5/26/2015
1-
1 μL 3` R primares
1 μL 3` F primares
2 μL PCR(ClpB) from 4/10/2015
12.5 μL supermix.
8 μL dd water.
Protocol:
95 °C 3 minutes
95 °C 30 seconds
72 °C 2 minutes 35 cycles
68 °C 1.5 minutes
Final elongation 68 °C for 5 minutes.
2-
1 μL 5` R primares
1 μL 5` F primares
2 μL PCR(ClpB) from 4/10/2015
12.5 μL supermix.
8 μL dd water.
Protocol:
95 °C 3 minutes
95 °C 30 seconds
72 °C 2 minutes 35 cycles
68 °C 1.5 minutes
Final elongation 68 °C for 5 minutes.
2-ClpB 5 prim(500bp)
empty
1-ClpB3 prim(500bp)
osama`s notebook
This blog is the ONS (Open Notebook Science) record for the work that I personally perform in the lab. It is posted informally and without peer review. Please feel free to comment and to contact me at osama.mahdi[at]my.ndsu.edu if there is something you're interested in. You can learn more about the lab on our wiki page at http://openwetware.org/wiki/Fisher. Thanks for visiting.
Friday, May 29, 2015
PCR for plasmidminipreb
5/20/2015
Plasmids from Plasmid minipreb for ClpX, ClpB and ChiT
Negative control: pJH1 with ClpB primares.
ChiT4 (band)
ChiT3 (band)
ChiT2
ChiT1
ClpB4
B3
B2
ladder
empty
B1 (band)
pJH1
ClpX4
X3
X2
X1
ladder
Plasmids from Plasmid minipreb for ClpX, ClpB and ChiT
Negative control: pJH1 with ClpB primares.
![]() |
1% agrose run for 2 h. |
ChiT4 (band)
ChiT3 (band)
ChiT2
ChiT1
ClpB4
B3
B2
ladder
empty
B1 (band)
pJH1
ClpX4
X3
X2
X1
ladder
Friday, May 22, 2015
Direct PCR for the insert clones
5/6/2015
Clones were grown on LB+ Hygromycin 250 mg/ml, direct sample was taken from the colony.
1 μL 3` R primares
1 μL 5` F primares
12.5 μL supermix.
10 μL dd water.
Protocol:
95 °C 3 minutes
95 °C 30 seconds
55 °C 2 minutes 30 cycles
68 °C 1.5 minutes
Final elongation 68 °C for 5 minutes.
ChiT B/r
ChiT,pJH1
ChiT PCR
ChiT3
ChiT2
ChiT1
ClpB,pJH1
ClpB,PCR
ClpB3
ClpB2
ClpB1
ClpX,pJH1
ClpX,PCR
ClpX3
ClpX2
ClpX1
ladder
Clones were grown on LB+ Hygromycin 250 mg/ml, direct sample was taken from the colony.
- Clones: ClpX1, X2, X3, X4, X5, X6, X7,X8 ,X9 ,X10 and X11
- ClpX primar with pJH1 clone as a control.
- ClpX PCR as a positive control.
- ClpB1, B2,B3, B4, B5, B6, B7and B8 .
- ClpB primar with pJH1 clone as a control.
- ClpB PCR as a positive control.
- ChiT1,T2,T3 and T4
- ChiT primar with pJH1 clone as a control,ChiT primar with B/r E. coli clone as a control.
- ChiT PCR as a positive control.
1 μL 3` R primares
1 μL 5` F primares
12.5 μL supermix.
10 μL dd water.
Protocol:
95 °C 3 minutes
95 °C 30 seconds
55 °C 2 minutes 30 cycles
68 °C 1.5 minutes
Final elongation 68 °C for 5 minutes.
ChiT B/r
ChiT,pJH1
ChiT PCR
ChiT3
ChiT2
ChiT1
ClpB,pJH1
ClpB,PCR
ClpB3
ClpB2
ClpB1
ClpX,pJH1
ClpX,PCR
ClpX3
ClpX2
ClpX1
ladder
Friday, April 24, 2015
Plasmid minipreb for ClpX, ClpB and ChiT
4/17/2015
Clones:
ClpX 1,2,3,4
ClpB 1,2,3,4
ChiT 1,2,3,4
Clones fromTransformation using chemically competent cells for ClpX,ClpB and ChiT + pJH1
Clones:
ClpX 1,2,3,4
ClpB 1,2,3,4
ChiT 1,2,3,4
Clones fromTransformation using chemically competent cells for ClpX,ClpB and ChiT + pJH1
Zyppy™ Plasmid Miniprep Kit was used Protocol
Monday, April 20, 2015
SOE PCR for clpX, ClpB and ChiT
4/10/2015
1-
1.5 μL ClpX 3` sample 1, 2/2/2015
1.5 μL ClpX 5` sample 2, 2/11.2015
1.5 μL ClpX 3` R primares
1.5 ClpX 5` F primares
20 micro supermix.
2-
1.5 μL ClpB 3` sample 1, 2/8/2015
1.5 μL ClpB 5` sample 3, 2/11.2015
1.5 μL ClpB 3` R primares
1.5 ClpB 5` F primares
20 micro supermix.
3-
1.5 μL ChiT 3` sample , 3/3/2015
1.5 μL ChiT 5` sample 4, 2/11.2015
1.5 μL ChiT 3` R primares
1.5 ChiT 5` F primares
20 micro supermix.
Protocol:
95 °C 3 minutes
95 °C 30 seconds
55 °C 2 minutes 30 cycles
68 °C 1.5 minutes
Final elongation 68 °C for 5 minutes.
1-
1.5 μL ClpX 3` sample 1, 2/2/2015
1.5 μL ClpX 5` sample 2, 2/11.2015
1.5 μL ClpX 3` R primares
1.5 ClpX 5` F primares
20 micro supermix.
2-
1.5 μL ClpB 3` sample 1, 2/8/2015
1.5 μL ClpB 5` sample 3, 2/11.2015
1.5 μL ClpB 3` R primares
1.5 ClpB 5` F primares
20 micro supermix.
3-
1.5 μL ChiT 3` sample , 3/3/2015
1.5 μL ChiT 5` sample 4, 2/11.2015
1.5 μL ChiT 3` R primares
1.5 ChiT 5` F primares
20 micro supermix.
Protocol:
95 °C 3 minutes
95 °C 30 seconds
55 °C 2 minutes 30 cycles
68 °C 1.5 minutes
Final elongation 68 °C for 5 minutes.
Friday, April 17, 2015
Transformation using chemically competent cells for ClpX,ClpB and ChiT + pJH1
4/1/2015
ClpX,ClpB and ChiT + pJH1
One Shot® Mach1™-T1R Chemically Competent E. coli
Transforming Competent Cells Perform the following before starting the transformation procedure:
• Equilibrate a water bath to 42°C.
• Warm the vial of S.O.C. Medium (supplied with the kit) to room temperature.
• Spread X-Gal onto LB agar plates containing antibiotic, if desired.
• Warm the selective plates in a 37°C incubator for 30 minutes (use one plate for each transformation).
If you are including the pUC19 control, make sure that you have one LB agar plate containing 100 µg/ml ampicillin.
Note: For optimal growth of Mach1™-T1R E. coli cells, it is essential that selective plates are prewarmed to 37°C prior to spreading. Transformation Procedure We recommend including the pUC19 control plasmid DNA supplied with the kit in your transformation experiment to verify the efficiency of the competent cells.
1. Thaw, on ice, one vial of One Shot® Mach1™-T1R Chemically Competent E. coli for each transformation.
2. Add 1 to 5 µl of the DNA (10 pg to 100 ng) into a vial of One Shot® cells and mix gently. Do not mix by pipetting up and down. If you are transforming the pUC19 control, add 1 µl (10 pg) into a separate vial of One Shot® cells and mix gently.
3. Incubate the vial(s) on ice for 30 minutes.
4. Heat-shock the cells for 30 seconds at 42°C without shaking.
5. Remove the vial(s) from the 42°C bath and place them on ice for 2 minutes.
6. Add 250 µl of room temperature S.O.C. Medium to each vial.
7. Cap the vial(s) tightly and shake horizontally at 37°C for 1 hour at 225 rpm in a shaking incubator.
8. Spread 25-100 µl of the transformation mix on a prewarmed selective plate. Store the remaining transformation mix at +4°C. Additional cells may be plated out the next day, if desired.
9. Invert the plate(s) and incubate at 37°C. If you are using ampicillin selection, visible colonies should appear within 8 hours, and blue/white screening can be performed after 12 hours. If you are selecting transformants with an antibiotic other than ampicillin, incubate plates overnight.
10. Select overnight-grown colonies and analyze by plasmid isolation, PCR, or sequencing.
For plasmid isolation, inoculate a single, overnight-grown colony in 2 ml of prewarmed selective media .
For optimal results, we recommend inoculating as much of the single colony as possible. Shake at 37°C for 4 hours before isolating the plasmid.
Result
1-ClpX + pJH1 ,on LB+ Hygromycine (+)
2-ClpB + pJH1 , on LB+ Hygromycine(+)
3- ChiT + pJH1, on LB+ Hygromycine (+)
4- PUC 19 on LB+ Ampenicillin, (+) positive control.
5- DH5 alfa on LB+ Ampenicillin (-) negative control.
6-PUC 19 and DH5 alfa on LB+ Hygromycine (-)
ClpX,ClpB and ChiT + pJH1
One Shot® Mach1™-T1R Chemically Competent E. coli
Transforming Competent Cells Perform the following before starting the transformation procedure:
• Equilibrate a water bath to 42°C.
• Warm the vial of S.O.C. Medium (supplied with the kit) to room temperature.
• Spread X-Gal onto LB agar plates containing antibiotic, if desired.
• Warm the selective plates in a 37°C incubator for 30 minutes (use one plate for each transformation).
If you are including the pUC19 control, make sure that you have one LB agar plate containing 100 µg/ml ampicillin.
Note: For optimal growth of Mach1™-T1R E. coli cells, it is essential that selective plates are prewarmed to 37°C prior to spreading. Transformation Procedure We recommend including the pUC19 control plasmid DNA supplied with the kit in your transformation experiment to verify the efficiency of the competent cells.
1. Thaw, on ice, one vial of One Shot® Mach1™-T1R Chemically Competent E. coli for each transformation.
2. Add 1 to 5 µl of the DNA (10 pg to 100 ng) into a vial of One Shot® cells and mix gently. Do not mix by pipetting up and down. If you are transforming the pUC19 control, add 1 µl (10 pg) into a separate vial of One Shot® cells and mix gently.
3. Incubate the vial(s) on ice for 30 minutes.
4. Heat-shock the cells for 30 seconds at 42°C without shaking.
5. Remove the vial(s) from the 42°C bath and place them on ice for 2 minutes.
6. Add 250 µl of room temperature S.O.C. Medium to each vial.
7. Cap the vial(s) tightly and shake horizontally at 37°C for 1 hour at 225 rpm in a shaking incubator.
8. Spread 25-100 µl of the transformation mix on a prewarmed selective plate. Store the remaining transformation mix at +4°C. Additional cells may be plated out the next day, if desired.
9. Invert the plate(s) and incubate at 37°C. If you are using ampicillin selection, visible colonies should appear within 8 hours, and blue/white screening can be performed after 12 hours. If you are selecting transformants with an antibiotic other than ampicillin, incubate plates overnight.
10. Select overnight-grown colonies and analyze by plasmid isolation, PCR, or sequencing.
For plasmid isolation, inoculate a single, overnight-grown colony in 2 ml of prewarmed selective media .
For optimal results, we recommend inoculating as much of the single colony as possible. Shake at 37°C for 4 hours before isolating the plasmid.
Result
1-ClpX + pJH1 ,on LB+ Hygromycine (+)
2-ClpB + pJH1 , on LB+ Hygromycine(+)
3- ChiT + pJH1, on LB+ Hygromycine (+)
4- PUC 19 on LB+ Ampenicillin, (+) positive control.
5- DH5 alfa on LB+ Ampenicillin (-) negative control.
6-PUC 19 and DH5 alfa on LB+ Hygromycine (-)
Ligation SOE PCR with pJH1
3/30/2015
ClpX, ClpB (insert)
pJH1 ,Δ dephosphatase and Δ SmaI (vector)
ClpX Insert 3 μL : pJH1 1 μL + 6 dH2O = total 10 μL
ClpB Insert 3 μL : pJH1 1 μL+ 6 dH2O = total 10 μL , brief centerfugation
Ligation using .neb.com/protocols
ClpX, ClpB (insert)
pJH1 ,Δ dephosphatase and Δ SmaI (vector)
ClpX Insert 3 μL : pJH1 1 μL + 6 dH2O = total 10 μL
ClpB Insert 3 μL : pJH1 1 μL+ 6 dH2O = total 10 μL , brief centerfugation
Ligation using .neb.com/protocols
Quick Ligation Protocol (M2200)
Buffers
Quick Ligation Reaction Buffer
Protocol
- Combine 50 ng of vector with a 3-fold molar excess of insert. Use NEBioCalculator to calculate molar ratios. Adjust volume to 10 μl with dH2O.
- Add 10 μl of 2X Quick Ligation Buffer and mix.
- Add 1μl of Quick T4 DNA Ligase and mix thoroughly.
- Centrifuge briefly and incubate at room temperature (25°C) for 5 minutes.
- Chill on ice, then transform or store at -20°C.
- Do not heat inactivate. Heat inactivation dramatically reduces transformation efficiency.
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