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Study Notes: Horizontal and Vertical Gel Systems

The primary aims of the electrophoresis apparatus are to:

  • maintain a uniform electric field across the gel
  • provide cooling to reduce thermal artefacts (aberrations) in the gel
  • allow access to the gel itself for sample loading and visual monitoring of the run.

There are two main types:

  • horizontal (generally agarose only)
  • vertical (generally polyacrylamide only).

The vertical gel can be further subdivided into two types:

  • slab gel
  • tube gel.

An example of an agarose horizontal gel is shown below but, as this section is specifically about polyacrylamide electrophoresis, it will not be discussed further.

A line drawing of a typical horizontal gel system. The tank is horizontal, with electrodes each end and sample wells at the negative electrode end.
This is an example of a typical horizontal gel system.

Vertical gel systems
There are many different brands of electrophoresis apparatus on the market made, by a number of different manufacturers. In earlier times laboratories often made their own apparatus out of Perspex and some of these are still used today. The following examples are typical of what is available commercially today but you should be aware that there are many variations on the market.

Slab gels
These are used for sequencing DNA (long gels) or for proteins (mini gels - 15 cm x 15 cm or smaller). The features common to all slab gel set-ups are listed below.

  • The gel is cast between two glass plates separated by spacers typically < 2 mm thick.
  • The gel is mounted so that the top is in contact with the negative electrode chamber and the bottom is in contact with the positive electrode chamber.
  • The only connection between the buffer containers is through the gel. This allows the use of discontinuous buffer systems unlike horizontal agarose systems where the chambers are connected by a liquid bridge and the gel is bathed in buffer.
  • Due to the electrical connection via the gel itself, precise and reproducible control of the voltage gradient across the gel is achieved.
  • Provision for cooling, as thin gels heat up rapidly under the electric field - often achieved by having a relatively large volume of buffer in both tanks, partially immersing the gel in the bottom tank buffer or having the glass gel cassette in contact with a metal plate that acts as a heat sink.

Mini gel systems because of their small size have shorter running times.

A line diagram of a typical DNA sequencing gel (polyacrylamide), in a vertical tank, the negative electrode chamber at the top (with the sample wells) and the positive electrode chamber at the bottom.

This is an example of a typical DNA sequencing gel (polyacrylamide).

A line diagram of a typical SDS-PAGE system, with the negative electrode chamber at the top, with sample wells and the positive electrode chamber at the bottom.

This is a diagram of a typical SDS-PAGE system.

Gels are cast between the two glass plates (often called the gel cassette) by temporarily sealing the bottom of the plates with tape or some other device, carefully pouring the gel solution between the plates and allowing it to polymerise. A special comb is inserted into the top of the plates to form the sample wells.

Tube gels
Are considered by some to be ‘yesterday’s technology’ as they were some of the first electrophoresis systems used and have been superseded for most applications. Gels are cast into a glass tube that is mounted in an apparatus to provide upper and lower buffer tanks, connected to the electric system. The tube itself acts as the ‘gel cassette’.

One common use for tube gels is for preparative electrophoresis where the band of protein (in this case a circular disc) can be easily excised from a stained gel for further processing and purification.

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