Epicentre® BioTechnologies has produced a product called the BuccalAmp™ DNA Extraction Kit. This kit is a very simple and rapid way of extracting DNA from various sources without any need for further purification of the extracted DNA.
The kit is sold with QuickExtract™ DNA Extraction Solution and Catch-All™ Sample Collection Swabs. Each kit is sold with 15 tubes of the DNA extraction solution and 15 of the swabs. The swabs are sterile and individually packed in a hard plastic casing that is easily resealed for transport to the laboratory for SNP analysis, infectious disease analysis, human and animal identification purposes.
The swabs themselves are foam swabs rather than the usual rayon or cotton varieties used by many laboratories and police forensic units as well as in hospitals. The swabs are very hardy and do not break up significantly even when rubbed on a coarse surface. Being made of foam they have an “open weave” style which increases the collection surface area as opposed to cotton and rayon swabs.
I have used the swabs along with the DNA extraction solution in a limited capacity to determine it’s effectiveness at producing a high quantity and quality of DNA for microsatellite analysis. I have had volunteers take a swab from one side of the cheek with a rayon swab and the other side of the cheek with a Catch-All™ swab.
I performed a standard Chelex extraction on the rayon swabs; the extraction consisted of a 56°C Proteinase K incubation step for 30 minutes, vortexing and then boiling for 8 minutes and transfer of the supernatant to a new tube.
For the Catch-All™ swab I followed the manufacturer’s instructions and rotated the swab 5 times in the QuickExtract™ DNA Extraction Solution and pressed the swab against the side when removing it to ensure that most of the DNA extraction remained in the tube. The tube was incubated at 65°C for 6 minutes, vortexed and boiled for 2 minutes. Although the concentration of DNA at the end of each extraction method was almost identical, the volume of the BuccalAmp™ DNA extract was double that of the Chelex method.
I tested both methods with a standardized set of rayon swabs spiked with an identical number of K562 cells. The extractions were performed as above and the average concentration of DNA was 0.944 ng/uL in 500 uL for BuccalAmp™ and 1.13 ng/uL in 250 uL for the Chelex extraction. Using BuccalAmp™ you end up with nearly double the total yield of DNA.
I have also tested a series of rayon swabs with an identical amount of blood dried on the swabs. I performed an extended incubation: 30 mins at 65°C, to allow the blood to elute and then boiled for 8 minutes using the BuccalAmp™ reagent. This generated an average concentration of 0.292 ng/uL in 500 uL, while the Chelex extraction gave a yield of 0.201 ng/uL in 250 uL.
The downstream microsatellite analysis of all samples was identical and without any fluorescent artifacts or quenching of 6-FAM, JOE, NED or ROX dyes. It’s easy to see that if a laboratory works with a lot of buccal or blood swabs or even throat swabs for infectious respiratory diseases, that this kit would increase throughput greatly. There is also the benefit of decreasing the chance of contamination as the swab is introduced to the DNA extraction solution and the tube remains closed until downstream applications are needed. With the Chelex extraction there are multiple tube opening steps and a final transfer to a new tube which significantly increases the risk of contamination.
All quantification was performed with a real-time quantitative PCR (qPCR) assay and included an internal control to test for inhibition of the PCR process. No inhibition of the PCR process was found in any of the samples tested.
There is also a cost saving involved when you consider the labor, pipette tips, and time required for a person to make and aliquot Chelex, Proteinase K and other solutions. In addition, the DNA extraction solution and swabs can be purchased separately. So you are free to experiment with the reagent using different swabs, or to use the swabs with your own extraction method. In our own (very limited) study, we obtained greater recovery of DNA using the Catch-All™ swabs versus the standard rayon swabs.