Beer DNA extraction

Requirements

The most important: a bootle of beer (33cl). In our first prototype, we used a Chimay red.

Needed consumables

Needed material

Beer DNA extraction

  1. Pre-cooled the centrifuge so that it starts at 4℃.

Extract the yeast from the beer

  1. Shake the beer bottle (a bit)
  2. Transfer into an 1000ml Erlenmeyer flask (the big glass that looks like a triangle)

    You can arefully shake it to remove a bit of CO2

  3. Transfer the beer (not the foam) into 50ml Falcon tubes using a large pipette

    • Make sure each tube gets the same quantity (to balance the centrifuge)
    • Put a lid on each tube but don’t close them until the next step (CO2 needs to be evacuated)
  4. Put the tubes (with the lids) in the centrifuge for 10min at full-speed and 4℃

    This step separates the liquid phase and the solid phase (which contains yeast among other things)

  5. Transfer the pellet, solid part on the bottom, into 5ml Eppendorf tubes
  6. Mix with 1ml neutral buffer (tris/buffer 7.4 1M) with a pipette
  7. Label the tubes
  8. Put the tubes into the centrifuge one more time for about 5 min at full-speed
  9. Transfer the pellet into 4 5ml Eppendorf tubes

Break the cell membranes of the yeasts

  1. Put the tubes into an ethanol bath (-80℃)
  2. Add 200µl of lysis buffer into each tube and suspend them
  3. Repeat 2 times
  4. Put the tubes into the ethanol bath for 2 min
  5. Put the tubes in boiling water (100℃) for 2 min
  6. Vortex the tubes for 30s

Extract the DNA from the cell

Now we want to extract DNA from the tubes, which also contains buffer and cell garbage (steps 17 to 22).

Gist: we add SPRI beads in a buffer containing PEG and NaCl so that the DNA binds to the beads. We use a magnet to capture the beads with the DNA. Then, we wash and repeat pretty much the same step: that time, beads will attach to the tube and the liquid will contain our DNA. In our case, we used an addition kit for this second step.

  1. Bind DNA to the magnetic beads
  2. Combine the content of the tubes into 2 50µl Eppendorf tubes
  3. Vortex the buffer with beads
  4. Compute the needed quantity of beads

We need a certain ratio of beads given the DNA we have

  1. Add the needed quantity of beads
  2. Incubate for 5 min
  3. Vortex the two samples
  4. Use either a magnet or a magnetic rack to attach the beads for 1 min
  5. Washing
  6. Remove carefully the liquid from the tubes using pipette
  7. Add µl of 70% Ethanol solution into each tube
  8. Put the tubes back to the magnetic rack
  9. Remove carefully the liquid, you can use a small centrifuge to help the process
  10. Dry for 2 min
  11. Check the purity with a spectrophotometer

To improve the purity, we a MinElute Reaction Kit 50 from Qiagen

  1. Put the samples in a column
  2. Centrifuge for 1 min at 17900G
  3. Add 750µl Buffer PE
  4. Centrifuge for 1 min at 17900G
  5. Remove the liquid from the tube and put the column back
  6. Centrifuge for 1 min to dry the column
  7. Transfer the column out into a new tube
  8. Add 11µl water
  9. Centrifuge for 1 min to elude the DNA from the column

    The liquid into the tube now contains the DNA

  10. Check the purity with a spectrophotometer
  11. Freeze the DNA until library preparation