DNA extraction kit Macherey & Nagel. Extraction was performed according to protocol. The leaf pieces were either frozen with liquid nitrogen and afterwards added to the mortar and pestle or water was added.
Open the Pollen:
Ribolyser:
6500 rpms* two times performed *30 seconds duration of the rotation *30 seconds pause
Media (cultivating bacteria):
LB = 20g LB powder filled up to 1L
Competent cells KRX from promega were used for transformation. Heat shock transformation were tested with the promega provided protocol and with the protocol from the iGEM Bielefeld team 2014:
Transformation via heat shock
Thaw 200 μL Chemo competent E.coli cells on ice
Add 0.5-5μL plasmid to 200 μL chemocompetent cells
Store cells on ice for 10-30 minutes
Heatshock for (60-)90 seconds at 42°C
Transfer transformation reaction to 1 mL SOC or LB Medium and incubate 1 hour at 37°C
Centrifuge 30 seconds at 11000 rpm and plate on selective LB Medium
Incubate overnight at 37°C
Plasmid isolation was performed with the analytic Jena plasmid isolation kit. The enclosed protocol was used. It was changed a bit as the elution step was done with water instead of elution buffer.
PCR:
Plant PCR were performed with Solis Biodyne Master Mix with the following protocol:
- 1µl Forward Primer
- 1µl Reverse Primer
- 4µl Master Mix (nucleotides, Taq polymerase) (Solis Biodyne)
- 12µl H2O
- 2µl Template DNA
Phusion PCR for cloning was performed with fermentas Phusion enzyme and the following protocol:
- 5x Phusion HF buffer (4µl)
- 10mM dNTPs (0,4µl)
- Forward primer (1µl)
- Reverse Primer (1µl)
- Template DNA (1µl)
- Phusion DNA polymerase (0,2µl)
- H2O (add to 20µl)
DNA Extraction from Xanthomonas campestris B100:
- Pick bacterial spots from the agar plate
- Dissolve cell with 0,9% NaCL solution (1mL)
- Centrifuge 5 min and 8000rpm
- Re-dissolve pellet in 1 mL steile Milli Q
- Heat 5 minutes at 98°C
- Centrifuge 5 minutes at 13500 rpm
- Collect supernatant in a new tube
- Store at -20°C, Measure DNA by Nanodrop
DNA extraction from Bacillus subtilis was performed by the protocol of the LMU Munich Team 2012: Isolation of chromosomal DNA from Bacillus subtilis for transformation (Cutting and Van der Horn, 1990)
- Mix 2.5 ml of an overnight culture with 2.5 ml SC buffer
- Harvest cells by centrifugation (5 min, 8000 rpm, RT)
- Resuspend cell pellet in 1 ml SC buffer
- Add 100 μl lysozyme and mix well
- Incubate for 15 min at 37°C
- Add 1 ml NaCl and mix well
- Filtrate the DNA solution with a 0.45 μm filter
- Use 100 μl for B. subtilis transformation
SC buffer (pH 7.0) NaCl
Sodium citrate
Lysozyme 2 mg/ml in SC buffer
NaCl 4 M
Gel electrophoresis:
TAE, 50x stock solution (provided by the supervisors); working solution 1x TAE
0,8%-2% agarose dissolved in 1x TAE
50x TAE:
242 g Tris Base
57.1 mL Glacial Acetic Acid
100 mL 0.5 M EDTA
pH:7.8
Nanodrop ND2000 Spectrophotometer from PeqLab was used for DNA measurements.
After the separation of the plasmids and another insert was not possible only by using specific primers, we used restriction enzymes to cut out the unnecessary insert. Herefore we used the restriction enzymes EcoR I, Pst I, Xba I and Not I. These were used by adding 4 nl DNA to 2µl Buffer, 1µl restriction enzymes and 12µl of water. After incubating this mix at 37°C we inactivated everything at 80°C for 20 minutes. Hereby we hoped to separate the psb1C3 (2070 bp) from the mCherry-insert (711 bp). You can find the exact procedure here on the 21.08.2018
.
Primers used for bet detection:
Bet1_1
ATGGGTGTTTTCAATTACGAAACTGAG
Bet1_2
TTAGTTGTAGGCATCGGAGTGTGCCAAGAGG
Pectin C, Pectin A, and Amylopectin were purchased by Carl Roth.
Pectinase from Aspergillus Niger, which was used in the pectin assay as a positive control, was purchased by Sigma
The experiments with liquid nitrogen and trypsin as well as the primer design strategy were especially supported by the supervisors. No antibiotics were handled by team members.