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Tech Tips: Getting DNA from Swabs

Mar 30, 2011
Suzanne Kennedy

A frequent question to our technical support team is how to isolate DNA from buccal swabs or swabbed material.  Here are our recommendations for performing an extraction of DNA from swabs based on feedback from our customers.  Whether or not to use bead beating depends on whether you are trying to isolate DNA from microbes or human (or host animal) cells.

The eukaryotic cells of the host will lyse easily with guanidine containing lysis buffers and proteinase K. These do not need to be mechanically broken open. However, microbial DNA isolation does need the force of mechanical lysis to obtain the optimal yields. So for this reason, we have several recommendations for working with swabs, depending on your sample type and how dirty it may be.

For human (host) DNA isolation from swabs or easy to lyse bacteria:

The Blood Spin DNA Kit may be used:

  1. With this kit, take the swab (of your choice) and brush the wall of the cheek up and down (8-10 times). Buccal swabs may be stored and shipped dry and at room temperature until ready for processing. 
  2. Place the swab in 200 ul of 10 mM Tris, 1 mM EDTA. If that volume does not cover your swab, increase it to 400 ul.
  3. Rotate the swab in the buffer to release the cells into the solution- give it a minute.
  4. Some swabs have a head that can be snapped off and left in the tube. If you have this type of swab, go ahead and break it off into the buffer. If you do not have this type of swab, remove it as described in step 7 below and continue to step 5.
  5. Add an equal volume of the Solution B1 (400 ul if you used 400 ul of TE buffer) from the blood spin kit and the proteinase K (10 ul).
  6. Let the sample digest for 30 minutes at 50-60C.
  7. Remove the swab by gently squeezing it against the wall of the tube to remove as much of the solution as possible. Then discard.
  8. Add an equal volume (400 ul) of 100% ethanol (Solution B2) and then bind the DNA to the column in two spins with 600 ul per spin.
  9. Proceed with the protocol as directed.

For human or bacterial cells:

Another option for human cells and bacterial cells that uses bead beating is the UltraClean Tissue and Cells DNA Isolation Kit. With this kit, we use our large garnet beads to lyse cells in the presence of a strong lysis buffer. This protocol also employs the proteinase K digest step to increase yields.

  1. With this kit, after taking the swab from the cheek cells (as described above) or environment, place it into a tube containing 1 ml of the Solution TD1 lysis buffer.  If you are looking for microbial DNA, place the swab into the  bead tube provided in the kit. Rotate the swab in the buffer to shake the cells into the solution. If possible, snap the head of the swab into the tube and let it incubate during digestion.
  2. Add the proteinase K provided and allow the sample to digest for 30 minutes at 55-60C.
  3. Remove the swab by squeezing off the excess liquid onto the side of the tube and remove as much of the liquid as you can. Discard the swab.
  4. Proceed with the vortex step in the protocol if you are looking for microbial cells and if not, you may proceed with the DNA binding to the Spin Filter step and continue as directed.

 For swabs collected from samples with PCR inhibitors:

Some of our customers are working with samples that contain a lot of PCR inhibitors. For example, some labs use rectal swabs from animals or babies to analyse the microbiota of the gut.  Swabs taken from the environmental may contain dust that will cause PCR inhibition.  So for these sample types, the BiOstic Bacteremia DNA Isolation Kit becomes the preferred choice. The Bacteremia Kit has a 2 ml bead tube that can accommodate a swab tip and contains our 0.15 mm garnet beads for optimal lysis of bacterial cells. The protocol uses a strong lysis buffer and employs our IRT method for removal of PCR inhibitors.

  1. Place the swab in the bead tube and add 450 ul of Solution CB1 (the lysis buffer in the kit).
  2. Rotate the swab in the buffer to release the cells into the solution- give it a minute.
  3. Snap the head off and leave in the tube if you have this type of swab otherwise, squeeze out as much liquid from the swab as you can and remove. 
  4. Perform the protocol as described, heating the sample at 70C for 15 minutes to help break the tougher microbes in the vortex step.
  5. Proceed with the protocol as directed.

The Bacteremia Kit is best for microbial samples because of the strong lysis and bead beating, however, if you have a sample with inhibitors but want human DNA (for example, a swab taken from a person who forgot to avoid eating or drinking before taking the sample), then you can use this kit too.

Do not use the bead beating tube and instead place the swab into a standard microcentrifuge tube containing Solution CB1 lysis buffer (450 ul) and let soak. Remove the swab after a few minutes and discard. Perform the heating step to lyse the cells and 10 ul of proteinase K may be used here during the incubation. Then proceed with the rest of the protocol starting with Solution CB2 which removes the inhibiting substances.

As you can see, we have a lot of options for swabbed samples depending on where it came from and the cell type of interest.  If you have any questions, or have an unusual sample and need advice, we’d love to help you with it. Just drop us an email at technical@mobio.com or leave a comment here on our blog.

Best,

Suzanne

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