Team:Freiburg/Notebook/1 August
From 2011.igem.org
Contents |
green light receptor
Qickchange PCR of CcaS
Investigators:Julia
repeating experiment from___, because we had no positive transformation, probably chosen wrong annealing temperature before.
blue light receptor
PCR
Investigators: Sophie
As our last PCRs of the LovTAP with the Gibson overhangs didn't work well, we now try a PCR with primers without overhangs for Gibson assembly.
Name: Sophie
| Date: 01.08.11 |
Continue from Experiment: PCR (Date): 27.07.11
(Name): Sandra, Sophie | |
Project Name: Blue Light |
PCR-Mixture for one Reaction:
For a 50 µl reaction use
32,5µl | H20 | Name |
10µl | 5x Phusion Buffer | of Primer |
2.5µl | Primer fw | P35 |
2.5µl | Primer dw | P36 |
1µl | dNTPs | of Template DNA |
1µl | DNA-Template | M35 (LovTAP) |
0.5 µl | Phusion (add in the end) |
What program do you use?
LovTAP ohne Ueberhaenge
To confirm the PCR-Product has the correct size, load 2 µl of the sample onto an agarose-gel.
How did you label the PCR-Product, where is it stored and what do you do next?
Labelled: M35 short; stored in Gibson Stuff box.
red light receptor
3A-assembly with pcyA and the terminator BBa_1006
Investigators:Julia
1.Digestion:
terminator (S21a), 26µl of the miniprep+ 12,1 µl H2O, cut with XbaI&PstI
pcyA (part BBa_I15009), 3 µl of miniprep + 35µl H2O, cut with EcoRI&SpeI
Vector-backbone (10 µl) pSB1T3, cut with EcoRI,PstI & DpnI
to each reation 5µl BSA(10x) and 5µl NEB buffer4 were added, digested at 37°C for two hours, inactivated at 80°C for 20min.
2.Ligation
2µl of digested pcyA,terminator and vector were added to 11µl H2O,2µl ligase buffer and 1µl T4 ligase.
Incubated at room temperature for 35 min, inactivated at 80°C for 20 min.
3.Transformation
Lysis cassette
Phage Lysis Cassette (K124017) + RBS (B0034)
Investigators: Theo
Digestion of 3A Assembly
Name: Theo | Date: 01.08.2011 |
Continue from Experiment : - | |
Project Name: Phage Lysis Cassette (K124017) + RBS (B0034) |
Procedure
- add H2O (38μl-DNA )
- 5 μl NEB4 buffer (stored at iGEM’s, -20°C)
- 5 μl 10x BSA (used 1:10 diluted sample stored at iGEM’s, -20°C)
- DNA (500 ng) (Vector:Insert ratio 1:3 in following Ligation)
- 1 μl restriction enzymes (stored at iGEM’s, -20°C)
- heat for 1-2 hours 37°C (6 hours if time)
- heat for 20 minutes 80°C (inactivation of enzymes)
- keep at 4°C if you cannot continue
Restriction enzymes you need to cut the vector, insert1 and insert 2:
Components | | | |||
DNA (500ng) | 10 | 9 | 8 | ||
BSA (10x) (5μl) | |||||
NEB4 Buffer (5μl) | |||||
Enzyme 1 (1μl) | EcoRI + DpnI | EcoRI | XbaI | ||
Enzyme 2 (1μl) | PstI | SpeI | PstI | ||
H2O (38 μl- DNA) | 27 | 29 | 30 | ||
In total 50 μl |
Documentation:
Why are you doing this experiment? Where are the samples stored? Antibiotica resistance, vector used etc.
A RBS (ribosome binding site) between the lamba cI regulated Promotor (R0051 of K098995) and the holin ATG of K124017 is absent. So a 3A assembly had to be performed in order to get a functioning Lysis cassette.
Resistance of RBS (B0034)=Cm and of Phage Lysis Cassette (K124017)=Amp, so the Vector is Tet (pSB1T3) |
Ligation
Name: Theo | Date: 01.08.2011 |
Continue from: 01.08.2011 Phage Lysis Cassette (K124017) + RBS (B0034) Digestion | |
Project Name: Phage Lysis Cassette (K124017) + RBS (B0034) Ligation |
Procedure
PCR tube:
total volume 20 μl
- add H2O (17 μl -X-Y-Z)
- add 2 μl Ligase Buffer 10x
- add Insert 1, Insert 2(when proceeding from 3A digestion use 2 μl of each)
- add Vector (20ng needed. When proceeding from 3A digestion use 2 μl)
- Add 1 μl T4-DNA Ligase
- Incubate 10-30 min at room temperature
- heat for 20 minutes at 80°C
- store at -20°C or directly proceed to transformation
Name of part | Ratio Insert:Vector
= 3:1 or 1:1 | Volume (μl) | |
X insert 1 | B0034 | 3:1 (1*3) | 3 |
Y insert 2 | K124017 | 3:1 (2*3) | 6 |
Z vector | pSB1T3 | 1:3 (1) | 1 |
H2O | 7 |
Documentation:
Why are you doing this experiment? Where are your parts stored? Name the parts for ligation etc.
Ligation step of 3A assembly.
Length of pSB1T3= ca 2200bp Length of K124017+Vector= ca 4500bp 4500/2200= ca 2 So 2*3 µl (since 3:1 is needed) = 6 µl
|
Transformation
Name: Theo | Date: 01.08.2011 |
Continue from : 01.08.2011 Phage Lysis Cassette (K124017) + RBS (B0034) Ligation
| |
Project Name: Phage Lysis Cassette (K124017) + RBS (B0034) |
Procedure
- take cells from -80°C freezer and put them on ice! (every eppi contains about 400 μl cells)
- thaw cells on ice 20 minutes
- pipette 50 μl cells and 2 μl DNA into eppi still on ice!
- Incubate for 30 minutes on ice
- Heat at 42°C for 60 sec
- Incubate on ice for 5 minutes
- Add 200 μl LB Broth
- Incubate for 2 hours at 37°C (cells with lysis cassette at 30°C!!)
- Plate 50 μl and 200μl on two different LB/Agar plates with appropriate antibiotic resistance
Documentation:
Why are you doing this experiment? Name of the sample? Where are they stored? Name the vector with inserts, antibiotika resistance etc.
New Composite Part in pSB1T3 Vector with modified K124017 containing a strong RBS in front of first ATG |
Precipitator
PCR
Name: Sophie
| Date: 01.08.11 |
Continue from Experiment: replay of PCR 19.07.11 (Date) 19.07.11
(Name) Ruediger | |
Project Name: GFP Pbd |
PCR-Mixture for one Reaction:
For a 50 µl reaction use
32,5µl | H20 | Name |
10µl | 5x Phusion Buffer | of Primer |
2.5µl | Primer fw | P28 |
2.5µl | Primer dw | P18 / P19/ P20 |
1µl | dNTPs | of Template DNA |
1µl | DNA-Template | S 14 (GFP) |
0.5 µl | Phusion (add in the end) |
What program do you use?
Ruediger PCR (modified by Tobi and me. First 10 cycles with 55°C, next cycles with 62°C annealing temperature.
To confirm the PCR-Product has the correct size, load 2 µl of the sample onto an agarose-gel.
How did you label the PCR-Product, where is it stored and what do you do next?