As the transformations did not work (B2, E1 and E2 in pET 43.1(a+) ) with TOP 10 competent cells, we take the products of the midiprep done on the 4th of August and we digest before redoing the transformation.
• Restriction enzymes: Xba I, Hind III (New England Biolabs, NEB)
• Restriction enzyme buffers
• 37 °C water bath
• Shaking incubator (INFORS HT)
• Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)
Method :
1. Realize a Mastermix and store it on ice :
Table 1: Volumes
Reactants
Volumes (µl)
Xba I
30
Hind III
30
Buffer 2.1
90
Distilled H2O
90
Total
150
2. In For each insert (B2, E1, E2), prepare 10 tubes of 1.5 ml (10 eppendorfs of miniprep products).
3. In each tube, put 25 μl of DNA and 5 μl of Master mix.
4. Let digest 2 hours at 37 °C, then incubate 5 minutes at 65 °C.
• Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)
• 1.5 ml eppendorfs
• Takara enzyme
• Primers S and AS
• dNTP mix 10 mM
• Tak Ex Buffer 6X
• Distilled H2O
• MgCl2
Method :
1. Prepare the following tubes :
Table 2 : Volumes
Mix with two primers
Mix with primer S only
Mix with primer AS only
Takara enzyme (µl)
6
6
6
Primer S (µl)
6
6
Ø
Primer AS (µl)
6
Ø
6
MgCl2 (µl)
15
15
15
dNTPs (µl)
15
15
15
Buffer (µl)
30
30
30
H2O (µl)
216
222
222
Total (µl)
294
294
294
2. For each mix, spread 49 µl of it in the samples.
3. Add 1 µl of DNA following the number of tubes :
Table 3 : Samples
Mix with two primers
Mix with primer S only
Mix with primer AS only
A1
tube 1
tube 2
tube 3
A2
tube 4
tube 5
tube 6
D1
tube 7
tube 8
tube 9
D2
tube 10
tube 11
tube 12
And tube 13 is the one without DNA
4. Launch the process of PCR.
5. Do an electrophoresis with the results of PCR
1. Use 1/10 volume of NaAc and 2.5 colume of ethanol for each insert :
Table 5 : Volumes
B2
E1
E2
NaAc (µl)
15
10
35
Ethanol (µl)
875
250
375
2. Resuspend B2⁄E1⁄E2 in 15 µl of H2O each.
3. We estimated the weight of each inserts :
m(B2) = 240 ng
m(E1) = 60 ng
m(E2) = 420 ng
Aim:
Prepare the transformation. Protocol: follow in this link
What we did in the lab: Materials:
• Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)
• Inserts B 2 /E 1 /E 2
• pET 43.1 (a+)
• TOP 10 X
• Distilled water
• Ligase
Method:
Use the following volumes :
Table 6
E1
E2
B2
pET 43.1 (a+)
E1 (µl)
15
Ø
Ø
Ø
E2 (µl)
Ø
15
Ø
Ø
B2 (µl)
Ø
Ø
15
Ø
pET 43.1 (a+) (µl)
4
4
4
4
Ligase (µl)
1
1
1
1
TOP 10 X (µl)
2.2
2.2
2.2
2.2
H2O (µL)
> Ø
> Ø
> Ø
> 15
>
Vtotal (µL)
> 22.2
> 22.2
> 22.2
> 22.2
Aim: Increase the quantity of DNA. Protocol: follow in this link
What we did in the lab: Materials:
• Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)
• Qiagen Miniprep kit
• Digestion enzyme XbaI and HindIII
• Digestion buffer 2.1
• 1.5 ml eppendorfs
• Electrophoresis cuve
• Distilled water
Method:
1. Use the Qiagen kit for our cultures from the 8th of August :
13 eppendorfs of B1.
20 eppendorfs of C2.
2. Digest the plasmid with the following volumes for each sample :
Table 7
Volumes (µl)
DNA
5
XbaI
1
HindIII
1
Buffer 2.1
2
H2O
11
Total
20
3. Analyze the digestion by electrophoresis on an agarose gel prepared with 1.05 g of agarose in 125 ml of TAE 1 X.
4. Launch the electrophoresis, following the deposit table :
C2 | ladder | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | ladder
B1 | ladder | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | Ø | Ø | Ø | 20 | ladder
Aim: Split the insert and the plasmid. Protocol: follow in this link
What we did in the lab: Materials:
• Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)
• Qiagen Miniprep kit
• Digestion enzyme XbaI and HindIII
• Digestion buffer 2 X
• 1.5 ml eppendorfs
• Distilled water
• Shaking incubator (INFORS HT)
Method:
1. Realize a master mix with :
Table 8
Volumes (µl)
XbaI
20
HindIII
20
Buffer 2 X
40
H2O
220
Total
300
2. Put μl of the master mix in each of the twenty 1.5 ml eppendorfs and add 5 μl of DNA.
3. Let incubate one hour at 37 °C and 150 rpm, then 5 minutes at 65 °C
Results The 10th of August, we realize that we forgot to put XbaI, so we respreads the previous mix on petri dishes with XbaI
Aim: We want to produce 5 μ g of dephosphorylated pET 43.1 (a+) from pET 43.1 (a+) at 400 ng⁄ml and we start with the digestion. Protocol: follow in this link
What we did in the lab: Materials:
• Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)
• Qiagen Miniprep kit
• Digestion enzyme XbaI and HindIII
• CutSmart buffer
• 1.5 ml eppendorfs
• Distilled water
• Shaking incubator (INFORS HT)
Method:
1. Put all the following reactants in a 1.5 ml eppendorf and let digest one hour at 37 °C :
Table 9
Volumes (µl)
DNA
12.5
XbaI
2
HindIII
4
Buffer CutSmart
5
H2O
26.5
Total
50
2. Inactivate the enzymes 5 minutes at 65 °C.
Aim: To produce proteins. What we did in the lab: Materials:
• Spectrophotometer Ultrospec 3100
• iPTG at 0.5 M
br/> Method:
1. Make two measures separated of 30 minutes :
Table 10
Sample
1
2
3
4
5
6
Time of addition of iPTG
Concentration (ng⁄μl)
B1 (1)
0.022
0.062
0.152
0.344
0.557
0.694
16 h 55
0.859
B1 (2)
0.185
0.417
0.693
15 h 25
0.956
B1 (3)
0.075
0.211
0.413
0.688
15 h 55
0.920
C2 (1)
0.060
0.166
0.350
0.627
0.699
16 h 25
0.905
C2 (2)
0.044
0.119
0.296
0.510
0.698
16 h 25
0.910
C2 (16)
0.080
0.230
0.445
0.689
15 h 55
0.907
2. When the DO reach 0.7 keep the last measure and centrifuge 3 minutes at 8000 g.
3. Throw away the supernatent and store at −20 °C.
4. Add iPTG to reach 0.3 mM.
Aim: Make the future ligation easier. Protocol: follow in this link
What we did in the lab: Materials:
• Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)
• onSAP
• CutSmart buffer
• 1.5 ml eppendorfs
• Distilled water
• Shaking incubator (INFORS HT)
Method:Method
1. Start with tube 2 (8.6 ng⁄μl in 46 μl) and use the following mix :
Table 11
Volumes ( μl)
DNA
46
CutSmart
6
H2O
6.7
onSAP
1.3
Total
60
2. Let incubate 30 minutes at 37 °C then 5 minutes at 65 °C.
3. Do the same for tube 1.
Aim: Check if the colonies we took contain the insert. Protocol: follow in this link
What we did in the lab
What we did in the lab Materials
• Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)
• Digestion enzyme XbaI and HindIII
• Digestion buffer 2.1
• 1.5 ml eppendorfs
• Distilled water
• Shaking incubator (INFORS HT)
• Inserts B2⁄E1⁄E2
Method
1. In a 1.5 ml eppendorf, put :
Table 12
Volumes (μl)
DNA
5
XbaI
1
H2O
11
HindIII
1
Buffer 2.1
2
Total
20
2. Let incubate one hour at 37 °C , then 5 minutes at −20 °C.