Team:TU-Munich/Notebook/Labjournal

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Week 1 22.4-28.4
Week 2 29.4-05.5
Week 3 06.5-12.5
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Labjournal

Week 1

Monday, April 22nd

Transformation of E. coli XL1 blue with Phytochrome B (2-908 N-terminal amino acids) (BBa_K801031, RFC25, pSB1C3)

Investigator: Jeff, Leonie, Rosario

Aim of the experiment: Transformation of Phytochrome B for protein fusion.

Procedure:

  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice.
  • 2 µl of DNA was added to 100 µl of competent cells and gently mixed.
  • 30 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding of 1 ml LB-medium to each tube.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • 100 µl of the cell suspension was plated on one chloramphenicol plate.
  • The rest were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated again on a new chlorampenicol plate.

Miniprep of pTUM100 with pGAL, pTEF1, pTEF2, pADH and RFC25 compatible RFP generator

Investigator: Jeff, Leonie, Rosario

Aim of the experiment: Miniprep of pTUM100 with pGAL, pTEF1, pTEF2, pADH and RFC25 compatible RFP generator

Procedure:

  • Miniprep was performed after manufacturer's protocol (QIAprep Miniprep, QIAGEN)

Sequencing of RFP-Generator (RFC25, pSB1C3)

Investigator: Jeff, Leonie, Rosario

Aim of the experiment: Sequencing of RFP-Generator (RFC25, pSB1C3)

Procedure:

Sequencing batch were prepared after manufacturer's protocol. (15 µl of plasmid DNA (50 - 100 ng) and 2 µl sequencing primer)

Tuesday, April 23rd

Picking of of E. coli XL1 blue with Phytochrome B (2-908 N-terminal amino acids) (BBa_K801031, RFC25, pSB1C3)

Investigator: Jeff, Leonie, Rosario, Florian

Aim of the experiment: Picking of of E. coli XL1 blue with Phytochrome B (2-908 N-terminal amino acids) (BBa_K801031, RFC25, pSB1C3)

Procedure:

  • pSB1C3 plasmid with BBa_K801031 (PhyB 2 - 908 aa, RFC25): Colonies were picked from chloramphenicol plates.
  • Picked pipette tips was transferred into cell-culture tubes with air-permeable, sterile cover. Each tube contain 4 mL of LB-medium + 4 µL chloramphenicol(1000x).
  • 4 colonies were picked.
  • These tubes were transferred in a cell culture shaker at 37 °C and were incubated overnight

Analytical digestion and gelelectrophoresis of RFP-generator (RFC25, pSB1C3, P4 & P5)

Investigator: Jeff, Leonie, Rosario, Florian

Aim of the experiment: Analytical digestion and gelelectrophoresis of RFP-generator (RFC25, pSB1C3, P4 & P5).


Procedure:

  • Batch for analytical digestion for P4 with NgoMIV+AgeI-HF
volume reagent
2.5 µl Plasmid DNA P4
2 µl NEBuffer 4 (10x)
0.25 µl NgoMIV (10 U/µl)
0.25 µl AgeI-HF (20 U/µl)
15 µl ddH2O
=20 µl TOTAL
  • Batch for analytical digestion for P5 with NgoMIV+AgeI-HF
volume reagent
2.5 µl Plasmid DNA P5
2 µl NEBuffer 4 (10x)
0.25 µl NgoMIV (10 U/µl)
0.25 µl AgeI-HF (20 U/µl)
15 µl ddH2O
=20 µl TOTAL
  • Incubation for 90 min at 37 °C.
  • Analytical gelelectrophoresis was performed at 90 V for 60 min.

Results:

1 kbp ladder DNA ladder P4 P5
Mutation successful Mutation successful!
  • Parts are compliant and do not contain RFC25 forbidden restriction sites.


TUM13 20130423 RFP Generator RFC25 AgeI NgoMIV.png

Sequencing of pTUM vectors with pGAL, pADH, pTEF1, pTEF2

Investigator: Jeff, Leonie, Rosario, Florian

Aim of the experiment: Sequencing of pTUM vectors with pGAL, pADH, pTEF1, pTEF2

Procedure:

Sequencing batch were prepared after manufacturer's protocol. (15 µl of plasmid DNA (50 - 100 ng) and 2 µl sequencing primer).

The different vectors we sequenced received the following barcodes:
- ADH in pTUM100: FR01002265
- TEF1 in pTUM100: FR01002266
- TEF2 in pTUM100: FR01002266
- GAL in pTUM100: FR01002268

Sequencing of TEF2 in pTUM100 was not interpretable. The other sequences were consistent with the sequences in the parts registry.

Wednesday, April 24th

Miniprep of Phytochrome B (2-908 N-terminal amino acids) (BBa_K801031, RFC25, pSB1C3)

Investigator: Jeff, Leonie, Florian

Aim of the experiment: Miniprep of Phytochrome B (2-908 N-terminal amino acids) (BBa_K801031, RFC25, pSB1C3).

Procedure:

  • Miniprep was performed after manufacturer's protocol (QIAprep Miniprep, QIAGEN)

Analytical digestion and gelelectrophoresis of Phytochrome B (2-908 N-terminal amino acids) (BBa_K801031, RFC25, pSB1C3), P7 - P10

Investigator: Jeff, Leonie, Florian

Aim of the experiment: Analytical digestion and gelelectrophoresis of Phytochrome B (2-908 N-terminal amino acids) (BBa_K801031, RFC25, pSB1C3), P7 - P10.

Procedure:

  • Batch for analytical digestion for P7 with NgoMIV+AgeI-HF
volume reagent
2.5 µl Plasmid DNA P7
2 µl NEBuffer 4 (10x)
0.25 µl NgoMIV (10 U/µl)
0.25 µl AgeI-HF (20 U/µl)
15 µl ddH2O
=20 µl TOTAL
  • Batch for analytical digestion for P8 with NgoMIV+AgeI-HF
volume reagent
2.5 µl Plasmid DNA P8
2 µl NEBuffer 4 (10x)
0.25 µl NgoMIV (10 U/µl)
0.25 µl AgeI-HF (20 U/µl)
15 µl ddH2O
=20 µl TOTAL
  • Batch for analytical digestion for P9 with NgoMIV+AgeI-HF
volume reagent
2.5 µl Plasmid DNA P9
2 µl NEBuffer 4 (10x)
0.25 µl NgoMIV (10 U/µl)
0.25 µl AgeI-HF (20 U/µl)
15 µl ddH2O
=20 µl TOTAL
  • Batch for analytical digestion for P10 with NgoMIV+AgeI-HF
volume reagent
2.5 µl Plasmid DNA P10
2 µl NEBuffer 4 (10x)
0.25 µl NgoMIV (10 U/µl)
0.25 µl AgeI-HF (20 U/µl)
15 µl ddH2O
=20 µl TOTAL
  • Incubation for 90 min at 37 °C.
  • Analytical gelelectrophoresis was performed at 90 V for 60 min.

Results:

1 kbp ladder DNA ladder P7 P8 P9 P10
Part is correct Part is correct Part is correct Part is correct


TUM13 20130424 PhytochromeB RFC25 AgeI NgoMIV.png

Transformation of E. coli XL1 blue with EreA and EreB (pDEST14)

Investigator: Jeff, Leonie, Florian

Aim of the experiment: Transformation of E. coli XL1 blue with EreA and EreB (pDEST14).

Procedure:

  • Plasmid DNA was received dried in paper from McMaster University.
  • DNA was resuspended in ddH2O
  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice.
  • 2 µl of DNA was added to 100 µl of competent cells and gently mixed.
  • 30 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding of 1 ml LB-medium to each tube.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • The transformated cells were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated on chlorampenicol and ampicillin plates.

Week 2

Monday, April 29nd

Miniprep of pRK792, pRK793, pRIL, ereA, ereB

Investigator: Leonie

Aim of the experiment: Miniprep of pRK792, pRK793, pRIL, ereA, ereB

Procedure:

  • Miniprep was performed after manufacturer's protocol (QIAprep Miniprep, QIAGEN)
  • Concentrations were determined by measuring the absorption:
Plasmid c [ng/µl]
pRK792 214,5
pRK793 154,3
pRIL 6,1
ereA 183,4
ereB 98,3
  • The procedure will have to be repeated for pRIL

Midiprep of RFC25 compatible RFP generator in (pSB1C3)

Investigator: Andreas, Florian

Aim of the experiment: Midiprep of RFC25 compatible RFP generator in (pSB1C3)

Procedure:

  • Midiprep was performed after manufacturer's protocol (QIAprep Midiprep, QIAGEN)

Tuesday, April 30th

Preparative digestion and gelelectrophoresis of mINF1 and Leptin with HindIII and EheI

Investigator: Louise, Johanna

Aim of the experiment: Testing the enzymes, since the earlier digestion with probably older enzymes did not work (no bands on gel) .

Procedure:

  • Batch for preparative digestion for mINF1 with HindIII and EheI
volume reagent
10 µl Plasmid DNA mINF11
5 µl Tango Buffer (10x)
2 µl HindIII (10 U/µl)
3 µl EheI (10 U/µl)
30 µl ddH2O
=50 µl TOTAL
  • Batch for preparative digestion for Leptin with HindIII and EheI
volume reagent
20 µl Plasmid DNA Leptin
5 µl Tango Buffer (10x)
2 µl HindIII (10 U/µl)
3 µl EheI (10 U/µl)
20 µl ddH2O
=50 µl TOTAL
  • Incubation for 3 h at 37 °C.

Transformation of E. coli XL1 blue with PSH21 (P17)

Investigator: Johanna, Louise

Aim of the experiment: Transformation of E. coli XL1 blue with PSH21.

Procedure:

  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice for 10 minutes.
  • 5 µl of DNA was added to 250 µl of competent cells and gently mixed.
  • 60 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding the DNA to 2 ml LB-medium.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • The transformated cells were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated on chlorampenicol and ampicillin plates.

Thursday, May 2nd

Miniprep of pSH21 (pAutoRex8) containing AlcR/AlcA promotor system

Investigator: Katrin

Aim of the experiment: Miniprep of pSH21 (pAutoRex8) containing AlcR/AlcA promotor system

Procedure:

  • Miniprep was performed after manufacturer's protocol (QIAprep Miniprep, QIAGEN)
  • The concentration was measured (900 ng/µl)


Friday, May 3rd

Transformation of E. coli XL1 blue with pSB1C3-GFP, pSB1C3-mkate2, pSB1C3-mCherry

Investigator: Andreas

Aim of the experiment: Transformation of E. coli XL1 blue with pSB1C3-GFP, pSB1C3-mkate2, pSB1C3-mCherry.

Procedure:

  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice for 10 minutes.
  • 5 µl of DNA was added to 250 µl of competent cells and gently mixed.
  • 60 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding the DNA to 2 ml LB-medium.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • The transformated cells were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated on chlorampenicol and ampicillin plates.

Plating of received E. coli containing biobricks

Investigator: Jeff, Andreas

Aim of the experiment: The received biobricks were already transformed in E. coli and were in an agar stabs. These E. coli cells were transferred with an inoculation loop on antibiotic selection plates and were incubated over night.

Operational sequence:

  • Bacterias containing plasmids with biobricks were transferred with a sterile inoculation loop on antibiotic plates and were incubated at 37 °C overnight.
  • The biobricks were:
Name Function
[[http://partsregistry.org/Part:BBa_K157004 BBa_K157004]] Fluoresceine A -binding derivative of a Lipocalin
[[http://partsregistry.org/Part:BBa_K863000 BBa_K863000]] bpul (laccase from Bacillus pumilus) with T7 promoter, RBS and HIS tag
[[http://partsregistry.org/Part:BBa_K909009 BBa_K909009]] cDNA of UV-B sensing protein UVR8 from Arabidopsis thaliana
[[http://partsregistry.org/Part:BBa_K337013 BBa_K337013]] constitutive promoter SV40
[[http://partsregistry.org/Part:BBa_K747096 BBa_K747096]] constitutive promoter CMV
[[http://partsregistry.org/Part:BBa_K414002 BBa_K414002]] constitutive promoter CaMV35S
[[http://partsregistry.org/Part:BBa_K147002 BBa_K147002]] xylE gene coding for catechol-1,2-dioxygenase
[[http://partsregistry.org/Part:BBa_E2020 BBa_E2020]] Cerulean
[[http://partsregistry.org/Part:BBa_K404319 BBa_K404319]] mCFP
[[http://partsregistry.org/Part:BBa_E0040 BBa_E0040]] GFPmut3b
[[http://partsregistry.org/Part:BBa_K592010 BBa_K592010]] amilGFP
[[http://partsregistry.org/Part:BBa_E2050 BBa_E2050]] mOrange
[[http://partsregistry.org/Part:BBa_K399001 BBa_K399001]] mStrawberry
[[http://partsregistry.org/Part:BBa_E1010 BBa_E1010]] mRFP1
[[http://partsregistry.org/Part:BBa_E2060 BBa_E2060]] mCherry
[[http://partsregistry.org/Part:BBa_K592012 BBa_K592012]] eforRed
[[http://partsregistry.org/Part:BBa_K592011 BBa_K592011]] cjBlue
[[http://partsregistry.org/Part:BBa_K864401 BBa_K864401]] aeBlue
[[http://partsregistry.org/Part:BBa_K592009 BBa_K592009]] amilCP, blue chromoprotein
[[http://partsregistry.org/wiki/index.php?title=Part:BBa_K414000 BBa_K414000]] RD29A Promoter + Strong Plant Kozak (RBS) + RFP
[[http://partsregistry.org/wiki/index.php?title=Part:BBa_K414006 BBa_K414006]] 35S Promoter + (Strong Plant RBS + GFP) From K414001
[[http://partsregistry.org/wiki/index.php?title=Part:BBa_K414007 BBa_K414007]] DREB1C promoter
[[http://partsregistry.org/wiki/index.php?title=Part:BBa_K678001 BBa_K678001]] alcA promoter
[[http://partsregistry.org/Part:BBa_K243004 BBa_K243004]] Short linker
[[http://partsregistry.org/Part:BBa_K243005 BBa_K243005]] Middle linker
[[http://partsregistry.org/Part:BBa_K243006 BBa_K243006]] Long Linker
[[http://partsregistry.org/Part:BBa_K243029 BBa_K243029]] GSAT Linker
[[http://partsregistry.org/Part:BBa_K243030 BBa_K243030]] SEG Linker


Sunday, May 5th

Picking of the plated E. coli containing biobricks and the parts received from LMU

Investigator: Florian

Aim of the experiment: The colonies from the plates were transferred into liquid LB medium, so that minipreps can be performed the next day.

Operational sequence:

  • Tubes with 5 ml LB medium and the corresponding antibiotic were prepared.
  • A single colony from each plate was transferred into a tube with a pipet tip.
  • The biobricks were:
Label Name Function
p19 mCherry in pSB1C3
p20 [[http://partsregistry.org/Part:BBa_K823039 BBa_K823039]] GFP in pSB1C3
p21 [[http://partsregistry.org/Part:BBa_K823029 BBa_K823029]] mKate2 in pSB1C3
p22 [[http://partsregistry.org/wiki/index.php?title=Part:BBa_K414006 BBa_K414006]] 35S Promoter + (Strong Plant RBS + GFP) From K414001
p23 [[http://partsregistry.org/Part:BBa_K414002 BBa_K414002]] constitutive promoter CaMV35S
p24 [[http://partsregistry.org/Part:BBa_K909009 BBa_K909009]] cDNA of UV-B sensing protein UVR8 from Arabidopsis thaliana
p25 [[http://partsregistry.org/Part:BBa_K399001 BBa_K399001]] mStrawberry
p26 [[http://partsregistry.org/wiki/index.php?title=Part:BBa_K414007 BBa_K414007]] DREB1C promoter
p27 [[http://partsregistry.org/Part:BBa_K863000 BBa_K863000]] bpul (laccase from Bacillus pumilus) with T7 promoter, RBS and HIS tag
p28 [[http://partsregistry.org/Part:BBa_K337013 BBa_K337013]] constitutive promoter SV40
p29 [[http://partsregistry.org/Part:BBa_K592011 BBa_K592011]] cjBlue
p30 [[http://partsregistry.org/wiki/index.php?title=Part:BBa_K678001 BBa_K678001]] alcA promoter
p31 [[http://partsregistry.org/Part:BBa_K592012 BBa_K592012]] eforRed
p32 [[http://partsregistry.org/Part:BBa_K592010 BBa_K592010]] amilGFP
p33 [[http://partsregistry.org/Part:BBa_K864401 BBa_K864401]] aeBlue
p34 [[http://partsregistry.org/Part:BBa_K404319 BBa_K404319]] mCFP
p35 [[http://partsregistry.org/wiki/index.php?title=Part:BBa_K414000 BBa_K414000]] RD29A Promoter + Strong Plant Kozak (RBS) + RFP
p36 [[http://partsregistry.org/Part:BBa_K592009 BBa_K592009]] amilCP, blue chromoprotein
p37 [[http://partsregistry.org/Part:BBa_K747096 BBa_K747096]] constitutive promoter CMV
p38 [[http://partsregistry.org/Part:BBa_K147002 BBa_K147002]] XylE dioxygenase (catechol dioxygenase)
p39 [[http://partsregistry.org/Part:BBa_K243005 BBa_K243005]] Middle linker
p40 [[http://partsregistry.org/Part:BBa_K243029 BBa_K243029]] GSAT Linker
p41 [[http://partsregistry.org/Part:BBa_E0040 BBa_E0040]] GFPmut3b
p42 [[http://partsregistry.org/Part:BBa_K243006 BBa_K243006]] Long Linker
p43 [[http://partsregistry.org/Part:BBa_K243030 BBa_K243030]] SEG Linker
p44 [[http://partsregistry.org/Part:BBa_K243004 BBa_K243004]] Short linker
p45 [[http://partsregistry.org/Part:BBa_K157004 BBa_K157004]] Fluoresceine A -binding derivative of a Lipocalin
p46 [[http://partsregistry.org/Part:BBa_E2060 BBa_E2060]] mCherry
p47 [[http://partsregistry.org/Part:BBa_E2020 BBa_E2020]] Cerulean
p48 [[http://partsregistry.org/Part:BBa_E1010 BBa_E1010]] mRFP1
p49 [[http://partsregistry.org/Part:BBa_E2050 BBa_E2050]] mOrange
  • There were no colonies on the plate with K864401 (p33), therefore the LB medium could not be infected
  • The tubes were placed into the incubator at 37 °C


Week 3

Monday, May 6th

Miniprep of the prepared E. coli containing biobricks and the parts from LMU

Investigators: Florian, Johanna, Jefferey

Aim of the experiment: A miniprep of the overnight culture of our E. coli containig our biobricks and LMU parts was performed using the Qiagen miniprep kit.

Procedure:

  • Miniprep was performed after manufacturer's protocol (QIAprep Miniprep, QIAGEN)
  • Resulting concentrations were determined by measuring the absorption:
Label Name Concentration [ng/µl]
p19 mCherry in pSB1C3 40,2
p20 GFP in pSB1C3 58,5
p21 mKate2 in pSB1C3 131,3
p22 35S Promoter + (Strong Plant RBS + GFP) From K414001 42,8
p23 constitutive promoter CaMV35S 39,3
p24 cDNA of UV-B sensing protein UVR8 from Arabidopsis thaliana 30,0
p25 mStrawberry 46,6
p26 DREB1C promoter 34,8
p27 bpul (laccase from Bacillus pumilus) with T7 promoter, RBS and HIS tag 52,5
p28 constitutive promoter SV40 58,7
p29 cjBlue 44,4
p30 alcA promoter 26,9
p31 eforRed 64,8
p32 amilGFP 59,3
p34 mCFP 78,4
p35 RD29A Promoter + Strong Plant Kozak (RBS) + RFP 61,2
p36 amilCP, blue chromoprotein 89,2
p37 constitutive promoter CMV 83,6
p38 XylE dioxygenase (catechol dioxygenase) 57,4
p39 Middle linker 64,3
p40 GSAT Linker 109,6
p41 GFPmut3b 118,1
p42 Long Linker 133,0
p43 SEG Linker 107,5
p44 Short linker 60,2
p45 Fluoresceine A -binding derivative of a Lipocalin 82,7
p46 mCherry 230,2
p47 Cerulean 25,7
p48 mRFP1 299,3
p49 mOrange 181,2


Sequencing of FluA, SV40, CaMV35S, xylE, LMU mKate2, LMU GFP, LMU mCherry, DREB1C, RD29A

Investigators: Andreas, Florian, Johanna, Jefferey, Rosario

Aim of the experiment: Sequencing of genes for which no prior sequencing results were available.

Procedure: The DNA was prepared for sequencing according to the Eurofins SmartSeq Kit protocol (15 µl of plasmid DNA (50 - 100 ng) and 2 µl sequencing primer).

The different genes we sequenced received the following barcodes:

Label Name Barcode
p45 FluA FR01002355
p28 SV40 FR01002356
p23 CaMV35S FR01002357
p38 xylE FR01002358
p21 LMU mKate2 FR01002359
p20 LMU GFP FR01002360
p19 LMU mCherry FR01002345
p46 mCherry FR01002346
p26 DREB1C FR01002347
p35 RD29A FR01002348

Preparation of ordered primers

Investigators: Andreas, Jefferey, Rosario

Aim of the experiment: Dissolving of primer pallets to provide a concentration of 100 pmol/µl

Procedure: We added an amount of water which gave us a final primer concentration of 100 pmol/µl.

Primers were labeled as follows:

Label Oligonr.
6 EreA_for
7 EreA_rev
8 EreA_SDM1_for
9 EreA_SDM1_rev
10 EreA_SDM2_for
11 EreA_SDM2_rev
12 EreA_SDM3_for
13 EreA_SDM3_rev
14 EreB_for
15 EreB_rev
16 EreB_SDM1_for
17 EreB_SDM1_rev
18 EreB_SDM2_for
19 EreB_SDM2_rev
20 EreB_SDM3_for
21 EreB_SDM3_rev

Tuesday, May 7th

PCR, purification and analytical geleletrophoresis of EreA (P15) and EreB (P16)

Investigator: Jeff, Louise, Florian, Rosario, Andi, Johanna

Aim of the experiment: PCR of EreA (P15) and EreB (P16).

Procedure:

Operational sequence:

  • PCR reaction mixture
volume reagent
10 µl 5x OneTaq Standard Reaction Buffer
1 µl 10 mM dNTPs
1 µl 10 µM Forward Primer (P15: O46 (EreA_for); P16: O31 (EreB_for))
1 µl 10 µM Reverse Primer (P15: O47 (EreA_rev); P16: O32 (EreB_rev))
0.25 µL OneTaq Hot Start DNA Polymerase (Finally: 1.25 units/50 µL)
1 µl Plasmid DNA (P15; P16)
35.75 µL ddH2O Water
=50 µL TOTAL
  • Mix with pipette
  • The gradient PCR program was performed after following scheme with following conditions (Tm=54 °C; ΔG=2 °C; P15 in row 11(=52 °C); P16 in row 1 (=54.0 °C)):
Initial denaturation 94 °C 30 s
30 cycles 94 °C 30 s
Tm=54 °C; ΔG=2 °C 60 s
68 °C 80 s
Final extension 68 °C 5 min
Hold 4 °C infinite
  • After PCR, the product was purified with QIAquick PCR Purification Kit, Qiagen.
  • 9 µl of the purified PCR products were mixed with 1 µl DNA loading buffer (10x) for analytical gelelectrophoresis
  • Analytical gelelectrophoresis was performed at 90 V for 60 min in 1% agarose gel.
1 kbp ladder F1 F2
Fragment-size like expected Fragment-size like expected

TUM13 20130507 P15 P16 PCR.png

Preparative digestion and gelelectrophoresis of PhyB (P9) and PIF3-20aa linker (P50) with AgeI and PstI as well as 20aalinker-PIF3 (P51) with EcoRI and NgoMIV

Investigator: Jeff, Andi, Florian, Rosario, Louise, Johanna

Aim of the experiment: Preparative digestion and gelelectrophoresis of PhyB (P9) and PIF3-20aa linker (P50) with AgeI and PstI as well as 20aalinker-PIF3 (P51) with EcoRI and NgoMIV .

Procedure:

  • Batch for preparative digestion of PhyB (P9) and PIF3-20aa linker (P50) with AgeI and PstI
volume reagent
20 µl Plasmid DNA P9/P50
4 µl NEBuffer 4
0.4 µl BSA (100x)
1 µl AgeI-HF
1 µl PstI-HF
13.6 µl ddH2O
=40 µl TOTAL
  • Batch for preparative digestion of 20aalinker-PIF3 (P51) with EcoRI and NgoMIV
volume reagent
20 µl Plasmid DNA P51
4 µl NEBuffer 4
1 µl EcoRI-HF
1 µl NgoMIV
14 µl ddH2O
=40 µl TOTAL
  • Incubation for 3 h at 37 °C.
  • 4 µl of DNA loading buffer (10x) were added to the reaction batches after digestion and were loaded on an 1% low-melting agarose gel for preparative gelelectrophoresis.
  • Preparative gelelectrophoresis was performed at 70 V for 90 min.
P9 digestion = F3 1 kbp ladder P50 digestion = F4 P51 digestion = F5
Fragment-size like expected; band was cut out Fragment-size like expected; band was cut out Fragment-size like expected; band was cut out

TUM13 20130507 P9 AgeI.PstI P50 AgeI.PstI P51 EcoRI.NgoMIV.png

  • Bands were extracted by QIAquick Gel Extraction Kit, QIAGEN.

Wednesday, May 8th

Preparative digestion and gelelectrophoresis of PCR product of EreA (F1) and EreB (F2) with XbaI & AgeI

Investigator: Jeff, Andi, Florian, Rosario, Louise

Aim of the experiment: Preparative digestion and gelelectrophoresis of PCR product of EreA (F1) and EreB (F2) with XbaI & AgeI.

Procedure:

  • Batch for preparative digestion of PCR product of EreA (F1) and EreB (F2) with XbaI & AgeI.
volume reagent
25 µl PCR product F1/F2
5 µl NEBuffer 4
0.5 µl BSA (100x)
1 µl AgeI-HF
1 µl XbaI
17.5 µl ddH2O
=50 µl TOTAL
  • Batch for preparative digestion of P52 for preperation of pSB1C3 vector:
volume reagent
20 µl Plasmid DNA P52
4 µl NEBuffer 4
0.4 µl BSA (100x)
1 µl AgeI-HF
1 µl XbaI
13.6 µl ddH2O
=40 µl TOTAL
  • Incubation for 3 h at 37 °C.
  • 5 µl of DNA loading buffer (10x) were added to the reaction batches for F1 & F2 and 4 µl of DNA loading buffer (10x) were added to the reaction batches for Pxx after digestion and were loaded on an 1% agarose gel for preparative gelelectrophoresis.
  • Preparative gelelectrophoresis was performed at 90 V for 60 min.
F1 digestion = F6 F2 digestion = F7 1 kbp ladder P52 digestion = F8
Length was like expected Length was like expected Length was like expected; the lower band was extracted

TUM13 20130508 F1 F2 P52 Xb.png

  • Bands were extracted by QIAquick Gel Extraction Kit, QIAGEN.

Ligation of F8+F6 (EreA in pSB1C3), F8+F7 (EreB in pSB1C3)

Investigator: Jeff, Andi, Florian, Rosario, Louise

Aim of the experiment: Ligation of F8+F6 (EreA in pSB1C3), F8+F7 (EreB in pSB1C3). Quickchanges have still to be performed.

Procedure:

Ligation batch for F8+F6 (EreA in pSB1C3), F8+F7 (EreB in pSB1C3):

  • Ligation batch for F8+F6
volume reagent
1.35 µl F8 (74.3 ng/µl, 2086 bp)
6.76 µl F6 (25.9 ng/µl, 1218 bp)
2 µl T4 ligase buffer (10x)
1 µl T4 ligase (1 U/µl)
8.89 µl ddH2O
=20 µl TOTAL
  • Ligation batch for F8+F7
volume reagent
1.35 µl F8 (74.3 ng/µl, 2086 bp)
8.78 µl F7 (20.6 ng/µl, 1257 bp)
2 µl T4 ligase buffer (10x)
1 µl T4 ligase (1 U/µl)
6.87 µl ddH2O
=20 µl TOTAL
  • Negative control was als prepared. Instead of the insert, the same volume of ddH2O was added to the reaction batches.
  • Cycled ligation has been performed after following protocol in a thermocycler:
100 cycles 12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
Hold 16 °C infinite


Lid temperature = 37 °C

Midiprep of cloning vector RFC25 RFP generating device

Investigators: Andreas, Rosario

Aim of the experiment: Midiprep of our cloning vector RFC25 RFP generating device.

Procedure: Midiprep was performed after manufacturer's protocol (QIAprep Midiprep, QIAGEN)

The yield of our vector was 1854 ng.

Thursday, May 9th

Transformation of E. coli XL1 blue with F8(pSB1C3)+F6(EreA) and F8(pSB1C3)+F7(EreB)

Investigator: Florian, Jeff, Leonie, Louise, Katrin, Ingmar

Aim of the experiment: Transformation of E. coli XL1 blue with F8(pSB1C3)+F6(EreA) and F8(pSB1C3)+F7(EreB). Quickchanges has now to be performed to remove forbidden restriction sites.

Procedure:

  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice.
  • 10 µl of ligation products F8+F6, F8+F7, F8 negative control were added to 100 µl of competent cells and gently mixed.
  • 30 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding of 1 ml LB-medium to each tube.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • 100 µl of the cell suspension was plated on one chloramphenicol plate.
  • The rest were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated again on a new chlorampenicol plate.

Friday, May 10th

Quick Change mutagenesis to remove mutations found by sequencing in our gene constructs

Investigator: Andi, Jeff, Rosario

Aim of the experiment: Deletion of found mutations.

Operational sequence

1. PCR general setup
Reaction batch 1

volume reagent
2.5 µl 10x Pfu Ultra II buffer
4 µl DNA template
1 µl 1:10 dilution of appropriate Oligo (= 5 pmol)
16.5 µl ddH2O
0.5 µl dNTP mix
0.5 µl Pfu Ultra II DNA polymerase (2.5 U / µl)

Reaction batch 2

volume reagent
2.5 µl 10x Pfu Ultra II buffer
4 µl DNA template
1 µl 1:10 dilution of appropriate Oligo (= 5 pmol)
16.5 µl ddH2O
0.5 µl dNTP mix
0.5 µl Pfu Ultra II DNA polymerase (2.5 U / µl)


PCR cycling parameters

Segment Cycles Temperature Time
1 1 95 °C 30 sec
2 12 95 °C 30 s
55 °C 1 min
68 °C 6 min
  • Having completed the PCR cycling parameters listed above both PCR reaction batches were mixed together and the cycling parameters listed above were one time more applied.
  • After the PCR was finished 1 µl of the DpnI restriction enzyme (10 U/µl)was added
  • Now the reaction was mixed gently and thoroughly, spinned down in a microcentrifuge for 1 minute, and immediately incubated at 37 °C for 1 hour to digest the parental supercoiled dsDNA


2. Used constructs and primers

Quickchange number Plasmid number Geneconstruct Oligo number
QC 1P27BPul_Laccase+ pSB1C3O26 & O27

Picking of transformed Plasmids F8 + F6

Investigator: Andi

Aim of the study: Picking from the overnight transformation of the ligated F8+F6, to see whether ligation is successful or not.

Operational sequence:

  • Picking and overnight culture after standard laboratory's protocol. (CamR LB-medium)



Investigator: Andi


PCR of TEV (P14, pRK793)

Investigator: Katrin, Jeff

Aim of the experiment: PCR, purification and analytical geleletrophoresis of TEV (P14, pRK793) to produce TEV with RFC25 pre- and suffx (still contains forbidden SpeI-site).

Procedure:

Operational sequence:

  • PCR reaction mixture
volume reagent
10 µl 5x OneTaq Standard Reaction Buffer
1 µl 10 mM dNTPs
1 µl 10 µM Forward Primer (O34 (TEV_fw))
1 µl 10 µM Reverse Primer (O35 (TEV_rv))
0.25 µL OneTaq Hot Start DNA Polymerase (Finally: 1.25 units/50 µL)
1 µl Plasmid DNA (P14)
35.75 µL ddH2O Water
=50 µL TOTAL
  • Mix with pipette
  • The PCR program was performed after following scheme with following conditions:
Initial denaturation 94 °C 30 s
30 cycles 94 °C 30 s
55 °C 60 s
68 °C 150 s
Final extension 68 °C 5 min
Hold 4 °C infinite
  • After PCR, the product was purified with QIAquick PCR Purification Kit, Qiagen.
  • Resulting product was labeled as F12.

Digestion of P61 with S1 Nuclease

Investigator: Katrin

Oligohybridization of O22 (MinMCS_for) and O23 (MinMCS_rev)

Investigator: Leonie


Preparation of ordered primers

Investigators: Andreas, Rosario, Katrin, Ingmar

Aim of the experiment: Dissolving of primer pallets to provide a concentration of 100 pmol/µl

Procedure: We added an amount of water which gave us a final primer concentration of 100 pmol/µl.

Primers were labeled as follows:

Label Oligonr.
24 BPU_for
25 BPU_rev
26 BPU_SDM1_for
27 BPU_SDM1_rev
28 BPU_SDM2_for
29 BPU_SDM2_rev
30 BPU_SDM3_for
31 BPU_SDM3_rev
32 BPU_SDM4_for
33 BPU_SDM4_rev
34 TEV_for
35 TEV_rev
36 TEV_t387c_for
37 TEV_t387c_rev
38 N_Split_TEV_for
39 N_Split_TEV_rev
40 C_Split_TEV_for
41 C_Split_TEV_rev
42 PIF6_2-100_for
43 PIF6_2-100_rev
44 p104AgeI a71g fw
45 p104AgeI a71g rev
46 xylE_for
47 xylE_rev
48 xylE_c312a_for
49 xylE_c312a_rev
50 xylE_g483a_for
51 xylE_g483a_rev
52 xylE_a834g_for
53 xylE_a834g_rev

Saturday, May 11th

Preparative digestion of PCR product of S219V pRK793 (F12) with XbaI & AgeI

Investigator: Louise

Aim of the experiment: Preparative digestion of PCR product of S219V pRK793 (F12) with XbaI & AgeI. Quickchange has still to be performed (forbidden SpeI restriction site).

Procedure:

  • Batch for preparative digestion of PCR product S219V pRK793 (F12) with XbaI & AgeI.
volume reagent
20 µl PCR product F12
4 µl NEBuffer 4
0.4 µl BSA (100x)
1 µl AgeI-HF
1 µl XbaI
13.6 µl ddH2O
=40 µl TOTAL
  • Incubation for 3 h at 37 °C
  • Digested products were purified to remove nucleotides and enzymes with QIAquick PCR Purification Kit, QIAGEN.
  • The digested fragment was labelled F15

Miniprep of overnight culture of transformated E.~coli XL1-Blue with F8 (pSB1C3) + F6 (EreA)

Investigator: Louise

Aim of the experiment: Miniprep of overnight culture of transformated E.~coli XL1-Blue with F8 (pSB1C3) + F6 (EreA) of 2 clones picked the day before

Procedure:

  • Miniprep was performed after manufacturer's protocol (QIAprep Miniprep, QIAGEN)
  • The plasmids were labelled as P63 and P64

Analytical digestion and gelelectrophoresis of P63 and P64 with AgeI-HF and XbaI

Investigator: Louise

Aim of the experiment: Analytical digestion and gelelectrophoresis of P63 and P64 with AgeI-HF and XbaI

Procedure:

  • Batch for analytical digestion of P63 and P64 with AgeI-HF and XbaI
volume reagent
2.5 µl Plasmid DNA P63/P64
2 µl NEBuffer 4 (10x)
0.2 µl BSA (100x)
0.25 µl XbaI(10 U/µl)
0.25 µl AgeI-HF (20 U/µl)
14.8 µl ddH2O
=20 µl TOTAL
  • Incubation for 90 min at 37 °C.
  • Analytical gelelectrophoresis was performed at 90 V for 60 min.


Analytical digestion of P63 with AgeI-HF and XbaI 1 kbp ladder Analytical digestion of P64 with AgeI-HF and XbaI
Insertion successful Insertion successful

TUM13 20130511 P63 P64 XbaI.png

Preparative digestion of PCR product of EreB (F2) with XbaI & AgeI

Investigator: Louise,Leonie,Johanna

Aim of the experiment: Preparative digestion of PCR product EreB (F2) with XbaI & AgeI (second try since there did not grow any transformed bacteria in the first time).

Procedure:

  • Batch for preparative digestion of PCR product and EreB (F2) with XbaI & AgeI.
volume reagent
20 µl PCR product F2
5 µl NEBuffer 4
0.5 µl BSA (100x)
1 µl AgeI-HF
1 µl XbaI
22.5 µl ddH2O
=50 µl TOTAL
  • Incubation for 3 h at 37 °C
  • The digested fragment was labelled F14


Purification and ligation of digested PCR product EreB (F14)

Investigator: Louise, Rosario

Aim of the experiment: PCR Purification and ligation of digested PCR product EreB (F14).

Procedure: PCR Purification of EreB PCR (F14)

  • To purify the digested Fragment(F14) the QIAquick PCR Purification Kit was used. The concentration of the purified product was found to be 5 ng/µl via Nano drop.

Ligation of F14 + F8(pSB1C3)

  • Ligation batch for F8+F14 (positive control)
volume reagent
1.35 µl F8 (74.3 ng/µl, 2086 bp)
15.65 µl F14 (5 ng/µl, 1257 bp)
2 µl T4 ligase buffer (10x)
1 µl T4 ligase (1 U/µl)
=20 µl TOTAL
  • Negative control was also prepared. Instead of the insert, the same volume of ddH2O was added to the reaction batch.
  • Cycled ligation has been performed after following protocol in a thermocycler:
99 cycles 12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
Hold 16 °C infinite


Lid temperature = 37 °C

Transformation of ligation products of F10 + F11 into E.coli Xl1-Blue

Investigator: Andi

Aim of the experiment:Transformation of the ligation products of F10 + F11 and the negative control in pTUM104 in XL1 Blue.

Operation Sequence

  • melting of 2x 200 µl Ca-competent E.coli XL1-Blue cells on ice
  • Preparing 4 Tubes with 100 µl of Ca-competent E.coli XL1-Blue cells
  • addition of 5 µl of the ligation products
  • incubation for 30 min on ice
  • heat shock for 5 min at 37 °C
  • transfer of cells to 1 ml LB-medium without antibiotics and incubate at 37°C and 180 rpm for 30 min
  • plate 100 µl on an Amp-LB-plate
  • sediment the leftover in a centrifuge (30 - 60 sec, 13 000 rpm) and resuspend the sediment in 100 µl LB-medium and plate it as well on an Amp-LB-plate

Transformation of Quickchange Product P62 into E.coli Xl1-Blue

Investigator: Andi

Aim of the experiment:Transformation of the Quickchange Product P62 and the negative control in XL1 Blue.

Operation Sequence

  • melting of 1x 200 µl Ca-competent E.coli XL1-Blue cells on ice
  • Preparing 4 Tubes with 50 µl of Ca-competent E.coli XL1-Blue cells
  • addition of 1 µl of the Quickchange Product
  • incubation for 30 min on ice
  • heat shock for 5 min at 37 °C
  • transfer of cells to 1 ml LB-medium without antibiotics and incubate at 37°C and 180 rpm for 30 min
  • plate 100 µl on an Amp-LB-plate
  • sediment the leftover in a centrifuge (30 - 60 sec, 13 000 rpm) and resuspend the sediment in 100 µl LB-medium and plate it as well on an Amp-LB-plate

Quickchange mutagenesis of pTUM104

Investigator: Ingmar

Aim of the experiment: Sequencing results showed a forbiden AgeI restriction site in this vector. The sdm will delete this restricition site

Procedure: PCR
Reaction batch 1

volume reagent
2.5 µl 10x Pfu Ultra II buffer
4 µl Plasmid P6 template
0.5 µl 1:10 dilution of O44 (10 pmol/µL)
16.5 µl ddH2O
0.5 µl dNTP mix
0.5 µl Pfu Ultra II DNA polymerase (2.5 U / µl)

Reaction batch 2

volume reagent
2.5 µl 10x Pfu Ultra II buffer
4 µl Plasmid P6 template
0.5 µl 1:10 dilution of O45 (10 pmol/µL)
16.5 µl ddH2O
0.5 µl dNTP mix
0.5 µl Pfu Ultra II DNA polymerase (2.5 U / µl)

PCR cycling parameters

Segment Cycles Temperature Time
1 1 95 °C 30 sec
2 10 95°C 30 sec
55°C 1 min
67°C 6 min
  • Having completed the PCR cycling parameters listed above both PCR reaction batches were mixed together and the cycling parameters listed above were one time more applied.
  • Digestion of the parental DNA with DpnI: Addition of 1 µl DpnI to the PCR batch and incubate for 1 h at 37 °C. The resulting product was named fragmet 14.

Transformation into E.coli Xl1-Blue Operation Sequence

  • melting of 100 µl Ca-competent E.coli XL1-Blue cells on ice
  • addition of 1 µl of the PCR product
  • incubation for 30 min on ice
  • heat shock for 5 min at 37 °C
  • transfer of cells to 1 ml LB-medium without antibiotics and incubate at 37°C and 180 rpm for 30 min
  • plate 100 µl on an Amp-LB-plate
  • sediment the leftover in a centrifuge (30 - 60 sec, 13 000 rpm) and resuspend the sediment in 100 µl LB-medium and plate it as well on an Amp-LB-plate

Sunday, May 12th

Analytical gelelectrophoresis of F15 (digested TEV PCR product)

Investigator: Jeff, Rosario

Aim of the experiment: Analytical gelelectrophoresis of F15 (digested TEV PCR product) to check whether PCR has worked.

Procedure:

  • 5 µl of F15 was mixed with 0.55 µl of DNA loading buffer (10x) and analytical gelelectrophoresis was performed at 1% agarose gel for 60 min at 90 V.

TUM13 20130512 PCR F12.png

  • PCR product has expected length

Transformation of E. coli XL1 blue with ligation product F8+F15 (TEV in pSB1C3, RFC25)

Investigator: Jeff, Rosario

Aim of the experiment: Transformation of E. coli XL1 blue with ligation product F8+F15 (TEV in pSB1C3, RFC25). Further quickchanges still have to be done.

Procedure:

  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice.
  • 10 µl of the ligation products were added to 200 µl of competent cells and gently mixed.
  • 30 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding of 1 ml LB-medium to each tube.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • 100 µl of the cell suspension was plated on one chloramphenicol plate.
  • The rest were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated again on a new chlorampenicol plate.

Transformation of E. coli XL1 blue with ligation products F8+F14 (EreB in pSB1C3, RFC25)

Investigator: Jeff, Rosario

Aim of the experiment: Transformation of E. coli XL1 blue with ligation product F8+F14 (EreB in pSB1C3, RFC25). Further quickchanges still have to be done.

Procedure:

  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice.
  • 10 µl of the ligation products were added to 200 µl of competent cells and gently mixed.
  • 30 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding of 1 ml LB-medium to each tube.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • 100 µl of the cell suspension was plated on one chloramphenicol plate.
  • The rest were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated again on a new chlorampenicol plate.

Transformation of E. coli XL1 blue with P23

Investigator: Jeff, Rosario

Aim of the experiment: Transformation of E. coli XL1 blue with P23 for insertion of miniMCS.

Procedure:

  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice.
  • 2 µl of DNA was added to 100 µl of competent cells and gently mixed.
  • 30 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding of 1 ml LB-medium to each tube.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • 100 µl of the cell suspension was plated on one chloramphenicol plate.
  • The rest were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated again on a new chlorampenicol plate.


Picking of transformed Plasmid F10+F11 (IRES from polio virus, blunt ligated with pSB1C3 for sequencing)

Investigator: Andi

Aim of the study: Picking of transformed Plasmid F10+F11 (AlcR blunt ligated with pSB1C3 for sequencing).

Operational sequence:

  • Picking and overnight culture after standard laboratory's protocol. (CamR LB-medium)
  • 10 colonies were picked.

Week 4


Monday, May 13th

Miniprep of overnight culture of transformated E.~coli XL1-Blue with F10+F11

Investigator: Rosario, Jeffery, Johanna, Flo, Leonie

Aim of the experiment: Miniprep of overnight culture of transformated E.~coli XL1-Blue F10+F11 of 10 clones picked the day before

Procedure:

  • Miniprep was performed after manufacturer's protocol (QIAprep Miniprep, QIAGEN)


Analyzing sequencing results

Investigator: Leonie,Johanna

Aim of the experiment: Comparison of the sequencing results with the Biobrick (BB) sequences.

Procedure: Using Geneious to align the sequencing results with the BB sequences.

LMU GFP in RFC 25(p20)

  • The provided sequence in the parts registry is totally wrong.
  • The comparison of the amino acid seqeunces reveals several point mutations.

TUM13 AlignmentforLMUGFP.png

FluA in RFC 25 (p45)

  • Did not yield sequencing results (does the primer bind ?)
  • No presence of RCF 25 standard restriction enzymes

mCherry in RFC 25 (p46)

  • Did not yield sequencing results (does the primer bind ?)
  • No presence of RCF 25 standard restriction enzymes

CaMV35S in RFC 25 (p23)

  • high identity
  • high match with HQ699544 (Blast)

LMU mKate2in RFC 25 (p21)

  • no continous ORF
  • Did not yield sequencing results

DREB1C promoter in RFC 25 (p26)

  • Present of fluorecent protein gene

xylE in RCF 25 (p38)

  • Did not yield sequencing results

SV40 in RCF 25 (p28)

  • sequencing result agrees with the laccases
  • the sequencing result can't be the one of SV40


Quickchange mutagenesis SDMI of p27

Investigator: Rosario, Jeff, Flo, Andi

Aim of the experiment: Sequencing results showed a forbidden restriction site in this vector. The sdm will delete this restricition site. The resulting Plasmid was labeled 65.

Procedure: PCR
Reaction batch 1

volume reagent
2.5 µl 10x Pfu Ultra II buffer
0.5 µl Plasmid P27 template
0.5 µl 1:10 dilution of O26 (10 pmol/µL)
20. 5 µl ddH2O
0.5 µl dNTP mix
0.5 µl Pfu Ultra II DNA polymerase (2.5 U / µl)

Reaction batch 2

volume reagent
2.5 µl 10x Pfu Ultra II buffer
0.5 µl Plasmid P27 template
0.5 µl 1:10 dilution of O27 (10 pmol/µL)
20.5 µl ddH2O
0.5 µl dNTP mix
0.5 µl Pfu Ultra II DNA polymerase (2.5 U / µl)

PCR cycling parameters

Segment Cycles Temperature Time
1 1 95 °C 30 sec
2 10 95°C 30 sec
55°C 1 min
67°C 4 min
  • Having completed the PCR cycling parameters listed above both PCR reaction batches were mixed together and the cycling parameters listed above were one time more applied, but the amount of cycles was increased to 20
  • Digestion of the parental DNA with DpnI: Addition of 1 µl DpnI to the PCR batch and incubate for 1 h at 37 °C.


Quickchange mutagenesis SDMI of p38

Investigator: Jeff, Flo, Andi, Rosario

Aim of the experiment: Sequencing results showed a forbidden restriction site in this vector. The sdm will delete this restricition site. The resulting Plasmid was labeled 67.

Procedure: PCR
Reaction batch 1

volume reagent
2.5 µl 10x Pfu Ultra II buffer
0,5 µl Plasmid P38 template
0.5 µl 1:10 dilution of O48 (10 pmol/µL)
20.5 µl ddH2O
0.5 µl dNTP mix
0.5 µl Pfu Ultra II DNA polymerase (2.5 U / µl)

Reaction batch 2

volume reagent
2.5 µl 10x Pfu Ultra II buffer
0.5 µl Plasmid P38 template
0.5 µl 1:10 dilution of O49 (10 pmol/µL)
20.5 µl ddH2O
0.5 µl dNTP mix
0.5 µl Pfu Ultra II DNA polymerase (2.5 U / µl)

PCR cycling parameters

Segment Cycles Temperature Time
1 1 95 °C 30 sec
2 10 95°C 30 sec
55°C 1 min
67°C 4 min
  • Having completed the PCR cycling parameters listed above both PCR reaction batches were mixed together and the cycling parameters listed above were one time more applied, but the amount of cycles have been increased to 20
  • Digestion of the parental DNA with DpnI: Addition of 1 µl DpnI to the PCR batch and incubate for 1 h at 37 °C.


Quickchange mutagenesis SDMI of P63

Investigator: Jeff, Rosario, Flo, Andi

Aim of the experiment: Sequencing results showed a forbidden restriction site in this vector. The sdm will delete this restricition site. The resulting Plasmid was labeled P66.

Procedure: PCR
Reaction batch 1

volume reagent
2.5 µl 10x Pfu Ultra II buffer
0.25 µl Plasmid P63 template; 1:2 dilution
0.5 µl 1:10 dilution of O8 (10 pmol/µL)
20.75 µl ddH2O
0.5 µl dNTP mix
0.5 µl Pfu Ultra II DNA polymerase (2.5 U / µl)

Reaction batch 2

volume reagent
2.5 µl 10x Pfu Ultra II buffer
0.25 µl Plasmid P63 template; 1:2 dilution
0.5 µl 1:10 dilution of O9 (10 pmol/µL)
20.75 µl ddH2O
0.5 µl dNTP mix
0.5 µl Pfu Ultra II DNA polymerase (2.5 U / µl)

PCR cycling parameters

Segment Cycles Temperature Time
1 1 95 °C 30 sec
2 10 95°C 30 sec
55°C 1 min
67°C 6 min
  • Having completed the PCR cycling parameters listed above both PCR reaction batches were mixed together and the cycling parameters listed above were one time more applied, the amount of cycles was raised to 20
  • Digestion of the parental DNA with DpnI: Addition of 1 µl DpnI to the PCR batch and incubate for 1 h at 37 °C.


Transformation of E. coli XL1 blue with P65

Investigator: Jeff, Rosario, Johanna, Andi, Flo, Leonie

Aim of the experiment: Transformation of E. coli XL1 blue with P65 .

Procedure:

  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice.
  • 2 µl of DNA was added to 100 µl of competent cells and gently mixed.
  • 30 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding of 1 ml LB-medium to each tube.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • 100 µl of the cell suspension was plated on one chloramphenicol plate.
  • The rest were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated again on a new chlorampenicol plate.


Transformation of E. coli XL1 blue with P66

Investigator: Jeff, Rosario, Flo, Johanna, Andi, Leonie

Aim of the experiment: Transformation of E. coli XL1 blue with P66.

Procedure:

  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice.
  • 2 µl of DNA was added to 100 µl of competent cells and gently mixed.
  • 30 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding of 1 ml LB-medium to each tube.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • 100 µl of the cell suspension was plated on one chloramphenicol plate.
  • The rest were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated again on a new chlorampenicol plate.

Transformation of E. coli XL1 blue with P67

Investigator: Jeff, Rosario, Johanna, Andi, Leonie, Flo

Aim of the experiment: Transformation of E. coli XL1 blue with P67.

Procedure:

  • CaCl2 competent E. coli XL1-Blue cells were put out from the stock in -80 °C freezer and were gently thawed on ice.
  • 2 µl of DNA was added to 100 µl of competent cells and gently mixed.
  • 30 min incubation on ice
  • 5 min. heat shock at 37 °C
  • Adding of 1 ml LB-medium to each tube.
  • Incubation for 45 min at 37 °C in the 180 rpm cell-culture shaker.
  • 100 µl of the cell suspension was plated on one chloramphenicol plate.
  • The rest were centrifuged for 1 min at 13000 rpm and the supernatant was dicarded.
  • The pellet was resuspended in 100 µl of LB-medium and this concentrated cell suspension was plated again on a new chlorampenicol plate.

Tuesday, May 14th

Analytical digestion of P15 and P19 to P52

Investigator: Leonie, Florian, Johanna

Aim of the experiment: Analytical digestion and gelelectrophoresis of P15 and P19 to P52 to check the sequencing results.

Procedure:

  • Batch for analytical digestion of P15 and P19 to P52
volume reagent
5 µl Plasmid DNA
5 µl Mastermix
=10 µl TOTAL

Batch of Mastermix

volume reagent
40 µl NEBuffer 4 (10x)
4 µl BSA (100x)
0.2 µl NotI(10 U/µl)
148 µl ddH2O
=200 µl TOTAL
  • Incubation for 90 min at 37 °C.
  • Analytical gelelectrophoresis was performed at 90 V for 60 min.

Gel 1

Gel 2

  • Discussion:
  • Gel 1, Row 1:
lane part plasmid band 1 band 2 result
2 EreA pDEST14 3,25 kb no cut, no restriction sites in pDEST14
3 mCherry(LMU) pSB1C3 2,0 kb 750 bp probably right
4 GFP(LMU)(845 bp) pSB1C3 2,0 kb 750 bp maybe switched with mKate2(LMU)
5 mKate2(LMU)(702 bp) pSB1C3 2,0 kb 900 bp maybe switched with GFP(LMU)
6 35S + Strong Plant + GFP(1775 bp) pSB1C3 2,0 kb 750 bp ?
7 UVR8(1332 bp) pSB1C3 2,0 kb 1,1 kb ?
8 mStrawberry(708 bp) pSB1C3 2,0 kb 1,4 kb ?
9 DREB1C promoter(463 bp) pSB1C3 2,5 kb probably only one cut -> one NotI site mutated
10 Laccase(1587 bp) pSB1C3 2,0 kb 1,3 kb ?
11 SV40(419 bp) pSB1C3 2,0 kb 1,6 kb this could be the laccase
12 cjBlue(696 bp) pSB1C3 2,0 kb 0,5 kb ?
  • Gel 1, Row 2:
lane part plasmid band 1 band 2 result
2 alcA (843 bp) pSB1C3 2,0 kb 0,7 kb ?
3 eforRed (681 bp) pSB1C3 plasmid plasmid bands (coiled, supercoiled, etc.)
4 amilGFP (699 bp) pSB1C3 2,0 kb 0,7 kb right part
5 mCFP (714 bp) pSB1C3 2,0 kb 0,7 kb right part
6 RD29A promoter (1535 bp) pSB1C3 2,0 kb 1,5 kb right part
7 amilCP (669 bp) pSB1C3 2,0 kb 0,7 kb right part
8 CMV promoter (580 bp) pSB1C3 2,0 kb 0,6 kb right part
9 middle linker (24 bp) pMA-BBFR 2,4 kb short insert went through the gel
10 GSAT (108 bp) pMA-BBFR 2,4 kb 0,1 kb right part
11 GFP(720 bp) pSB1A2 ?
12 long linker (36 bp) pMA-BBFR 2,4 kb short insert went through the gel
  • Gel 2:
lane part plasmid band 1 band 2 result
2 SEG linker (108 bp) pMA-BBFR 2,4 kb short insert went through the gel
3 short linker (12 bp) pMA-BBFR 2,4 kb short insert went through the gel
4 FluA (522 bp) pMA-BBFR 2,4 kb 0,5 kb right part
5 mCherry (769 bp) pSB2K3 4,4 kb 0,75 kb right part
6 Cerulean (778 bp) pSB2K3 ?
7 mRFP1 (706 bp) pSB2K3 4,4 kb 0,7 kb right part
8 mOrange (769 bp) pSB2K3 4,4 kb 0,75 kb right part
9 PIF3-20aa (366 bp) pSB1C3 2,0 kb 0,35 kb right part
10 20aa-PIF3 (366 bp) pSB1C3 2,0 kb 0,35 kb two plasmids and two insert can be seen
11 LexA (ca. 6 kb) pSB1C3 > 8 kb only one cut, huge plasmid


Picking of Plasmid P23 (CaMV35S) and Ligation Product F8 + F15 (TEV)

Investigator: Jeff, Florian

Aim of the study: Picking of Plasmid P23 (CaMV35S) and Ligation Product F8 + F15 (TEV) for Miniprep.

Operational sequence:

  • Picking and overnight culture after standard laboratory's protocol. (CamR LB-medium)
  • 1 colony of P23 were picked.
  • 7 colonies of F8 + F15 were picked.

Sequencing of P63 & P64

Investigators: Louise

Aim of the experiment: Sequencing of genes for which no prior sequencing results were available.

Procedure: The DNA was prepared for sequencing according to the Eurofins SmartSeq Kit protocol (15 µl of plasmid DNA (50 - 100 ng) and 2 µl sequencing primer).

The different genes we sequenced received the following barcodes:

Label Name Barcode1 Barcode2
p63 EreA FR01002349 FR01002350
p64 EreA FR01002351 FR01002352

Wednesday, May 15th

Preparative digestion of psB1C3-RFP-generator (P60) and another psB1C3 (P8) as well as P64 (EreA in defect psB1C3 (F8)) with XbaI & AgeI

Investigator: Louise,Leonie,Johanna

Aim of the experiment:Preparative digestion of psB1C3-RFP-generator (P60) and another psB1C3 (P8) as well as P64 (EreA in defect psB1C3 (F8)) with XbaI & AgeI to recover EreA and prepare two new vectors for cloning.

Procedure:

  • Batch for preparative digestion of PCR product and EreB (F2) with XbaI & AgeI.
volume reagent
20 µl Plasmid (P8,P60,P64)
4 µl NEBuffer 4
0.4 µl BSA (100x)
1 µl AgeI-HF
1 µl XbaI
13.6 µl ddH2O
=40 µl TOTAL
  • Incubation for 2.5 h at 37 °C
  • The digested fragments were labelled F17(P8), F18(P60), F19(P64)

PCR, purification and analytical geleletrophoresis of and EreB (P16)

Investigator: Jeff, Louise

Aim of the experiment: PCR of EreB (P16).

Procedure:

Operational sequence:

  • PCR reaction mixture
volume reagent
10 µl 5x OneTaq Standard Reaction Buffer
1 µl 10 mM dNTPs
1 µl 10 µM Forward Primer (O31 (EreB_for))
1 µl 10 µM Reverse Primer (O32 (EreB_rev))
0.25 µL OneTaq Hot Start DNA Polymerase (Finally: 1.25 units/50 µL)
1 µl Plasmid DNA (P15; P16)
35.75 µL ddH2O Water
=50 µL TOTAL
  • Mix with pipette
  • The PCR program TMKS was performed after following scheme:
Initial denaturation 94 °C 30 s
30 cycles 94 °C 30 s
52 °C 60 s
68 °C 80 s
Final extension 68 °C 5 min
Hold 4 °C infinite
  • After PCR, the product was purified with QIAquick PCR Purification Kit, Qiagen.
  • 4 µl of the purified PCR products were mixed with 0.4 µl DNA loading buffer (10x) for analytical gelelectrophoresis
  • Analytical gelelectrophoresis was performed at 90 V for 30 min in 1% agarose gel.
1 kbp ladder F16
Fragment-size like expected

TUM13 20130515 PCR P16.png

Purification and ligation of digested products F17, F18, F19

Investigator: Jeff, Louise

Aim of the experiment: Purification and ligation of digested products F17, F18, F19.

Procedure:

  • To purify the digested Fragments the QIAquick PCR Purification Kit was used. The concentration of the purified product was found to be XX ng/µl via Nano drop.

Ligation of F19 + FXX(pSB1C3)

  • Ligation batch for F19+FXX (positive control)
volume reagent
1.35 µl F8 (74.3 ng/µl, 2086 bp)
X µl F14 (5 ng/µl, 1257 bp)
2 µl T4 ligase buffer (10x)
1 µl T4 ligase (1 U/µl)
=20 µl TOTAL
  • Negative control was also prepared. Instead of the insert, the same volume of ddH2O was added to the reaction batch.
  • Cycled ligation has been performed after following protocol in a thermocycler:
99 cycles 12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
12 °C 60 s
22 °C 60 s
Hold 16 °C infinite


Analytical digestion and analytical gelelectrophoresis of P90-P97 (TEV protease, XbaI+AgeI) and P97 (CaMV p35S, XbaI+PstI)

Investigator: Jeff

Aim of the experiment: Analytical digestion and analytical gelelectrophoresis of P90-P97 (TEV protease, XbaI+AgeI) and P97 (CaMV p35S, XbaI+PstI).

Procedure:

  • Mastermix for analytical digestion of P90-P96 with XbaI+AgeI-HF:
volume reagent
16 µl NEBuffer 4 (10x)
1.6 µl BSA (100x)
2 µl XbaI (20 U/µl)
2 µl AgeI-HF (20 U/µl)
118.4 µl ddH2O
=140 µl TOTAL
  • Batch for digestion of P90-P96 with XbaI+AgeI-HF:
volume reagent
2.5 µl Plasmid DNA
17.5 µl Mastermix
=20 µl TOTAL
  • Batch for digestion of P90-P96 with XbaI+AgeI-HF:
volume reagent
2.5 µl Plasmid DNA
2 µl NEBuffer 4 (10x)
0.2 µl BSA (100x)
0.25 µl XbaI (20 U/µl)
0.25 µl AgeI-HF (20 U/µl)
14.8 µl ddH2O
=20 µl TOTAL
  • Incubation for 90 min at 37 °C.
  • Analytical gelelectrophoresis was performed at 90 V for 60 min.

Results:

1 kbp ladder DNA ladder Digestion of P90 Digestion of P91 Digestion of P92 Digestion of P93 Digestion of P94 Digestion of P95 Digestion of P96 Digestion of P97
Insert has expected length Insert has expected length Insert has expected length Insert has expected length Corrupt Insert has expected length Insert has expected length Corrupt
  • The inserts for TEV semm to be right in the most cases, but the backbone has mutated and it should be cloned into a new pSB1C3 with new same restriction enzymes (XbaI+AgeI)!
  • The forward sequencing of CaMV p35S is right but the analytical digestion is wrong. Maybe further parts are downstream of the promoter?! Reverse sequencing should be performed for further analysis.

TUM13 20130515 P90-P96 XbaI.png

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