Several BTCI Biotechnology Field Trips feature analysis of DNA by means of agarose gel electrophoresis. We have adopted the use of certain products in order to improve the efficiency and safety of the experience that we offer to students. BTCI realizes that these products may or may not be in common use in other teaching laboratories. In the spirit of enabling teachers to translate BTCI protocols to activities in their own classrooms, we offer this brief summary of how BTCI does gel electrophoresis, along with other options that teachers may use.
Running Buffer
An important consideration when running agarose gel electrophoresis is the selection of a running buffer. At BTCI, sodium borate (SB) solution is the running buffer of choice in our teaching labs. Our reason for using it instead of more conventional electrophoresis running buffers (TBE or TAE) is straightforward: SB dissipates heat much better than TBE or TAE, allowing us to run gels at a higher voltage. This allows students to get quality electrophoresis results in a much shorter amount of time.
| Feature |
Sodium Borate |
TBE/TAE |
| Running Voltage |
200 to 250V |
130 V |
| Running Time |
20 to 25 min. |
45 min. |
| Downstream Compatabilities |
None |
DNA may be extracted from gel for downstream use |
Jenkins, K. & Bielec, B. (2006). Running DNA Mini-Gels in 20 Minutes or Less Using Sodium Boric Acid Buffer. The American Biology Teacher, 68(9), 544-546. With permission from the National Association of Biology Teachers.
Fluorescent DNA Stain
BTCI uses a product from Fotodyne called FOTO/VisionTM to visualize DNA in a gel instead of ethidium bromide (EtBr). Because of the way that DNA stains bind to DNA molecules, there is often concern that they are mutagenic, carcinogenic or both. One particular measure of a chemical compound's mutagenicity is called the Ames test. Ethidium bromide has been found to be a mutagen in this test. As such, there are concerns about ethidium bromide's use, containment, and disposal in teaching laboratories. FOTO/VisionTM is an example of a fluorescent DNA-binding dye that does not show mutagenicity in the Ames test. Using a non-mutagenic DNA stain like FOTO/VisionTM allows BTCI to offer students a more interactive field trip experience while minimizing a common safety concern in the laboratory.
| Feature |
FOTO/VisionTM
|
Ethidium Bromide |
| Mutagenicity |
Not mutagenic in Ames test |
Mutagenic in Ames test |
| Disposal Considerations |
None |
Liquids must be filtered through activated charcoal. Solids must be incinerated. |
| Staining Mode |
Incorporated into sample loading dye; not used as a gel or buffer additive. |
Gel or Buffer additive; Can stain DNA during or after electrophoresis |
| Reusability |
None |
Staining solution can be reused many times. |