Contents 1 Tuesday 29th July 1.1 Lab Work 1.1.1 A - The frame coli Odor free 1.1.1.1 PCR 1.1.2 C - Salicylate Inducible Suppressing System 1.1.2.1 Digestion 1.1.2.2 Segregate Process by Electrophoresis 1.1.3 D - Lemon scent 1.1.3.1 Transformation of electrocompetent cells 1.1.3.2 PCR of BBa_K762100

Tuesday 29th July

Lab Work

A - The frame coli Odor free

PCR

by Romain

Strains used: E. coli MG1655Z1 and E. coli MG1655, and oligonucleotides used: FTR-Apra-F and FTR-Apra-R.

Protocol

Add into a PCR tube the following:

Component	For a total volume of 50μl
H2O	27.25μl
Green GoTaq buffer 5X	10μl
dNTPs	1μl
FTR-Apra-F	2μl
FTR-Apra-R	2μl
DMSO	1.5μl
MgCl2	4μl
Bacterial culture	2μl
Green GoTaq enzyme	0.25μl

Tube was placed in PCR machine with the following parameters.

Cycle step	Temperature	Time	Cycle
Initial denaturation	95°C	5 min	1
Denaturation	95°C	30 s	30
Annealing	60°C	30 s	30
Extension	72°C	2 min	30
Final extension	72°C	5 min	1
Final extension	12°C	hold	1

The different bacterial cultures in each tubes:

1. Tube 1: MG1655Z1 10I
2. Tube 2: MG1655 100II
3. Tube 3: MG1655 50I
4. Tube 4: MG1655 100I
5. Tube 5: MG1655Z1 10II
6. Tube 6: MG1655 50II
7. Tube 7: MG1655Z1 10I positive control with plasmid

Results of the PCR: The electrophoresis revealed nothing

New PCR with different enyme.

Strains used: MG1655 and MG1655Z1, and oligonucleotides used: FTR-Apra-F and FTR-Apra-R.

Protocol

Add into a PCR tube the following:

Component	For a total volume of 50μl
H2O	37.25μl
DreamTaq buffer 10X	5μl
dNTPs	1μl
FTR-Apra-F	1μl
FTR-Apra-R	1μl
DMSO	2.5μl
Bacterial culture	2μl
DreamTaq enzyme	0.25μl

Tube was placed in PCR machine with the following parameters.

Cycle step	Temperature	Time	Cycle
Initial denaturation	95°C	5 min	1
Denaturation	95°C	30 s	30
Annealing	60°C	30 s	30
Extension	72°C	2 min	30
Final extension	72°C	5 min	1
Final extension	12°C	hold	1

1. Tube 1: MG1655Z1 10I
2. Tube 2: MG1655 100II
3. Tube 3: MG1655 50I
4. Tube 4: MG1655 100I
5. Tube 5: MG1655Z1 10II
6. Tube 6: MG1655 50II
7. Tube 7: MG1655Z1 10I positive control with plasmid

Results of the PCR: The electrophoresis revealed successfully the DNA!

C - Salicylate Inducible Suppressing System

Digestion

by Fabio

After the experiments done yesterday, we are sure to manipulate the right plasmid from both BioBricks and also that we have a good concentration of them. Now it's time to start the Assembly procedure in order to concatenate both BioBricks.

• BioBrick BBa_J61051 (Salicylate promoter + NahR) as Part A
• BioBrick BBa_K228001 (RNA suppressor) as Part B

The enzymes used were:

• EcoRI and SpeI for BBa_J61051
• SpeI and XbaI for BBa_K228001

TODO: Illustration of the process

BioBrick Assembly - Digest Reaction Protocol

Segregate Process by Electrophoresis

by Fabio

First we tested both products of the digestions in order to verify the success of the reaction (Process A), which remained for 25 minutes in 100V. Once the sizes of the digestion's products confirmed, we did the Process B (1 hour in 100V) in order to segregate a good amount of DNA to the next step.

Process A

1. BBa_J61051
2. BBa_K228001

Process B

1. BBa_J61051 strains from the bottom band of process A

Results:

• A #1: Success, we can clearly see the vector and the core of the BioBrick after the digestion.
• A #2: Success, the digested BioBrick was cut one time and has the expected size.
• B: Success, we have a very good concentration of the BBa_J61051's core.

BioBrick Assembly - Segregate Process Protocol

D - Lemon scent

Transformation of electrocompetent cells

by Arnaud & Terry

Strain used: DY330. Plasmid used: pJBEI-6409 (code for enzymes to produce limonene from glucose in E. coli)

Make 2 électroporations in cold electroporation cuvettes:

• A control cuvette(without DNA): 50µl of DY330.
• A second cuvette: 50µl of DY330 culture + 1µl of pJBEI-6409 plasmid.

Electroporation : 2500V, 132W, 40µF.

After that, add 1ml of cold LB in each cuvette and transfer in 2 tubes to incubate during 1 to 2h at 30°C.

Spread on 4 dishes LB + Cm:

• 100µl of control (without plasmid)
• 50µl of transformed DY330 with pJBEI-6409
• 100µl of transformed DY330 with pJBEI-6409
• The rest of transformed DY330 with pJBEI-6409 (concentrate in approximately 150µl)

Incubate for the weekend at 30°C.

PCR of BBa_K762100

by Sean

Oligonucleotides used: iPS66, iPS67

Oligonucleotides were diluted twice from 100µM to 50µM.

Protocol

Add into a PCR tube the following:

Component	For a total volume of 50μl
H2O	35.5μl
Phusion buffer 5X	10μl
dNTPs	1μl
iPS66	1μl
iPS67	1μl
BBa_K762100	1μl
Phusion DNA polymerase	0.25μl

Tube was placed in PCR machine with the following parameters.

Cycle step	Temperature	Time	Cycle
Initial denaturation	98°C	1 min	1
Denaturation	98°C	15 s	25 - 30
Annealing	55°C	variable	25 - 30
Extension	72°C	45 s	25-30
Final extension	72°C	10 min	1
Final extension	8°C	hold	1

Members there:

• Instructors and advisors: Alice, Solenne and Sylvie.
• Students: Arnaud, Fabio, Romain, Sean and Terry.

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