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.