I think it would be difficult to prepare a polyacrylamide gel in the same manner as an agarose gel. Polyacrylamide gels are usually quite thin (1 or 1.5 mm thick is typical). If you tried to polymerize a gel that thin in an agaorse gel tray, it probably wouldn't polymerize because of too much exposure to air. Also, it would be nearly impossible to cast the wells, and they would not be able to hold much volume.

Before slab gels for PAGE were introduced, gels used to be cast in glass tubes that were oriented vertically. This is a good orientation when you need to have different cathode and anode buffers, as on isoelectric focusing. It would be very challenging to keep the two buffers separate in a horizontal gel.

I suspect that at least one reason that agarose gels are cast horizontally is that they are not strong enough to stand up under their own weight if they were cast vertically when low agarose concentrations are used. Other than that, it is a much simpler way to cast gels when there is no need for them to be vertical; it allows the gels to be made fairly thick to allow a relatively large volume well; it makes casting and loading the wells easy; it allows the gel to be completely submerged in running buffer to keep it cool, and so forth.

I think it would be difficult to prepare a polyacrylamide gel in the same manner as an agarose gel. Polyacrylamide gels are usually quite thin (1 or 1.5 mm thick is typical). If you tried to polymerize a gel that thin in an agaorse gel tray, it probably wouldn't polymerize because of too much exposure to air. Also, it would be nearly impossible to cast the wells, and they would not be able to hold much volume.

Before slab gels for PAGE were introduced, gels used to be cast in glass tubes that were oriented vertically. This is a good orientation when you need to have different cathode and anode buffers, as on isoelectric focusing. It would be very challenging to keep the two buffers separate in a horizontal gel.

I suspect that at least one reason that agarose gels are cast horizontally is that they are not strong enough to stand up under their own weight if they were cast vertically when low agarose concentrations are used. Other than that, it is a much simpler way to cast gels when there is no need for them to be vertical; it allows the gels to be made fairly thick to allow a relatively large volume well; it makes casting and loading the wells easy; it allows the gel to be completely submerged in running buffer to keep it cool, and so forth.

Dear Rehab Zaki,

The first reason is that SDS-PAGE gels have two component gels – the stacking gel and the resolving gel.  The vertical system allows you to make them sequentially. You add the resolving gel first and then once it is set, you add the stacking gel. It would be very difficult, if not impossible, to make a gel like this in a horizontal system.

The second reason is that oxygen inhibits the polymerization of SDS-PAGE gels. Ammonium persulfate (APS) in the SDS-PAGE gel mix decays to produce free radical SO4- ions, which react with the acrylamide molecules in the presence of TEMED to initiate polymerization. Molecular oxygen can react with, and mop up, the free radical SO4- ions and inhibit the polymerization reaction.  Sandwiching it between two plates keeps oxygen away from the gel mix. So in an open, horizontal system the polymerization reaction would not proceed efficiently.

In this instance the reagents used in SDS-PAGE gels are relatively expensive, so it would not be cost effective to pour them like agarose gels as you need much thicker gels. So it is more cost effective to make thinner gels.

Good question i have also learned lots more things from this. :-)

Note : Collected.

And finally, you also can use polyacrylamide gels to separate DNA fragments, e.g. if they are small and you need high resolution. And then you use, because of all the above reasons, a vertical gel for DNA.

Horizontal Gel Electrophoresis

In horizontal gel electrophoresis, a gel is cast in a horizontal orientation and submerged in running buffer within the gel box. The gel box is divided into two compartments, with agarose gel separating the two. As previously stated, an anode is located at one end, while a cathode is located at the other. The ionic running buffer allows for a charge gradient to be created when a current is applied. In addition, the buffer serves to cool the gel, which heats up as a charge is applied. The running buffer is often recirculated to prevent a pH gradient from forming.Horizontal electrophoresis; gel being removed after sample run. Photo courtesy of Accuris by Benchmark Scientific

Since the two compartments of a horizontal gel system are connected through the running buffer, it is not possible to utilize horizontal systems with a discontinuous buffer system. Additionally, acrylamide cannot be used for horizontal systems because gels are cast in a tray which is exposed to atmospheric oxygen. Oxygen inhibits the polymerization of acrylamide, and thus, interferes with the creation of the gel. The ease-of-use of a horizontal system makes this an ideal choice for most DNA and RNA applications.

Vertical Gel Electrophoresis

A vertical gel method is slightly more complex than its horizontal counterpart. A vertical system utilizes a discontinuous buffer system, where the top chamber contains the cathode and the bottom chamber contains the anode. A thin gel (less than 2 mm) is poured between two glass plates and mounted so that the bottom of the gel is submerged in buffer in one chamber and the top is submerged in buffer in another chamber. When current is applied, a small amount of buffer migrates through the gel from the top chamber to the bottom chamber.

Unlike horizontal systems, the buffer can only flow through the gel, which allows for precise control of voltage gradients during separation. When combined with the smaller pore size of the acrylamide gel, greater separation and resolution can be achieved with this system compared to horizontal systems.