
 
===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.
+
Construct the concentration of Hg(II) ions for induction
-
Pick the clone of pPbra+T3 pol. Prepare the plasmid DNA.
+
    Final Concentration/M Volume/μL Original Concentration/M
-
===9.6===
+
-
Do the PCR of antigen 43 using Hifi Taq DNA polymerase.
+
-
Digest merP+GFP+TCP with EcoRl and Spel. Put it into PSB3K3 backbone.
+
1. 5*10-5 25 10-3
-
Connect pPbra+T3 pol with 1-23L. pick the single clone. Prepare the plasmid DNA.
+
2. 3*10-5 15 10-3
-
Do the ligation and transformation.
+
3. 10-5 5 10-3
-
Pick the clone of Pbad+T3 pol.
+
4. 8*10-6 4 10-3
-
Make competent cell containing pc+merR+merp+rbs+T3pol. Transform T3 promoter into it.
+
5. 5*10-6 2.5 10-3
-
Induce the expression using different concentration of IPTG.
+
6. 3*10-6 1.5 10-3
-
Re-suspend the cell. Measure the GFP intensity by a microplate reader.
+
7. 10-6 0.5 10-3
-
===9.7===
+
-
Digest merP+GFP+TCP with EcoRl and Pstl to put it into PSB3K3.
+
-
Send pbra+T3 pol+terminator for sequencing.
+
8. 8*10-7 4 10-4
-
Identify the pBAD+T3 pol using electrophoresis.
+
9. 5*10-7 2.5 10-4
-
Make competent cells of pc+merR+merp+rbs+T3pol.
+
10. 3*10-7 1.5 10-4
-
Transform T3 promoter into it.
+
11. 10-7 0.5 10-4
-
===9.8===
+
-
Re-suspend the cell.
+
-
Measure the GFP intensity using microplate reader.
+
12. 8*10-8 4 10-5
-
PCR antigen 43 using hifi Taq DNA polymerase.
+
13. 5*10-8 2.5 10-5
-
===9.9===
+
-
PCR Rbs+agn 43 using agn for/rev primer to identify it.
+
-
Digest the correct ones using EcoRl and Spel.
+
14. 3*10-8 1.5 10-5
-
Send the correct ones for sequencing.
+
15. 10-8 0.5 10-5
-
Transform T3 promoter into cells containing pc+merR+merp+rbs+T3pol.
+
16. 8*10-9 0.4 10-5
-
Send pBAD+T3 pol for sequencing.
+
17. 5*10-9 25 10-7
-
pPbra+T3pol+terminator done.
+
18. 3*10-9 15 10-7
-
Measure the GFP intensity using a microplate reader.
+
19. 10-9 5 10-7
-
===9.12===
+
-
Digest rbs+agn43 with EcoRl and Xbal. Digest PhiR73+Po promoter with EcoRl and Spel.
+
-
Identify them using electrophoresis.
+
20. 0 0 0
-
Retrieve the gel.
 
-
Do the ligation and transformation.
 
-
Pick the clone.
+
===9.5===
-
===9.13===.
+
 
-
Digest Antigen 43 with EcoRl and Xbal. Digest PhiR73+Po promoter+rbs with EcoRl and Spel.
+
Learn the protocol for preparation of competent cells for transformation for bi-transformation
 +
 
 +
Pick up one colony from each agar plate: J23109 and J23112
 +
 
 +
Grow the culture overnight
 +
 
 +
 
 +
 
 +
===9.6===
 +
 
 +
Re-activate the culture of J23109 and J23112 in fresh LB with ampicilin and kanamyclin
 +
 
 +
Measure the value of OD600
 +
 
 +
Induced with Hg(II) ions of different concentration for 2hrs
 +
 
 +
Centrifugation at 5000r for 5min
 +
 
 +
Resuspension with PBS
 +
 
 +
Measure the value of OD600 and GFP with ELISA
 +
 
 +
 
 +
 
 +
===9.7===
 +
 
 +
Learn about Western Blot with Boxuan Zhao
-
Identify them using electrophoresis.
 
-
===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.
+
Design the traffic light assay
-
===9.16===
+
 
-
Digest PSB1A2 and PSB1A3.
+
LacZ full length (RBS: B0034) BBa_I1732017 2_3K 3093bp pSB1A2
 +
 
 +
LacZ α fragment BBa_I732006 1_23H 234bp pSB1AK3
 +
 
 +
Plasmid1: 1_18I MerR (pSB3K3)
 +
 
 +
Plasmid2: PmerT - LacZ full length / LacZ α fragment (pSB1C3)
 +
 
 +
X-GAL assay
 +
 
 +
 
 +
 
 +
Positive Transformation of 2_3K and 1_23H: TansMAX
 +
 
 +
 
 +
 
===9.17===
===9.17===
-
Digest PSB1C3 with EcoRI and Spel.
 
-
Digest antigen 43 with EcoRl and Spel.
+
Pick up 2 colonies from each agar plate: 2_3K and 1_23H
 +
 
 +
Grow the culture for 12hrs
 +
 
 +
Mini-Prep
 +
 
 +
Get the plasmids: 2_3K (LacZ full length_ pSB1A2)
 +
 
 +
1_23H (LacZ α fragment_ pSB1AK3)
 +
 
 +
 
 +
 
 +
===9.18===
 +
 
 +
Digestion (20μL):
 +
 
 +
LacZ full length: 5μL
 +
 
 +
SpeI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer4): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Digestion (20μL):
 +
 
 +
LacZα fragment: 5μL
 +
 
 +
SpeI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer4): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel Extraction
 +
 
 +
 
 +
 
 +
FAILED(T_T)
 +
 
 +
Wrong enzyme used
 +
 
 +
 
 +
 
 +
===9.19===
 +
 
 +
Digestion (20μL):
 +
 
 +
LacZ full length: 5μL
 +
 
 +
XbaI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer3): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Digestion (20μL):
 +
 
 +
LacZ α fragment: 5μL
 +
 
 +
XbaI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer3): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel Extraction
 +
 
 +
The band for LacZ full length is clear but not for LacZ α fragment
 +
 
 +
Change method
 +
 
 +
PCR from 1_23H by EasyPFU SuperMix (20μL)
 +
 
 +
2*EasyPFU SuperMix: 10μL
 +
 
 +
ddH2O: 7μL
 +
 
 +
Primer_Univ_For: 1.5μL
 +
 
 +
Primer_Univ_Rev:1.5μL
 +
 
 +
Template: 0.3μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel Extraction
 +
 
 +
There should be one band for LacZ α fragment: 250bp
 +
 
 +
 
 +
 
 +
===9.20===
 +
 
 +
Digestion (20μL):
 +
 
 +
RBS_pSB1A2: 5μL
 +
 
 +
SpeI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer2): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel Extraction
 +
 
 +
Get the RBS_pSB1A2 backbone digested with SpeI and PstI
 +
 
 +
Digestion (20μL):
 +
 
 +
PmerT_pSB1C3: 5μL
 +
 
 +
SpeI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer2): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel Extraction
 +
 
 +
Get the PmerT_pSB1C3 backbone digested with SpeI and PstI
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (LacZ α fragment digested with XbaI and PstI): 6μL
 +
 
 +
Vector (RBS_pSB1A2 backbone digested with SpeI and PstI): 2μL
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (LacZ full length digested with XbaI and PstI): 6μL
 +
 
 +
Vector (PmerT_pSB1C3 backbone digested with SpeI and PstI): 2μL
 +
 
 +
Transformation of RBS-LacZ α fragment (pSB1A2)
 +
 
 +
 
-
Do the ligation and transformation.
 
===9.21===
===9.21===
-
Retract the whole genome of K12 strain.
+
 
 +
No recognizable colonies grew on the agar plates (T_T)
 +
 
 +
FAILED (>.<||)
 +
 
 +
Forgot to digest the PCR product
 +
 
 +
 
 +
 
 +
Digestion (20μL):
 +
 
 +
1_23H PCR product: 5μL
 +
 
 +
XbaI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer3): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Purification of the digested product
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (LacZ α fragment digested with XbaI and PstI): 6μL
 +
 
 +
Vector (RBS_pSB1A2 backbone digested with SpeI and PstI): 2μL
 +
 
 +
Transformation of RBS-LacZ α fragment (pSB1A2)
 +
 
 +
Transformation of PmerT-LacZ full length (pSB1C3)
 +
 
 +
 
 +
 
===9.22===
===9.22===
-
Nest PCR of antigen 43 using new template and new primers.
 
-
Put antigen 43 into PSB1C3.
+
Pick up 6 colonies from each agar plate of RBS-LacZ α fragment (pSB1A2) and PmerT-LacZ full length (pSB1C3)
 +
 
 +
Grow the culture for 12hrs
 +
 
 +
Mini-prep of PmerT-LacZ full length (pSB1C3)
 +
 
 +
Digestion (20μL):
 +
 
 +
PmerT-LacZ full length (pSB1C3): 5μL
 +
 
 +
XbaI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer3): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis to verify
 +
 
 +
Band No.1, 2, 3, 6 are of correct size
 +
 
 +
DNA Sequencing
 +
 
 +
To get the plasmid: PmerT-LacZ full length (pSB1C3)
 +
 
 +
 
 +
 
 +
Mini-prep of RBS-LacZ α fragment (pSB1A2)
 +
 
 +
Digestion (20μL):
 +
 
 +
RBS-LacZ α fragment (pSB1A2): 5μL
 +
 
 +
XbaI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer3): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis to verify
 +
 
 +
Band No.1, 2, 3, 4, 5, 6 are all of correct size
 +
 
 +
 
-
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.
+
PCR to get RBS-LacZ α fragment by FastPFU (50μL)
-
Identify them using electrophoresis.
+
5*phusionHF buffer: 10μL
 +
 
 +
2.5mM dNTPs: 5μL
 +
 
 +
Polymerase: 1μL
 +
 
 +
Primer_Univ_For: 1.5μL
 +
 
 +
Primer_Univ_Rev:1.5μL
 +
 
 +
Template: 0.2μL
 +
 
 +
ddH2O: 32μL
 +
 
 +
Electrophoresis
 +
 
 +
Excise the band of 250bp
 +
 
 +
Gel Extraction
 +
 
 +
Digestion (20μL):
 +
 
 +
RBS-LacZ α fragment: 5μL
 +
 
 +
XbaI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer3): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Purification of digested product
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (LacZ α fragment digested with XbaI and PstI): 6μL
 +
 
 +
Vector (PmerT_pSB1C3 backbone digested with SpeI and PstI): 2μL
-
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.
+
Transformation: Trans5α
 +
 
 +
Pick up 6 colonies from the agar plate: PmerT- RBS-LacZ α fragment (pSB1C3)
 +
 
 +
Grow the culture for overnight
 +
 
-
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.
+
Mini-prep of PmerT- RBS-LacZ α fragment (pSB1C3)
 +
 
 +
Digestion (20μL):
 +
 
 +
PmerT- RBS-LacZ α fragment (pSB1C3): 5μL
 +
 
 +
XbaI: 1μL
 +
 
 +
PstI: 1μL
 +
 
 +
Buffer (NEBuffer3): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis to verify
 +
 
 +
Band No.1, 2, 3, 4, 5, 6 are all of correct size
 +
 
 +
DNA Sequencing
 +
 
 +
To get the plasmid: PmerT- RBS-LacZ α fragment (pSB1C3)
 +
 
-
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.
+
Construct the mutant promoter P88 and P3 into the traffic light system
 +
 
 +
 
 +
 
===9.27===
===9.27===
-
Attend the seminar.
+
 
 +
Annealing to form the promoter from designed primers (95℃ 5min):
 +
 
 +
Primer_For_P88: 1.5μL
 +
 
 +
Primer_Rev_P88:1.5μL
 +
 
 +
Phosphorylation (37℃ 30min):
 +
 
 +
[ADD]
 +
 
 +
PNK: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
ddH2O: 4μL
 +
 
 +
Ligation:
 +
 
 +
[ADD]
 +
 
 +
Ligase: 1μL
 +
 
 +
Vector (RBS-LacZ α fragment _pSB1A2 backbone digested with EcoRI and XbaI): 1μL
 +
 
 +
Transformation: Trans5α
 +
 
 +
 
 +
 
 +
Annealing to form the promoter from designed primers (95℃ 5min):
 +
 
 +
Primer_For_P3: 1.5μL
 +
 
 +
Primer_Rev_P3:1.5μL
 +
 
 +
Phosphorylation (37℃ 30min):
 +
 
 +
[ADD]
 +
 
 +
PNK: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
ddH2O: 4μL
 +
 
 +
Ligation:
 +
 
 +
[ADD]
 +
 
 +
Ligase: 1μL
 +
 
 +
Vector (RBS-LacZ α fragment _pSB1A2 backbone digested with EcoRI and XbaI): 1μL
 +
 
 +
Transformation: Trans5α
 +
 
 +
 
 +
 
 +
Annealing to form the promoter from designed primers (95℃ 5min):
 +
 
 +
Primer_For_P88: 3μL
 +
 
 +
Primer_Rev_P88: 3μL
 +
 
 +
Phosphorylation (37℃ 30min):
 +
 
 +
[ADD]
 +
 
 +
PNK: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
ddH2O: 1μL
 +
 
 +
Ligation:
 +
 
 +
[ADD]
 +
 
 +
Ligase: 2μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert: (LacZ full length digested with XbaI and PstI): 6μL
 +
 
 +
Vector (pSB1C3 backbone digested with EcoRI and PstI): 2μL
 +
 
 +
Transformation: Trans5α
 +
 
 +
 
 +
 
 +
Annealing to form the promoter from designed primers (95℃ 5min):
 +
 
 +
Primer_For_P3: 3μL
 +
 
 +
Primer_Rev_P3: 3μL
 +
 
 +
Phosphorylation (37℃ 30min):
 +
 
 +
[ADD]
 +
 
 +
PNK: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
ddH2O: 1μL
 +
 
 +
Ligation:
 +
 
 +
[ADD]
 +
 
 +
Ligase: 2μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert: (LacZ full length digested with XbaI and PstI): 6μL
 +
 
 +
Vector (pSB1C3 backbone digested with EcoRI and PstI): 2μL
 +
 
 +
Transformation: Trans5α
 +
 
 +
 
 +
 
===9.28===
===9.28===
-
Connect T7+PhiR73+Po promoter+rbs+antigen 43.
 
-
Do the ligation and transformation.
+
No recognizable colonies grew on the agar plates (T_T)
 +
 
 +
REPEAT
 +
 
 +
 
-
PCR the T3 promoter+PhiR73+Po promoter.
 
===9.29===
===9.29===
-
Retrieve the PCR product.
 
-
Digest the product using EcoRl and Spel.
+
Still no recognizable colonies grew on the agar plates (TAT)
 +
 
 +
Change the ratio of different components
 +
 
 +
Annealing to form the promoter from designed primers (95℃ 5min):
 +
 
 +
Primer_For_P88: 15μL
 +
 
 +
Primer_Rev_P88:15μL
 +
 
 +
Phosphorylation (37℃ 30min):
 +
 
 +
[ADD]
 +
 
 +
PNK: 1μL
 +
 
 +
Ligase buffer: 3.5μL
 +
 
 +
ddH2O: 1μL
 +
 
 +
Ligation:
 +
 
 +
[ADD]
 +
 
 +
Ligase: 5μL
 +
 
 +
Ligase buffer: 1.5μL
 +
 
 +
Vector (RBS-LacZ α fragment _pSB1A2 backbone digested with EcoRI and XbaI): 10μL
 +
 
 +
Transformation: Trans5α
 +
 
 +
 
 +
 
 +
Annealing to form the promoter from designed primers (95℃ 5min):
 +
 
 +
Primer_For_P3: 15μL
 +
 
 +
Primer_Rev_P3:15μL
 +
 
 +
Phosphorylation (37℃ 30min):
 +
 
 +
[ADD]
 +
 
 +
PNK: 1μL
 +
 
 +
Ligase buffer: 3.5μL
 +
 
 +
ddH2O: 1μL
 +
 
 +
Ligation:
 +
 
 +
[ADD]
 +
 
 +
Ligase: 5μL
 +
 
 +
Ligase buffer: 1.5μL
 +
 
 +
Vector (RBS-LacZ α fragment _pSB1A2 backbone digested with EcoRI and XbaI): 10μL
 +
 
 +
Transformation: Trans5α
 +
 
 +
 
 +
 
 +
Annealing to form the promoter from designed primers (95℃ 5min):
 +
 
 +
Primer_For_P88: 7μL
 +
 
 +
Primer_Rev_P88: 7μL
 +
 
 +
Phosphorylation (37℃ 30min):
 +
 
 +
[ADD]
 +
 
 +
PNK: 1μL
 +
 
 +
Ligase buffer: 1.7μL
 +
 
 +
ddH2O: 1μL
 +
 
 +
Ligation:
 +
 
 +
[ADD]
 +
 
 +
Ligase: 5μL
 +
 
 +
Ligase buffer: 3.3μL
 +
 
 +
Insert: (LacZ full length digested with XbaI and PstI): 6μL
 +
 
 +
Vector (pSB1C3 backbone digested with EcoRI and PstI): 10μL
 +
 
 +
ddH2O: 9μL
 +
 
 +
Transformation: Trans5α
 +
 
 +
 
 +
 
 +
Annealing to form the promoter from designed primers (95℃ 5min):
 +
 
 +
Primer_For_P3: 7μL
 +
 
 +
Primer_Rev_P3: 7μL
 +
 
 +
Phosphorylation (37℃ 30min):
 +
 
 +
[ADD]
 +
 
 +
PNK: 1μL
 +
 
 +
Ligase buffer: 1.7μL
 +
 
 +
ddH2O: 1μL
 +
 
 +
Ligation:
 +
 
 +
[ADD]
 +
 
 +
Ligase: 5μL
 +
 
 +
Ligase buffer: 3.3μL
 +
 
 +
Insert: (LacZ full length digested with XbaI and PstI): 6μL
 +
 
 +
Vector (pSB1C3 backbone digested with EcoRI and PstI): 10μL
 +
 
 +
ddH2O: 9μL
 +
 
 +
Transformation: Trans5α
-
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.
+
Still no recognizable colonies grew on the agar plates (TT_TT)
 +
 
 +
Hand over this work to Ying Sheng
==October==
==October==
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+
[<html><a href="#top">TOP</a></html>]
-
===10.1===
+
===10.3===
-
Digest pTET+T7 pol using EcoRl and Spel.
+
-
Retrieve the gel.
+
Prepare PARTS
-
Connect T3 promoter+PhiR73+Po promoter+ antigen 43.
 
-
Do the ligation and transformation.
 
-
===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.
+
 
 +
Change backbone
 +
 
 +
(1) T7-RBS-DsbA-MBP_pSB1K3=>T7-RBS-DsbA-MBP_pSB1C3
 +
 +
(2) RBS-LacZ α fragment _pSB1A2=> RBS-LacZ α fragment _pSB1C3
 +
 +
 
 +
 
 +
Digestion (20μL):
 +
 
 +
pSB1C3: 5μL
 +
 
 +
EcoRI-HF: 0.5μL
 +
 
 +
PstI: 0.5μL
 +
 
 +
Buffer (NEBuffer4): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Digestion (20μL):
 +
 
 +
T7-RBS-DsbA-MBP_pSB1K3: 5μL
 +
 
 +
EcoRI-HF: 0.5μL
 +
 
 +
PstI: 0.5μL
 +
 
 +
Buffer (NEBuffer4): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Digestion (20μL):
 +
 
 +
RBS-LacZ α fragment _pSB1A2: 5μL
 +
 
 +
EcoRI-HF: 0.5μL
 +
 
 +
PstI: 0.5μL
 +
 
 +
Buffer (NEBuffer4): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel extraction
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (T7-RBS-DsbA-MBP digested with EcoRI-HF and PstI): 6μL
 +
 
 +
Vector (pSB1C3 backbone digested with EcoRI and PstI): 2μL
 +
 
 +
Transformation: Mach-T1
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (RBS-LacZ α fragment digested with EcoRI-HF and PstI): 6μL
 +
 
 +
Vector (pSB1C3 backbone digested with EcoRI and PstI): 2μL
 +
 
 +
Transformation: Mach-T1
 +
 
 +
 
 +
 
===10.5===
===10.5===
-
Do the auto-aggregation assay.
 
-
===10.7===
 
-
Digest merp+GFP using Spel and Pstl.
 
-
Digest TCP using Xbal and Pstl.
+
Pick up 3 colonies from each agar plates
 +
 
 +
Grow the culture for 12hrs
 +
 
 +
Mini-Prep
 +
 
 +
Verification
 +
 
 +
DNA Sequencing
 +
 
 +
To get the plasmid: T7-RBS-DsbA-MBP (pSB1C3) and RBS-LacZ α fragment (pSB1C3)
 +
 
 +
SUBMIT the plasmids
 +
 
 +
Positive Transformation of T7-RBS-DsbA-MBP (pSB1C3) and RBS-LacZ α fragment (pSB1C3)
 +
 
 +
 
 +
 
 +
===10.6===
 +
 
 +
Pick up 1 colonies from each agar plates
 +
 
 +
Grow the culture for 12hrs
 +
 
 +
SUBMIT the culture preserved with glycerol
 +
 
 +
 
 +
 
 +
Brief Characterization of PmerT-LacZ full length and PmerT-RBS-LacZ α fragment
 +
 
 +
Re-activate the culture to OD600 0.4~0.6
 +
 
 +
Centrifugation (5000r 5min)
 +
 
 +
Resuspension with ddH2O (0.01M Xgal added)
 +
 
 +
Induced by Hg(II) ions of different concentrations from 10-3M to 10-7M
 +
 
 +
(pictures see in PDF)
 +
 
 +
-
Do the ligation and transformation.
 
===10.8===
===10.8===
-
Identify the digested product using electrophoresis.
 
-
Do the ligation and transformation.
+
DNA sequencing shows that P88 / P3-LacZ α fragment (pSB1C3) are correct
 +
 
 +
Positive Transformation
 +
 
 +
Pick up one colony from each agar plate
 +
 
 +
Grow the culture overnight
 +
 
 +
 
 +
 
===10.9===
===10.9===
-
Prepare the plasmid DNA.
 
-
Identify them using PCR.
+
Digestion (20μL):
 +
 
 +
J23114_pSB3K3: 10μL
 +
 
 +
EcoRI-HF: 0.5μL
 +
 
 +
PstI: 0.5μL
 +
 
 +
Buffer (NEBuffer4): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel extraction
 +
 
 +
PCR from P88-LacZ α fragment_pSB1C3 by EasyPFU SuperMix (20μL)
 +
 
 +
2*EasyPFU SuperMix: 10μL
 +
 
 +
ddH2O: 7μL
 +
 
 +
Primer_Univ_For: 1.5μL
 +
 
 +
Primer_Univ_Rev:1.5μL
 +
 
 +
Template: 0.3μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel Extraction
 +
 
 +
There should be one band for P88-RBS-LacZ α fragment: 350bp
 +
 
 +
PCR from P3-LacZ α fragment_pSB1C3 by EasyPFU SuperMix (20μL)
 +
 
 +
2*EasyPFU SuperMix: 10μL
 +
 
 +
ddH2O: 7μL
 +
 
 +
Primer_Univ_For: 1.5μL
 +
 
 +
Primer_Univ_Rev:1.5μL
 +
 
 +
Template: 0.3μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel Extraction
 +
 
 +
There should be one band for P3-RBS-LacZ α fragment: 350bp
 +
 
 +
Digestion (20μL):
 +
 
 +
P88-RBS-LacZ α fragment PCR product: 5μL
 +
 
 +
EcoRI-HF: 0.5μL
 +
 
 +
PstI: 0.5μL
 +
 
 +
Buffer (NEBuffer4): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Digestion (20μL):
 +
 
 +
P3-RBS-LacZ α fragment PCR product: 5μL
 +
 
 +
EcoRI-HF: 0.5μL
 +
 
 +
PstI: 0.5μL
 +
 
 +
Buffer (NEBuffer4): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Purification of the digested PCR product
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (P88-RBS-LacZ α fragment digested with EcoRI-HF and PstI): 6μL
 +
 
 +
Vector (pSB3K3 backbone digested with EcoRI and PstI): 2μL
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (P3-RBS-LacZ α fragment digested with EcoRI-HF and PstI): 6μL
 +
 
 +
Vector (pSB3K3 backbone digested with EcoRI and PstI): 2μL
 +
 
 +
Transformation: Trans5α
 +
 
 +
 
-
Send the correct ones for sequencing.
 
===10.10===
===10.10===
-
Antigen 43 clone step done.
 
-
Connect ptet+T7 pol with T7 promoter+PhiR73+Po promoter+ antigen 43.
+
Pick up 6 colonies from each plate
 +
 
 +
Grow the culture for 12hrs
 +
 
 +
Colony PCR by EasyTaq SuperMix
 +
 
 +
Template: 0.2μL
 +
 
 +
Primer_Univ_For: 1μL
 +
 
 +
Primer_Univ_Rev: 1μL
 +
 
 +
2*EasyTaq SuperMix: 5μL
 +
 
 +
ddH2O:3μL
 +
 
 +
Electrophoresis to verify
 +
 
 +
 
 +
 
 +
Pick up one colony from plates: 1_18E and J23117
 +
 
 +
Grow the culture for 12hrs
 +
 
 +
 
 +
 
 +
 
-
Do the ligation and transformation.
 
===10.11===
===10.11===
-
Do the auto-aggregation assay.
+
 
 +
Fail in cultivating overnight culture
 +
 
 +
PHAGE appeared??? (>…<)
 +
 
 +
Pick up another 6 colonies from each plate
 +
 
 +
Grow the culture for 12hrs
 +
 
 +
Colony PCR by EasyTaq SuperMix
 +
 
 +
Template: 0.2μL
 +
 
 +
Primer_Univ_For: 1μL
 +
 
 +
Primer_Univ_Rev: 1μL
 +
 
 +
2*EasyTaq SuperMix: 5μL
 +
 
 +
ddH2O:3μL
 +
 
 +
Electrophoresis to verify
 +
 
 +
 
 +
 
===10.12===
===10.12===
-
Do the auto-aggregation assay.
+
 
 +
Fail in cultivating overnight culture again (T_T)
 +
 
 +
Pick up another 5 colonies from each plate
 +
 
 +
Grow the culture in fresh LB with 1/10 kanamyclin for 12hrs
 +
 
 +
Colony PCR by EasyTaq SuperMix
 +
 
 +
Template: 0.2μL
 +
 
 +
Primer_Univ_For: 1μL
 +
 
 +
Primer_Univ_Rev: 1μL
 +
 
 +
2*EasyTaq SuperMix: 5μL
 +
 
 +
ddH2O:3μL
 +
 
 +
Electrophoresis to verify
 +
 
 +
 
 +
 
===10.13===
===10.13===
-
Measure the result.
+
 
 +
Mini-prep
 +
 
 +
Get the plasmids: P88-RBS-LacZα fragment_pSB3K3
 +
 
 +
P3-RBS-LacZα fragment_pSB3K3
 +
 
 +
Re-activate the culture: 1_18E and J23117
 +
 
 +
Make them competent cells for bi-transformation
 +
 
 +
Transformation:
 +
 
 +
Competent cell 1_18E: P88-RBS-LacZα fragment_pSB3K3
 +
 
 +
Competent cell J23117: P3-RBS-LacZα fragment_pSB3K3
 +
 
 +
 
 +
 
 +
===10.14===
 +
 
 +
Pick up 3 colonies from each agar plate
 +
 
 +
Grow the culture overnight
 +
 
 +
 
 +
 
===10.15===
===10.15===
-
Attend group seminar.
 
-
Do the auto-aggregation assay.
+
Brief Characterization of P88-RBS-LacZ α fragment and P3- RBS-LacZ α fragment
-
===10.16-10.21===
+
 
-
Connect merp+GFP with TCP.
+
Re-activate the culture to OD600 0.4~0.6
 +
 
 +
Centrifugation (5000r 5min)
 +
 
 +
Resuspension with ddH2O (0.01M Xgal added)
 +
 
 +
Induced by Hg(II) ions of different concentrations from 10-3M to 10-7M
 +
 
 +
 
 +
 
 +
NO COLOR CHANGE (! _ !)
 +
 
 +
 
 +
 
 +
[10.16-10.23] Prepare for GRE test
 +
 
 +
 
 +
 
 +
===10.24===
 +
 
 +
Pick up 6 colonies from each agar plate: J23109_pSB3K3
 +
 
 +
Grow the culture overnight
 +
 
 +
 
 +
 
 +
===10.25===
 +
 
 +
Mini-prep
 +
 
 +
Get the plasmid: J23109_pSB3K3
 +
 
 +
Digestion (20μL):
 +
 
 +
J23109_pSB3K3: 10μL
 +
 
 +
EcoRI-HF: 0.5μL
 +
 
 +
PstI: 0.5μL
 +
 
 +
Buffer (NEBuffer4): 2μL
 +
 
 +
ddH2O: 12μL
 +
 
 +
Electrophoresis
 +
 
 +
Gel extraction
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (P88-RBS-LacZα fragment_pSB3K3): 6μL
 +
 
 +
Vector (pSB3K3 backbone digested with EcoRI and PstI): 2μL
 +
 
 +
Ligation (10μL):
 +
 
 +
Ligase: 1μL
 +
 
 +
Ligase buffer: 1μL
 +
 
 +
Insert (P3-RBS-LacZα fragment_pSB3K3): 6μL
 +
 
 +
Vector (pSB3K3 backbone digested with EcoRI and PstI): 2μL
 +
 
 +
Transformation: TransT1-phage [14:00-0:00]
 +
 
 +
Pick up one colony from plates: 1_18E and J23117
 +
 
 +
Grow the culture for 12hrs [19:30-7:30]
 +
 
 +
 
 +
 
 +
===10.26===
 +
 
 +
Pick up 6 colonies from each plate
 +
 
 +
Grow the culture for 12hrs [0:30-12:30]
 +
 
 +
Colony PCR by EasyTaq SuperMix
 +
 
 +
Template: 0.2μL
 +
 
 +
Primer_Univ_For: 1μL
 +
 
 +
Primer_Univ_Rev: 1μL
 +
 
 +
2*EasyTaq SuperMix: 5μL
 +
 
 +
ddH2O:3μL
 +
 
 +
Electrophoresis to verify
 +
 
 +
 
 +
 
 +
Re-activate the culture of 1_18E and J23117 [7:30-11:30]
 +
 
 +
Make them competent cells for bi-transformation [12:00-13:00]
 +
 
 +
 
 +
 
 +
Mini-prep [12:30-13:30] Helped by Haoqian Zhang
 +
 
 +
Get the plasmids P88-RBS-LacZα fragment_pSB3K3
 +
 
 +
P3-RBS-LacZα fragment_pSB3K3
 +
 
 +
 
 +
 
 +
Transformation: TransT1-phage [13:30-15:00]
 +
 
 +
Competent cell 1_18E: P88-RBS-LacZα fragment_pSB3K3
 +
 
 +
Competent cell J23117: P3-RBS-LacZα fragment_pSB3K3
 +
 
 +
[15:00-1:00]
 +
 
 +
===10.27===
 +
 
 +
Pick up 3 colonies on each agar plate
 +
 
 +
Grow the culture for 12hrs [1:30-13:30]
 +
 
 +
Re-activate the culture [13:30-15:30]
 +
 
 +
 
 +
 
 +
Brief Characterization of PmerT-LacZ full length and PmerT-RBS-LacZ α fragment
 +
 
 +
Re-activate the culture to OD600 0.4~0.6
 +
 
 +
Centrifugation (5000r 5min)
 +
 
 +
Resuspension with ddH2O (0.01M Xgal added)
 +
 
 +
Induced by Hg(II) ions of different concentrations from 10-3M to 10-7M [16:00-10:00]
 +
 
-
Connect pc+merR with terminator.
 
-
Transform these two plasmid into one single strain.
 
-
Antigen 43 auto-aggregation assay.  Analyse the result.
 
-
===10.21-10.25===
 
-
Upload and edit parts of our group.
 
-
[[https://2010.igem.org/Team:Peking/Notebook/ZRLiu TOP]]
 
 +
[<html><a href="#top">TOP</a></html>]
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Latest revision as of 10:35, 27 October 2010




   Zairan Liu's Notes
                                                                                                                                                goto her page
I am responsible for the construction of metal binding peptide periplasm display module for Pb(II). This module aims at binding Pb(II) ions in the periplasmic space using the engineered anti-parallel coiled coil which is transported with the help of DsbA signal sequence. During the process several other intermediate plasmids are also constructed. Furthermore, I contribute to the characterization of Pc promoters of different intensity.


download her notes

Contents


July

Mon Tue Wed Thu Fri Sat Sun
- - - - 1 2 3
4 5 6 7 8 9 10
11 12 13 14 15 16 17
18 19 20 21 22 23 24
25 26 27 29 29 30 31
- - - - - - -

[TOP]

7.5

Purification of digested PCR product: merP, merT, and merC

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (merP / merT / merC digested with EcoRI and PstI): 7μL

Vector (pSB1A2 backbone digested with EcoRI and PstI): 1μL

Transformation: Trans5α

7.6

No recognizable colonies grew on the agar plates (T_T)

Digestion (20μL):

pSB1A2: 5μL

EcoRI: 1μL

PstI: 1μL

Buffer (EcoRI Buffer): 2μL

ddH2O: 12μL

Electrophoresis

Gel Extraction


PCR to get merP, merT and merC fragments by Phusion (20μL)

5*phusionHF buffer: 4μL

2.5mM dNTPs: 1.6μL

Polymerase: 0.2μL

Primer_For:1μL

Primer_Rev: 1μL

Template: 0.5μL

ddH2O: 11.7μL


7.7

Electrophoresis

Gel Extraction

merT: 351bp

merP: 256bp

merC: 423bp

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (merP / merT / merC digested with EcoRI and PstI): 7μL

Vector (pSB1A2 backbone digested with EcoRI and PstI): 1μL

Transformation: Trans5α


7.8

Pick up 3 colonies from each agar plate

Grow the culture overnight

[7.9-7.19 Field Practices @ Yantai & Beijing (^_<)] [7.20-7.21 Home @ Nanjing (#_#)] [7.22-7.24 World Exhibit @ Shanghai (*~*)Orz] [7.25 Home @ Nanjing (#_#)]

7.26

Design the PbrR Metal Binding Peptide (MBP) Construction

PCR from pbrR to get the N terminal and C terminal of MBP by PFUEasyMix (20μL)

EasyMix: 10μL

ddH2O: 9μL

Primer_For_N: 0.5μL

Primer_Rev_N:0.5μL

Template (pbrR): 0.5μL

=>Get the metal binding domain of pbrR as the N terminal for MBP_STD

EasyMix: 10μL

ddH2O: 9μL

Primer_For_C: 0.5μL

Primer_Rev_C:0.5μL

Template (pbrR): 0.5μL

=>Get the metal binding domain of pbrR as the C terminal for MBP_STD

Linker are designed into Primer_Rev_N and Primer_For_C


7.27

Electrophoresis

Gel Extraction


N C

Digestion:

N terminal: EcoRI+BspEI+NEBuffer3

C terminal: BspEI+PstI+NEBuffer3

Purification of digestion product

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert1 (N terminal digested with EcoRI and BspEI): 3μL

Insert2 (C terminal digested with BspEI and PstI): 3μL

Vector (pSB1K3 backbone digested with EcoRI and PstI): 2μL


7.28

Transformation: OmniMAX

Pick up 3 colonies from the agar plate

Grow the culture overnight


7.29

Mini-Prep

Verification

DNA Sequencing

To get the plasmid: pbrR_MBP_STD (pSB1K3)


PCR from pbrR to get the N terminal and C terminal of MBP by EasyPFU (50μL)

10*EasyPFU buffer: 5μL

2.5mM dNTPs: 5μL

Polymerase: 1μL

Primer_For_N’:1μL

Primer_Rev_N’: 1μL

Template (pbrR): 0.2μL

ddH2O: 36.8μL

=>Get the metal binding domain of pbrR as the N terminal for MBP_COM

10*EasyPFU buffer: 5μL

2.5mM dNTPs: 5μL

Polymerase: 1μL

Primer_For_C’:1μL

Primer_Rev_C’: 1μL

Template (pbrR): 0.2μL

ddH2O: 36.8μL

=>Get the metal binding domain of pbrR as the C terminal for MBP_COM

Linker are designed into Primer_Rev_N’ and Primer_For_C’

Electrophoresis

Gel Extraction

Digestion:

N terminal: NdeI+BspEI+NEBuffer3

C terminal: BspEI+XhoI+NEBuffer3


7.30

Purification of digested product

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert1 (N terminal digested with NdeI and BspEI): 3μL

Insert2 (C terminal digested with BspEI and XhoI): 3μL

Vector (pET21a backbone digested with NdeI and XhoI): 2μL

Transformation: OmniMAX


7.31

Pick up 3 colonies from the agar plate

Grow the culture for 12hrs

Mini-Prep

Verification

DNA Sequencing

To get the plasmid: pbrR_MBP_COM (pET21a)

August

Mon Tue Wed Thu Fri Sat Sun
1 2 3 4 5 6 7
8 9 10 11 12 13 14
15 16 17 18 19 20 21
22 23 24 25 26 27 28
29 30 31 - - - -

[TOP]

8.3

Design the DsbA-MBP Construction


PCR from pbrR to get the N terminal and C terminal of MBP by EasyPFU SuperMix (50μL)

2*EasyPFU SuperMix: 25μL

ddH2O: 20.8μL

Primer_For_N: 2μL

Primer_Rev_N:2μL

Template (pbrR): 0.2μL

=>Get the metal binding domain of pbrR as the N terminal for DsbA-MBP

2*EasyPFU SuperMix: 25μL

ddH2O: 20.8μL

Primer_For_C: 2μL

Primer_Rev_C:2μL

Template (pbrR): 0.2μL

=>Get the metal binding domain of pbrR as the C terminal for DsbA-MBP

Linker are designed into Primer_Rev_N and Primer_For_C

Electrophoresis to verify

Purification of PCR product

Digestion:

N terminal: XbaI+BspEI+NEBuffer3

C terminal: BspEI+XhoI+NEBuffer3

8.4

Purification of digested product

Digestion (20μL):

pET39b: 5μL

SpeI: 1μL

XhoI: 1μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Electrophoresis

Gel Extraction

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert1 (N terminal digested with XbaI and BspEI): 3μL

Insert2 (C terminal digested with BspEI and XhoI): 3μL

Vector (pET39b backbone digested with SpeI and XhoI): 2μL

Transformation: OmniMAX


8.5

Mini-Prep

Verification: Digestion (20μL):

Plasmid: 5μL

NdeI: 1μL

XhoI: 1μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Electrophoresis to verify

NdeI(1030) XhoI(174) MBP(abt 500bp)

Correct band=1030-174+500=1356

DNA Sequencing

To get the plasmid: DsbA-MBP (pET39b)


8.10

Design and the T7-RBS-DsbA-MBP Construction


1st Round of Nest PCR by EasyPFU SuperMix (50μL)

2*EasyPFU SuperMix: 25μL

ddH2O: 20.8μL

Primer_For (T7-RBS-DsbA-F1): 2μL

Primer_Rev (PbrR-MBP-C’-R):2μL

Template (DsbA-MBP): 0.2μL

=>RBS is prefixed to DsbA-MBP

Electrophoresis


FAILED!!!(TAT)


REPEAT-PCR with Gradient

Gradient: T=60℃ G=5

Electrophoresis


Gel extraction

8.11

2nd Round of Nest PCR by EasyPFU SuperMix (50μL)

2*EasyPFU SuperMix: 25μL

ddH2O: 20.8μL

Primer_For (T7-RBS-DsbA-F2): 2μL

Primer_Rev (PbrR-MBP-C’-R):2μL

Template (1st Round of Nest PCR product (RBS-DsbA-MBP)): 0.2μL

=>T7 is prefixed to 1st Round of Nest PCR product (RBS-DsbA-MBP)

Electrophoresis

Gel extraction


8.12

Digestion (20μL):

2nd Round of Nest PCR product (T7-RBS-DsbA-MBP): 5μL

EcoRI: 1μL

SpeI: 1μL

Buffer (EcoRI Buffer): 2μL

ddH2O: 12μL

Purification of digested product


Digestion (20μL):

pSB1C3: 5μL

EcoRI: 1μL

SpeI: 1μL

Buffer (EcoRI Buffer): 2μL

ddH2O: 12μL

Electrophoresis

Gel Extraction

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (T7-RBS-DsbA-MBP digested with EcoRI and SpeI): 6μL

Vector (pSB1K3 backbone digested with EcoRI and SpeI): 2μL

Transformation: OmniMAX


8.13

Pick up 5 colonies from each agar plate

Grow the culture overnight


8.14

Mini-Prep

Verification: Digestion (20μL):

Plasmid: 5μL

PstI: 1μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Electrophoresis to verify

There should be two bands; one is about 3000bp and the other is 600bp

Verification: PCR by EasyTaq SuperMix

Template: 0.2μL

Primer_Univ_For: 1μL

Primer_Univ_Rev: 1μL

2*EasyTaq SuperMix: 5μL

ddH2O:3μL

Electrophoresis to verify

There should be one band, which is about 1200bp

DNA Sequencing

To get the plasmid: DsbA-MBP (pET39b)


8.16

FAILED (T~T)

Why?

Because the reverse primer cannot specifically distinguish the C terminal from the N terminal of the MBP, new primer including the sequence of His-tag is designed in order to recognize the C terminal only


Hand over this work to Donghai Liang

[8.17-8.31] Physical Training

September

Mon Tue Wed Thu Fri Sat Sun
- - 1 2 3 4 5
6 7 8 9 10 11 12
13 14 15 16 17 18 19
20 21 22 23 24 25 26
27 28 29 30 - - -

[TOP]

9.1

Digestion (20μL):

pSB1C3: 5μL

EcoRI: 1μL

PstI: 1μL

Buffer (EcoRI Buffer): 2μL

ddH2O: 12μL

Electrophoresis

Gel Extraction

Digestion (20μL):

pbrR_MBP_STD (pSB1A2): 5μL

EcoRI: 1μL

PstI: 1μL

Buffer (EcoRI Buffer): 2μL

ddH2O: 12μL

Electrophoresis

Gel Extraction

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (PbrR_MBP_STD digested with EcoRI and SpeI): 6μL

Vector (pSB1C3 backbone digested with EcoRI and SpeI): 2μL

Transformation: OmniMAX


9.2

Mini-Prep

Verification: Digestion (20μL):

Plasmid: 5μL

EcoRI: 1μL

PstI: 1μL

Buffer (EcoRI Buffer): 2μL

ddH2O: 12μL

Electrophoresis to verify

There should be one band, which is about 500bp

DNA Sequencing

To get the plasmid: pbrR-MBP (pSB1C3)


9.3

Construct the concentration of Hg(II) ions for induction 

   Final Concentration/M Volume/μL Original Concentration/M

1. 5*10-5 25 10-3

2. 3*10-5 15 10-3

3. 10-5 5 10-3

4. 8*10-6 4 10-3

5. 5*10-6 2.5 10-3

6. 3*10-6 1.5 10-3

7. 10-6 0.5 10-3

8. 8*10-7 4 10-4

9. 5*10-7 2.5 10-4

10. 3*10-7 1.5 10-4

11. 10-7 0.5 10-4

12. 8*10-8 4 10-5

13. 5*10-8 2.5 10-5

14. 3*10-8 1.5 10-5

15. 10-8 0.5 10-5

16. 8*10-9 0.4 10-5

17. 5*10-9 25 10-7

18. 3*10-9 15 10-7

19. 10-9 5 10-7

20. 0 0 0


9.5

Learn the protocol for preparation of competent cells for transformation for bi-transformation

Pick up one colony from each agar plate: J23109 and J23112

Grow the culture overnight


9.6

Re-activate the culture of J23109 and J23112 in fresh LB with ampicilin and kanamyclin

Measure the value of OD600

Induced with Hg(II) ions of different concentration for 2hrs

Centrifugation at 5000r for 5min

Resuspension with PBS

Measure the value of OD600 and GFP with ELISA


9.7

Learn about Western Blot with Boxuan Zhao


9.15

Design the traffic light assay

LacZ full length (RBS: B0034) BBa_I1732017 2_3K 3093bp pSB1A2

LacZ α fragment BBa_I732006 1_23H 234bp pSB1AK3

Plasmid1: 1_18I MerR (pSB3K3)

Plasmid2: PmerT - LacZ full length / LacZ α fragment (pSB1C3)

X-GAL assay


Positive Transformation of 2_3K and 1_23H: TansMAX


9.17

Pick up 2 colonies from each agar plate: 2_3K and 1_23H

Grow the culture for 12hrs

Mini-Prep

Get the plasmids: 2_3K (LacZ full length_ pSB1A2)

1_23H (LacZ α fragment_ pSB1AK3)


9.18

Digestion (20μL):

LacZ full length: 5μL

SpeI: 1μL

PstI: 1μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Digestion (20μL):

LacZα fragment: 5μL

SpeI: 1μL

PstI: 1μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Electrophoresis

Gel Extraction


FAILED(T_T)

Wrong enzyme used


9.19

Digestion (20μL):

LacZ full length: 5μL

XbaI: 1μL

PstI: 1μL

Buffer (NEBuffer3): 2μL

ddH2O: 12μL

Digestion (20μL):

LacZ α fragment: 5μL

XbaI: 1μL

PstI: 1μL

Buffer (NEBuffer3): 2μL

ddH2O: 12μL

Electrophoresis

Gel Extraction

The band for LacZ full length is clear but not for LacZ α fragment

Change method

PCR from 1_23H by EasyPFU SuperMix (20μL)

2*EasyPFU SuperMix: 10μL

ddH2O: 7μL

Primer_Univ_For: 1.5μL

Primer_Univ_Rev:1.5μL

Template: 0.3μL

Electrophoresis

Gel Extraction

There should be one band for LacZ α fragment: 250bp


9.20

Digestion (20μL):

RBS_pSB1A2: 5μL

SpeI: 1μL

PstI: 1μL

Buffer (NEBuffer2): 2μL

ddH2O: 12μL

Electrophoresis

Gel Extraction

Get the RBS_pSB1A2 backbone digested with SpeI and PstI

Digestion (20μL):

PmerT_pSB1C3: 5μL

SpeI: 1μL

PstI: 1μL

Buffer (NEBuffer2): 2μL

ddH2O: 12μL

Electrophoresis

Gel Extraction

Get the PmerT_pSB1C3 backbone digested with SpeI and PstI

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (LacZ α fragment digested with XbaI and PstI): 6μL

Vector (RBS_pSB1A2 backbone digested with SpeI and PstI): 2μL

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (LacZ full length digested with XbaI and PstI): 6μL

Vector (PmerT_pSB1C3 backbone digested with SpeI and PstI): 2μL

Transformation of RBS-LacZ α fragment (pSB1A2)


9.21

No recognizable colonies grew on the agar plates (T_T)

FAILED (>.<||)

Forgot to digest the PCR product


Digestion (20μL):

1_23H PCR product: 5μL

XbaI: 1μL

PstI: 1μL

Buffer (NEBuffer3): 2μL

ddH2O: 12μL

Purification of the digested product

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (LacZ α fragment digested with XbaI and PstI): 6μL

Vector (RBS_pSB1A2 backbone digested with SpeI and PstI): 2μL

Transformation of RBS-LacZ α fragment (pSB1A2)

Transformation of PmerT-LacZ full length (pSB1C3)


9.22

Pick up 6 colonies from each agar plate of RBS-LacZ α fragment (pSB1A2) and PmerT-LacZ full length (pSB1C3)

Grow the culture for 12hrs

Mini-prep of PmerT-LacZ full length (pSB1C3)

Digestion (20μL):

PmerT-LacZ full length (pSB1C3): 5μL

XbaI: 1μL

PstI: 1μL

Buffer (NEBuffer3): 2μL

ddH2O: 12μL

Electrophoresis to verify

Band No.1, 2, 3, 6 are of correct size

DNA Sequencing

To get the plasmid: PmerT-LacZ full length (pSB1C3)


Mini-prep of RBS-LacZ α fragment (pSB1A2)

Digestion (20μL):

RBS-LacZ α fragment (pSB1A2): 5μL

XbaI: 1μL

PstI: 1μL

Buffer (NEBuffer3): 2μL

ddH2O: 12μL

Electrophoresis to verify

Band No.1, 2, 3, 4, 5, 6 are all of correct size


9.23

PCR to get RBS-LacZ α fragment by FastPFU (50μL)

5*phusionHF buffer: 10μL

2.5mM dNTPs: 5μL

Polymerase: 1μL

Primer_Univ_For: 1.5μL

Primer_Univ_Rev:1.5μL

Template: 0.2μL

ddH2O: 32μL

Electrophoresis

Excise the band of 250bp

Gel Extraction

Digestion (20μL):

RBS-LacZ α fragment: 5μL

XbaI: 1μL

PstI: 1μL

Buffer (NEBuffer3): 2μL

ddH2O: 12μL

Purification of digested product

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (LacZ α fragment digested with XbaI and PstI): 6μL

Vector (PmerT_pSB1C3 backbone digested with SpeI and PstI): 2μL


9.24

Transformation: Trans5α

Pick up 6 colonies from the agar plate: PmerT- RBS-LacZ α fragment (pSB1C3)

Grow the culture for overnight


9.25

Mini-prep of PmerT- RBS-LacZ α fragment (pSB1C3)

Digestion (20μL):

PmerT- RBS-LacZ α fragment (pSB1C3): 5μL

XbaI: 1μL

PstI: 1μL

Buffer (NEBuffer3): 2μL

ddH2O: 12μL

Electrophoresis to verify

Band No.1, 2, 3, 4, 5, 6 are all of correct size

DNA Sequencing

To get the plasmid: PmerT- RBS-LacZ α fragment (pSB1C3)


9.26

Construct the mutant promoter P88 and P3 into the traffic light system


9.27

Annealing to form the promoter from designed primers (95℃ 5min):

Primer_For_P88: 1.5μL

Primer_Rev_P88:1.5μL

Phosphorylation (37℃ 30min):

[ADD]

PNK: 1μL

Ligase buffer: 1μL

ddH2O: 4μL

Ligation:

[ADD]

Ligase: 1μL

Vector (RBS-LacZ α fragment _pSB1A2 backbone digested with EcoRI and XbaI): 1μL

Transformation: Trans5α


Annealing to form the promoter from designed primers (95℃ 5min):

Primer_For_P3: 1.5μL

Primer_Rev_P3:1.5μL

Phosphorylation (37℃ 30min):

[ADD]

PNK: 1μL

Ligase buffer: 1μL

ddH2O: 4μL

Ligation:

[ADD]

Ligase: 1μL

Vector (RBS-LacZ α fragment _pSB1A2 backbone digested with EcoRI and XbaI): 1μL

Transformation: Trans5α


Annealing to form the promoter from designed primers (95℃ 5min):

Primer_For_P88: 3μL

Primer_Rev_P88: 3μL

Phosphorylation (37℃ 30min):

[ADD]

PNK: 1μL

Ligase buffer: 1μL

ddH2O: 1μL

Ligation:

[ADD]

Ligase: 2μL

Ligase buffer: 1μL

Insert: (LacZ full length digested with XbaI and PstI): 6μL

Vector (pSB1C3 backbone digested with EcoRI and PstI): 2μL

Transformation: Trans5α


Annealing to form the promoter from designed primers (95℃ 5min):

Primer_For_P3: 3μL

Primer_Rev_P3: 3μL

Phosphorylation (37℃ 30min):

[ADD]

PNK: 1μL

Ligase buffer: 1μL

ddH2O: 1μL

Ligation:

[ADD]

Ligase: 2μL

Ligase buffer: 1μL

Insert: (LacZ full length digested with XbaI and PstI): 6μL

Vector (pSB1C3 backbone digested with EcoRI and PstI): 2μL

Transformation: Trans5α


9.28

No recognizable colonies grew on the agar plates (T_T)

REPEAT


9.29

Still no recognizable colonies grew on the agar plates (TAT)

Change the ratio of different components

Annealing to form the promoter from designed primers (95℃ 5min):

Primer_For_P88: 15μL

Primer_Rev_P88:15μL

Phosphorylation (37℃ 30min):

[ADD]

PNK: 1μL

Ligase buffer: 3.5μL

ddH2O: 1μL

Ligation:

[ADD]

Ligase: 5μL

Ligase buffer: 1.5μL

Vector (RBS-LacZ α fragment _pSB1A2 backbone digested with EcoRI and XbaI): 10μL

Transformation: Trans5α


Annealing to form the promoter from designed primers (95℃ 5min):

Primer_For_P3: 15μL

Primer_Rev_P3:15μL

Phosphorylation (37℃ 30min):

[ADD]

PNK: 1μL

Ligase buffer: 3.5μL

ddH2O: 1μL

Ligation:

[ADD]

Ligase: 5μL

Ligase buffer: 1.5μL

Vector (RBS-LacZ α fragment _pSB1A2 backbone digested with EcoRI and XbaI): 10μL

Transformation: Trans5α


Annealing to form the promoter from designed primers (95℃ 5min):

Primer_For_P88: 7μL

Primer_Rev_P88: 7μL

Phosphorylation (37℃ 30min):

[ADD]

PNK: 1μL

Ligase buffer: 1.7μL

ddH2O: 1μL

Ligation:

[ADD]

Ligase: 5μL

Ligase buffer: 3.3μL

Insert: (LacZ full length digested with XbaI and PstI): 6μL

Vector (pSB1C3 backbone digested with EcoRI and PstI): 10μL

ddH2O: 9μL

Transformation: Trans5α


Annealing to form the promoter from designed primers (95℃ 5min):

Primer_For_P3: 7μL

Primer_Rev_P3: 7μL

Phosphorylation (37℃ 30min):

[ADD]

PNK: 1μL

Ligase buffer: 1.7μL

ddH2O: 1μL

Ligation:

[ADD]

Ligase: 5μL

Ligase buffer: 3.3μL

Insert: (LacZ full length digested with XbaI and PstI): 6μL

Vector (pSB1C3 backbone digested with EcoRI and PstI): 10μL

ddH2O: 9μL

Transformation: Trans5α


9.30

Still no recognizable colonies grew on the agar plates (TT_TT)

Hand over this work to Ying Sheng

October

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10.3

Prepare PARTS


10.4

Change backbone

(1) T7-RBS-DsbA-MBP_pSB1K3=>T7-RBS-DsbA-MBP_pSB1C3

(2) RBS-LacZ α fragment _pSB1A2=> RBS-LacZ α fragment _pSB1C3


Digestion (20μL):

pSB1C3: 5μL

EcoRI-HF: 0.5μL

PstI: 0.5μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Digestion (20μL):

T7-RBS-DsbA-MBP_pSB1K3: 5μL

EcoRI-HF: 0.5μL

PstI: 0.5μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Digestion (20μL):

RBS-LacZ α fragment _pSB1A2: 5μL

EcoRI-HF: 0.5μL

PstI: 0.5μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Electrophoresis

Gel extraction

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (T7-RBS-DsbA-MBP digested with EcoRI-HF and PstI): 6μL

Vector (pSB1C3 backbone digested with EcoRI and PstI): 2μL

Transformation: Mach-T1

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (RBS-LacZ α fragment digested with EcoRI-HF and PstI): 6μL

Vector (pSB1C3 backbone digested with EcoRI and PstI): 2μL

Transformation: Mach-T1


10.5

Pick up 3 colonies from each agar plates

Grow the culture for 12hrs

Mini-Prep

Verification

DNA Sequencing

To get the plasmid: T7-RBS-DsbA-MBP (pSB1C3) and RBS-LacZ α fragment (pSB1C3)

SUBMIT the plasmids

Positive Transformation of T7-RBS-DsbA-MBP (pSB1C3) and RBS-LacZ α fragment (pSB1C3)


10.6

Pick up 1 colonies from each agar plates

Grow the culture for 12hrs

SUBMIT the culture preserved with glycerol


Brief Characterization of PmerT-LacZ full length and PmerT-RBS-LacZ α fragment

Re-activate the culture to OD600 0.4~0.6

Centrifugation (5000r 5min)

Resuspension with ddH2O (0.01M Xgal added)

Induced by Hg(II) ions of different concentrations from 10-3M to 10-7M

(pictures see in PDF)


10.8

DNA sequencing shows that P88 / P3-LacZ α fragment (pSB1C3) are correct

Positive Transformation

Pick up one colony from each agar plate

Grow the culture overnight


10.9

Digestion (20μL):

J23114_pSB3K3: 10μL

EcoRI-HF: 0.5μL

PstI: 0.5μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Electrophoresis

Gel extraction

PCR from P88-LacZ α fragment_pSB1C3 by EasyPFU SuperMix (20μL)

2*EasyPFU SuperMix: 10μL

ddH2O: 7μL

Primer_Univ_For: 1.5μL

Primer_Univ_Rev:1.5μL

Template: 0.3μL

Electrophoresis

Gel Extraction

There should be one band for P88-RBS-LacZ α fragment: 350bp

PCR from P3-LacZ α fragment_pSB1C3 by EasyPFU SuperMix (20μL)

2*EasyPFU SuperMix: 10μL

ddH2O: 7μL

Primer_Univ_For: 1.5μL

Primer_Univ_Rev:1.5μL

Template: 0.3μL

Electrophoresis

Gel Extraction

There should be one band for P3-RBS-LacZ α fragment: 350bp

Digestion (20μL):

P88-RBS-LacZ α fragment PCR product: 5μL

EcoRI-HF: 0.5μL

PstI: 0.5μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Digestion (20μL):

P3-RBS-LacZ α fragment PCR product: 5μL

EcoRI-HF: 0.5μL

PstI: 0.5μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Purification of the digested PCR product

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (P88-RBS-LacZ α fragment digested with EcoRI-HF and PstI): 6μL

Vector (pSB3K3 backbone digested with EcoRI and PstI): 2μL

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (P3-RBS-LacZ α fragment digested with EcoRI-HF and PstI): 6μL

Vector (pSB3K3 backbone digested with EcoRI and PstI): 2μL

Transformation: Trans5α


10.10

Pick up 6 colonies from each plate

Grow the culture for 12hrs

Colony PCR by EasyTaq SuperMix

Template: 0.2μL

Primer_Univ_For: 1μL

Primer_Univ_Rev: 1μL

2*EasyTaq SuperMix: 5μL

ddH2O:3μL

Electrophoresis to verify


Pick up one colony from plates: 1_18E and J23117

Grow the culture for 12hrs



10.11

Fail in cultivating overnight culture

PHAGE appeared??? (>…<)

Pick up another 6 colonies from each plate

Grow the culture for 12hrs

Colony PCR by EasyTaq SuperMix

Template: 0.2μL

Primer_Univ_For: 1μL

Primer_Univ_Rev: 1μL

2*EasyTaq SuperMix: 5μL

ddH2O:3μL

Electrophoresis to verify


10.12

Fail in cultivating overnight culture again (T_T)

Pick up another 5 colonies from each plate

Grow the culture in fresh LB with 1/10 kanamyclin for 12hrs

Colony PCR by EasyTaq SuperMix

Template: 0.2μL

Primer_Univ_For: 1μL

Primer_Univ_Rev: 1μL

2*EasyTaq SuperMix: 5μL

ddH2O:3μL

Electrophoresis to verify


10.13

Mini-prep

Get the plasmids: P88-RBS-LacZα fragment_pSB3K3

P3-RBS-LacZα fragment_pSB3K3

Re-activate the culture: 1_18E and J23117

Make them competent cells for bi-transformation

Transformation:

Competent cell 1_18E: P88-RBS-LacZα fragment_pSB3K3

Competent cell J23117: P3-RBS-LacZα fragment_pSB3K3


10.14

Pick up 3 colonies from each agar plate

Grow the culture overnight


10.15

Brief Characterization of P88-RBS-LacZ α fragment and P3- RBS-LacZ α fragment

Re-activate the culture to OD600 0.4~0.6

Centrifugation (5000r 5min)

Resuspension with ddH2O (0.01M Xgal added)

Induced by Hg(II) ions of different concentrations from 10-3M to 10-7M


NO COLOR CHANGE (! _ !)


[10.16-10.23] Prepare for GRE test


10.24

Pick up 6 colonies from each agar plate: J23109_pSB3K3

Grow the culture overnight


10.25

Mini-prep

Get the plasmid: J23109_pSB3K3

Digestion (20μL):

J23109_pSB3K3: 10μL

EcoRI-HF: 0.5μL

PstI: 0.5μL

Buffer (NEBuffer4): 2μL

ddH2O: 12μL

Electrophoresis

Gel extraction

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (P88-RBS-LacZα fragment_pSB3K3): 6μL

Vector (pSB3K3 backbone digested with EcoRI and PstI): 2μL

Ligation (10μL):

Ligase: 1μL

Ligase buffer: 1μL

Insert (P3-RBS-LacZα fragment_pSB3K3): 6μL

Vector (pSB3K3 backbone digested with EcoRI and PstI): 2μL

Transformation: TransT1-phage [14:00-0:00]

Pick up one colony from plates: 1_18E and J23117

Grow the culture for 12hrs [19:30-7:30]


10.26

Pick up 6 colonies from each plate

Grow the culture for 12hrs [0:30-12:30]

Colony PCR by EasyTaq SuperMix

Template: 0.2μL

Primer_Univ_For: 1μL

Primer_Univ_Rev: 1μL

2*EasyTaq SuperMix: 5μL

ddH2O:3μL

Electrophoresis to verify


Re-activate the culture of 1_18E and J23117 [7:30-11:30]

Make them competent cells for bi-transformation [12:00-13:00]


Mini-prep [12:30-13:30] Helped by Haoqian Zhang

Get the plasmids P88-RBS-LacZα fragment_pSB3K3

P3-RBS-LacZα fragment_pSB3K3


Transformation: TransT1-phage [13:30-15:00]

Competent cell 1_18E: P88-RBS-LacZα fragment_pSB3K3

Competent cell J23117: P3-RBS-LacZα fragment_pSB3K3

[15:00-1:00]

10.27

Pick up 3 colonies on each agar plate

Grow the culture for 12hrs [1:30-13:30]

Re-activate the culture [13:30-15:30]


Brief Characterization of PmerT-LacZ full length and PmerT-RBS-LacZ α fragment

Re-activate the culture to OD600 0.4~0.6

Centrifugation (5000r 5min)

Resuspension with ddH2O (0.01M Xgal added)

Induced by Hg(II) ions of different concentrations from 10-3M to 10-7M [16:00-10:00]



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