Protocols

• 
  
  2D detection of IPTG and HSL
  
  Organization and preparation
  
  
• 
  
  Culture medium and culture conditions
  
  First work on BioBricks
  
  
• 
  
  Genetic methods
  
  First creation of own BioBricks
  
  
• 
  
  Analytical methods
  
  Improving our chip technology
  
  

2D detection of IPTG and HSL

Chip production

Cell preparation

1. over night culture of sensor cells (50 mL in a 250 mL flask with) max. 16 h
2. centrifuge all 50 mL by 3000 g for 10 min at RT (21 °C).
3. discard the supernatant
4. re-suspend the pellet in 1 mL tempered (~21 °C) LB-medium .

Agar preparation

1. autoclave 50 mL medium with 1.5 % (w/v) agarose (has to be multiplied with the number of chips prepared).
2. cool it down to 45 °C in a water bath.

Chip preparation

1. mix the cooled medium with the cells by inverting gently.
2. pour it in the chip form, avoiding bubble formation (!).
3. wait for approximately 20 min until the agar has solidified.
4. cut out the chips with a scalpel.
5. put two chips into a labeled petri dish and store additional 4 chips in labeled petri dishs in the refrigerator.
6. incubate two chips for 1 h at 37 °C prior to induction.

Sensor-chip manufacturing XXX

Measurement of fluorescence

Culture medium and culture conditions

Media

LB medium

1. weight components

   5 g/L NaCl

   10 g/L tryptone

   5 g/L yeast extract

   (15 g/L agar for plates)

2. fill up to 1 L with deionized water
3. mix well by shaking
4. autoclave
   1. autoclaving tape, caps slightly unscrewed
   2. base of the pot has to be covered with deionized water
   3. close lid
   4. heat level 3 until the pressure valve opens
   5. reduce heat level to 1.5
   6. set timer to 20 minutes
   7. turn heater off
   8. wait until the pressure valve retracts (30-45 minutes)
   9. open, close caps & shake
5. for plates, wait until you can touch the bottle (<60 °C, clean bench!)
6. add antibiotics (1 µL/mL) and shake (gloves!)

TB medium

1. components 1:

   4 mL/L glycerol

   12 g/L tryptone

   24 g/L yeast extract

2. fill up to 900 mL with deionized water
3. mix well by shaking
4. autoclave
5. components 2:

   0.17 M KH₂PO₄

   0.72 M K₂HPO₄

6. dissolve in 100 mL deionized water and sterilize it by passing it through a filter
7. after autoclaving and cooling down, add sterile phosphate solutions

Hartmans minimal medium (HM)

M9 minimal medium (M9)

SOC

1. components

   0,5 % yeast extract

   2 % tryptone

   10 mM NaCl

   2.5 mM KCl

   20 mM MgSO₄

2. fill up with deionized water
3. adjust to pH 7.5 with NaOH
4. after autoclaving, add 20 mM sterile glucose solution (filter sterilization)

Molecular biological methods

Cloning

Restriction Digest

Ligation

Gibson Assembly

The Gibson Assembly was conducted according to the protocol published by New England Biolabs.

1. Set up the reaction according to the table below on ice (2-3 fragment assembly).
2. Incubate samples in a thermocycler at 50°C for 15 minutes when 2 or 3 fragments are being assembled or 60 minutes when 4-6 fragments are being assembled. Following incubation, store samples on ice or at –20°C for subsequent transformation.
3. Transform NEB 5-alpha Competent E. coli cells with 2 μl of the assembly reaction, following the transformation protocol.

Transformation

Heat Shock

1. thaw cells on ice
2. add 1 µL of plasmid DNA
3. incubate on ice for 30 min
4. heat shock at 42 °C for 60 s
5. incubate on ice for 5 min
6. add 200 µL of SOC media
7. incubate at 37 °C for 2 h
8. plate 20  and 200 µL on plates supplemented with the appropiate antibiotic

Electroporation

1. add 1 μL plasmid to electrocompetent cells
2. put DNA/ cell suspension in electroporation cuvette
3. wipe dry the electroporator
4. use a small plastic pipette to place the cells
5. pulse: 2.5 kV, 200-400 Ω, 25 μF (for E.coli)
6. immediatly add 1 mL LB and incubate for 2 h at 37 °C
7. plate 50 μL on selective medium plate
8. centrifuge the rest (3000 g, 20 min), discard supernatant, re-suspend the pellet in 50 μL LB and plate it on selective medium plate

PCR

We have used several different types of PCR throughout our project:

• colony PCR
• check PCR
• gradient PCR
• SOE PCR
• touchdown PCR
• QuikChange(Ligation-During-Amplification)

The scope of appplication as well as the conduct are described below.

Colony PCR /Check PCR

With GoTaq Mast Mix

• 12.5 µl GoTaq Master Mix
• 1 µl primer_F
• 1 µl primer_R
• pick colony with tip and suspend in PCR tube
• 9.5 µl ddH₂O

gradient PCR

SOE PCR

touchdown PCR

QuikChange

Analytical methods

Agarose gel electrophoresis

Separation of DNA or RNA

1. take 5µl of the PCR product
2. mix with 1µl loading dye
3. apply onto agarose gel together with a marker
4. run at 120°C for 40 minutes for a full gel

SDS-PAGE

Cell preparation

• lysis cell pellet in lysis buffer
• centrifuge for 15 min at 13.000 rpm
• mix the supernatant with 2x lammli buffer with β-mercaptoethanol
• denatured for 5 min at 95 °C
• sample to the gel

For some SDS-PAGEs, we used BioRad ready made gels.

The recipe of the self-made SDS is as follows:

1.5x Buffer

• 1.5 M Tris-Cl pH = 8.8
• in 1 L is 40 ml 10 % SDS

Gels

Run gel

• apply the prepared samples together with a protein marker on the gel
• run the gel for 10 min at 60 V and after that for ca. 60 min at 120 V

Bradford assay

Determination of protein concentration

Measurement of fluorescence

The measurement of fluorescence was performed using the Synergy Mx (BioTek) microplate reader and the Gen5 software.

• volume of sample in each well: 100µl
• measure GFP fluorescence at an excitation wavelength of 496 nm and an emission wavelength at 516 nm

Measurement of optical density

Depending on the number of samples, two different devices were used for measurement of optical density, the Unico Spectrophotometer 1201 (Fisher Bioblock Scientific) and the Synergy Mx (BioTek) microplate reader.