The Buffer Puffer self-recirculating gel box from Owl Separation Systems is a simple way of recirculating the buffer in an electrophoresis apparatus to prevent the formation of pH or ion gradients. Buffer from one end of the gel box travels through a tube to the other end, allowing the buffer to recirculate without the need for pumps, tubing, or other cumbersome accessories. Bubbles at the end near the positive electrode provide the force to push the buffer back to the other end of the gel box. It is ideal for RNA gels where an ion gradient may cause glyoxalated RNA to dissociate. It is also useful for gels that need to run for several hours, since buffer recirculation encourages even migration of nucleic acids.
When we first started running gels for Northern blots in our lab, we faced the choice of formaldehyde or glyoxal/DMSO. I wanted to avoid toxic formaldehyde and I had heard that glyoxalated RNA tends to give sharper bands on a Northern. However, glyoxal gels require an inconvenient buffer recirculation system. In another laboratory where I used a pump and rubber tubing, I frequently flooded my bench with buffer. In my current lab, we didn’t even have a gel box that could accommodate a pump. I tried manually recirculating the buffer with a serological pipet periodically, but this method was clearly not the most convenient. In my experience with the Buffer Puffer system, the gel box does not overheat even after running for a few hours and the RNA is intact. Therefore, we can leave a gel running without constantly needing to monitor it. Finally, purchasing the Buffer Puffer for RNA gels forced our lab to have a dedicated gel box for RNA work rather than simply trying to decontaminate one of our DNA gel boxes every time we do a Northern blot.
On the other hand, if you are having problems because your running buffer is incompatible with your sample-loading buffer, even the recirculating gel box will overheat. When my gel box was steaming prior to purchasing the Buffer Puffer, I thought that the new gel box might solve my problem. In this case, I was using a commercially available glyoxal/DMSO loading dye that does not work with low ionic strength buffers. Therefore, I would caution researchers to troubleshoot before investing in a new gel box.
The obvious advantage of a self-recirculating gel box is that it does not require anything to be attached to it and does not make a mess. Another nice feature is that the gel-casting tray has removable end barriers that don’t require tape and don’t leak. Owl also sells a number of accessories such as additional combs and casting trays to meet the needs of individual labs.
One regret that I have is that I purchased a much larger model than our lab needs. As a result, we need a large volume of RNase-free buffer and we have to run our gels for a few hours. There is a smaller model available that may be more suitable for some labs. Another disadvantage is that researchers who prefer to start buffer recirculation after the nucleic acid has migrated out of the wells do not have that option. However, we have not had a problem with the buffer recirculating during the first several minutes.
I suspect that many researchers would find the Buffer Puffer very useful but are unaware that this type of gel box is available.
Tara Lauriat
Graduate Student
Mount Sinai School of Medicine
New York, NY