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 mA for 40 minutes for a full gel

SDS-PAGE

Cell preparation

• lysis of 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

This assay is used for the determination of protein concentration of a sample.

• mix Bradford solution with ddH₂O in a ratio of 1:4
• make linear range for BSA 125–1,000 μg/mL in 1 mL cuvettes with one cuvette as a blank
• mix equal amounts of BSA and samples that concentration is to be known (1-3 µL) with 1 mL of 1x Bradford solution, vortex and incubate 5 min. at room temperature
• measure OD at spectrophotometer at 595 nm
• build a graph from the date of BSA linear range measurement with a concentration against OD and count the concentration of your samples.

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.