Team:Aachen/Notebook/Protocols/Analytical methods

From 2014.igem.org

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(→Bradford assay)
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This assay is used for determination of protein concentration.  
This assay is used for determination of protein concentration.  
* mix Bradford solution with ddH{{sub|2}}O 1:4
* mix Bradford solution with ddH{{sub|2}}O 1:4
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* make linear range for BSA 125–1,000 μg/ml in 1 mL cuvetts with one cuvett as a blank and samples, that concentration have to be known
+
* make linear range for BSA 125–1,000 μg/ml in 1 mL cuvetts with one cuvett as a blank
-
* mix equal ammount of BSA and samples (1-3 µL) with 1 mL of 1xBradford solution, vortex and incubate 5 min. at room temperature
+
* mix equal ammount of BSA and samples that concentration is to be known (1-3 µL) with 1 mL of 1xBradford solution, vortex and incubate 5 min. at room temperature
* measure OD at spectrophotometer at 595 nm
* measure OD at spectrophotometer at 595 nm
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* bild a graph from the date of BSA linear range measurement with a concentration against OD and count the concentration of your sample.
+
* bild 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 ==
== Measurement of fluorescence ==

Revision as of 15:16, 12 October 2014

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

0.75 mm 12 % RUNNING Gel 1 mm 4 % STACKING Gel
1x 2x 4x 1x 2x 4x
H2O 1.65 mL 3.3 mL 6.6 mL 1.5 mL 3 mL 6 mL
1.5x Gel Buffer 1.3 mL 2.6 mL 5.2 mL 0.65 mL 1.3 mL 2.6 mL
30 % Acrylamide (37.5:1) 2 mL 4 mL 8 mL 0.325 mL 0.65 mL 1.3 mL
10 % APS 50 µL 100 µL 200 µL 25 µL 50 µL 100 µL
TEMED 10 µL 20 µL 40 µL 5 µL 10 µL 20 µL

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 determination of protein concentration.

  • mix Bradford solution with ddH2O 1:4
  • make linear range for BSA 125–1,000 μg/ml in 1 mL cuvetts with one cuvett as a blank
  • mix equal ammount of BSA and samples that concentration is to be known (1-3 µL) with 1 mL of 1xBradford solution, vortex and incubate 5 min. at room temperature
  • measure OD at spectrophotometer at 595 nm
  • bild 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.

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