Team:Paris Saclay/Notebook/September/6
Contents
Tuesday 6th September
Lab work
Visualization
Q5 PCR on dCas9 ST - GFP 11 in pSB1C3, FRB in pJET and GFP 1.9 in pUC19
By Maxence
Q5 PCR was performed on plasmids with the following protocol:
For each 50μl of reaction, mix the following reagents :
- 1µL of plasmid
- 1µ of dNTPs (10mM)
- 1µL of each primer mix (10µM)
- 10µL of Q5 buffer (5X)
- 0,5µL of Q5 high fidelity polymerase
- 35,5µL of nuclease free water
Mix gently and aliquot 50μl of the mix into the PCR tubes on ice. Perform PCR as follow:
| Step | Temperature | Time |
|---|---|---|
| Initial denaturation | 98°C | 30sec |
| 30 cycles | 98°C | 10sec |
| Tm | 20sec | |
| 72°C | t | |
| Final Extension | 72°C | 2min |
| Hold | 4°C | $\infty$ |
Primers used were:
| Matrix | dCas9 ST - GFP 11 in pSB1C3 clones 6 and 8 | FRB in pJET clones 4 and 9 | GFP 1.9 in pUC19 |
|---|---|---|---|
| Primers | iPS152 and iPS151 | iPS149 and iPS150 | iPS84 and iPS140 |
| Tm | 57,5°C | 56,7°C | 72°C |
| t | 1 min 30 | 20 sec | 30 sec |
PCR Clean-up of PCR products
By Maxence
PCR products obtained were cleaned up by using the NucleoSpin Gel and PCR Clean-up kit protocol.
NanoDrop Measurements
By Maxence
| Sample | Concentration (ng/µL) |
|---|---|
| PCR fragment GFP 11 clone 6 - pSB1C3 | 187.23 |
| PCR fragment GFP 11 clone 8 - pSB1C3 | 156.85 |
| PCR fragment FRB clone 4 - pSB1C3 | 75.67 |
| PCR fragment FRB clone 9 - pSB1C3 | 246.41 |
| PCR fragment GFP 1.9 - pSB1C3 | 22.06 |
Gel of cleaned up PCR products
By Maxence
After amplification, 3 µL of each cleaned up PCR products and 5 µL of DNA ladder were placed in wells and migrated at 100V during 30 min.
PCR products expected were :
| PCR products | Expected band size (bp) |
|---|---|
| GFP 11- pSB1C3 | 2500 |
| FRB | 374 |
| GFP 1.9 | X |
GEL GEL GEL
Linearization of PCR product GFP 11 - pSB1C3 from clone 8
By Maxence
PCR product GFP 11 - pSB1C3 has been linearized for further Gibson application by using DpnI treatment :
- 30µL of cleaned up PCR product GFP 11 - pSB1C3
- 4µL of fast digest buffer
- 1µL of DpnI
- 5µL of water
The mix was placed 10 minutes at 37°C and was cleaned by using the NucleoSpin Gel and PCR Clean-up kit protocol.
