Team:Paris Saclay/Notebook/September/12

Monday 12th September

Lab work

Visualization

Glycerol stocks of clones 7, 9, 15 and 16 containing FRB - GFP11 in pSB1C3

"By Maxence"

The glycerol stock of the bacteria with the following plasmids were made.

  • pPS16_009 (FRB - GFP11) clone 7
  • pPS16_009 (FRB - GFP11) clone 9
  • pPS16_014 (FRB - GFP11) clone 15
  • pPS16_014 (FRB - GFP11) clone 16

500µL of liquid culture and 250 µL of glycerol 60% were mixed and put at -20°C.

A MODIFIER

Plasmids extraction of clones 7, 9, 15 and 16 containing FRB - GFP11 in pSB1C3

"By Maxence"

The following plasmids were extracted using the "Charge Switch-Pro Plasmid Miniprep" kit:

  • pPS16_009 (FRB - GFP11) clone 7
  • pPS16_009 (FRB - GFP11) clone 9
  • pPS16_014 (FRB - GFP11) clone 15
  • pPS16_014 (FRB - GFP11) clone 16

Samples preparation for sequencing

By Maxence

20 µL of plasmids pSB1C3 FRB - GFP 11 (clones 7, 9, 15 and 16) were sent to be sequenced. 20 µL of the primers iPS83 (5µM) and iPS84 (5µM) were sent for sequencing.

A VERIFIER

NanoDrop Measurements

By Maxence

Sample Concentration (ng/µL)
PCR product GFP 1.9 from 9th September
 438.11
pSB1C3 from 22nd August
 31.61
PCR fragment gblock 1.1 from 9th September
 239.41
PCR fragment gblock 1.2 from 9th September
 195.92
PCR fragment gblock 2.1 from 9th September
 165.99
PCR fragment gblock 2.2 from 9th September
 143.45

Gibson of cleaned up PCR products GFP 1.9 from 9th September x pSB1C3 treated by DpnI from 22nd August

By Maxence

Gibson was performed with cleaned up PCR products GFP 1.9 (insert) (obtained the 9th September) x pSB1C3 treated by DpnI (plasmid) (obtained the 22nd August) with the following protocol:

For each 20μl of reaction, mix the following reagents :

  • 0.2 µL of insert
  • 3.16 µL of plasmid
  • 6.64 µL of water
  • 10 µL of buffer mix

Two controls were done: one without insert and one without buffer (water was added in order to have a total of 20 µL). The PCR was performed as follow : 1 hour at 50°C.

Transformation of DH5a cells with GFP 1.9 in pSB1C3 obtained by Gibson

By Maxence

Dh5a cells were transformed with pSB1C3 containing GFP 1.9, or controls (no buffer mix and plasmid alone) using the usual protocol.

gblock 1.1 - 1.2 and gblock 2.1 - 2.2 Ligation

By Maxence

gBlocks pPS16_003 and pPS16_004 were ligated together as following :

  • 8 µL of pPS16_00 PCR product from 9th September
  • 8 µL of pPS16_004 PCR product from 9th September
  • 2 µL of Buffer T4 10X
  • 2 µL of ligase T4 enzyme

This strategy aims to obtain fragment 1.

gBlocks pPS16_003 and pPS16_004 were ligated together as following :

  • 8 µL of pPS16_00 PCR product from 9th September
  • 8 µL of pPS16_004 PCR product from 9th September
  • 2 µL of Buffer T4 10X
  • 2 µL of ligase T4 enzyme

This strategy aims to obtain fragment 2.

The ligation product was put at rooming temperature for 2 hours.

A MODIFIER

Clean-up of Ligation products

By Maxence

Ligation products obtained were cleaned up by using the NucleoSpin Gel and PCR Clean-up kit protocol.

NanoDrop Measurements

By Maxence

Sample Concentration (ng/µL)
gblock 1.1 and gblock 1.2 cleaned-up Ligation product
 194
gblock 2.1 and gblock 2.2 cleaned-up Ligation product
 157


PCR of cleaned up Ligation products (fragment 1 and fragment 2) with 3% DMSO

By Maxence

As the annealing temperature (Tm) seems too high to obtain good results for fragments 1 and 2 amplification, DMSO was used in order to reduce the annealing temperature during the PCR. For that purpose, PCR was performed with the following protocol.

For each 50μl of reaction, mix the following reagents :

  • 1 µL of matrix
  • 1 µL of dNTPs (10mM)
  • 2.5 µL of each primer mix (10µM)
  • 10 µL of buffer (5X)
  • 0,5 µL of Phusion polymerase
  • 31 µL of nuclease free water
  • 1.5 µL of DMSO

Mix gently and aliquot 50 μl 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
60°C 30sec
72°C 1 min
Final Extension 72°C 2min
Hold 4°C $\infty$ 
Primers used were:
Matrix Products from Ligation of gblock 1.1 and gblock 1.2 (fragment 1) Products from Ligation of gblock 1.1 and gblock 1.2 (fragment 2)
Primers iPS140 and iPS122 iPS 123 and iPS84

Gel of 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)
Fragment 1 1920
Fragment 2 1831

GEL bizare 1

A large smearing in agarose gel of PCR products was obtained. As this result was not usable, a new PCR was run by diluting the Ligations products : 1/100, 1/10,000 and 1/1,000,000.

GEL bizare 2

A large smearing in agarose gel of PCR products was also obtained, but the smears were seemed to decrease with the dilution rate.