Anyone who has done a lot of PCR has also run a lot of agarose gels! The standard method for analyzing and purifying PCR products involves pouring an agarose gel (percentage of the gel depends on the product base pair size). This involves weighing agarose, adding buffer, boiling, adding ethidium bromide, pouring the gel and then waiting for it to harden. Needless to say, this takes time and effort that could be better used running experiments, setting up more PCR reactions, etc.
Invitrogen has developed several systems that eliminate the need to pour your own agarose gels. There is the basic E-Gel® for 12-16 samples (depending on whether you buy the single or double comb version), the E-Gel® 48 and the E-Gel® 96. The E-Gel® system consists of a base unit that provides the current and the precast agarose gels themselves. There are two separate bases available – one for the smaller 12 sample gel and one for the high-throughput 48 and 96 well gels. The gels come individually packaged and once opened can be easily snapped into the base and then loaded. The time can then be set (for the basic base the only options are 15 and 30 minutes); the samples are then run on the gel with an automatic stop. This is probably my favorite feature, as there is nothing worse than forgetting to stop your gel and having all that precious DNA sample run off the gel into the buffer.
I have had the E-Gel® 48 system for a while now and I really enjoy it. It is easy to use and eliminates the time and hassle of pouring gels, dealing with ethidium bromide and buffers, and worrying about the current and time. It also allows me to load up to 48 samples with a multi-channel pipettor, which increases my throughput and saves more time. The run time can be adjusted if the product bands are close together or the samples need to be better separated but usually a 20 minute run is sufficient to resolve the bands.
There are several drawbacks to using the E-Gel® 48 system, however. The main one is the limitation to only 3 percentages of gels (1%, 2% and 4%). While these are usually sufficient, it is sometimes necessary to have a more specific percentage for better resolution of PCR products. I often have wanted a 1.2 or 1.5% gel to use, and occasionally pour my own gels to separate PCR reactions I know don’t resolve well on the precast gels. Another drawback is the reliability on Invitrogen to have the gels you need in stock. The gels often seem to be on backorder, occasionally up to a month. There’s nothing worse than having to pour your own gels when you’ve been spoiled with this precast system! Purifying DNA bands can also be a problem; although possible, it is somewhat complicated. The gels are enclosed in a plastic cassette, which is great when handling the gels to avoid ethidium contamination or drying of the gel, but it is very hard to get the gel (and thus the DNA) separated from the cassette. (It is easier with the 12-well basic system, however, and there are specific gels and tools for this purpose.) Another drawback is the price: a box of 8 gels costs roughly $160, or about $20 per gel. This is quite pricey compared to the ~$2 per gel to pour your own. It can also be a waste if you don’t have enough samples to fill the wells as the gels cannot be reused. The smaller system can be used for smaller sample sizes but that requires an additional base system and different gels to be kept on hand.
Overall, I love this system. If you have the money to spend for the ease and convenience of eliminating all the pain and complications of pouring and running agarose gels, dealing with ethidium bromide and buffers, power units, etc., I would highly recommend investing in one of the E-Gel® systems.
Research Associate
Department of Ophthalmology
University of California, San Francisco