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It seems in electrophoresis, agrose gel always runs horizontally, and SDS-PAGE gel always runs vertically, why?

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  • $\begingroup$ Be careful saying always, as in science you can rarely make an all-encompassing statement like that. Gels are traditionally run in those formats, but there are exceptions for a variety of reasons. $\endgroup$ – MattDMo Nov 24 '15 at 19:32
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When you stand general agarose gel vertically, the gel is slippery coming out from the bottom; although, some run vertically.

To polymerize acrylamide, it is good idea to avoid air because oxygen inhibits polymerization of acrylamide. You would get an air tight condition, pouring acrylamide between glass plates, but how could you run gel made between glass plates. When you set such gel plates horizontally, how do you load samples? Then, it is easier to set gel plates vertically.

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  • $\begingroup$ Yes, if you poured acrylamide into a horizontal slab mold it would take a very long time to polymerize, AND that top surface would dry out (unless you had a buffer layer on top of it, or plastic wrap, or similar). $\endgroup$ – mdperry Nov 25 '15 at 0:52
  • $\begingroup$ Why does the agrose slippery out from the bottom if it runs vertically? $\endgroup$ – sunboyharry Nov 26 '15 at 5:04
  • $\begingroup$ @sunboyharry Agarose does not adhere enough on glass plates to hold its position. I can not explain it via the physical and chemical properties, though. $\endgroup$ – 243 Nov 26 '15 at 18:13
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Generally, one would want to run all the gels vertically to save the space. The gel slab has to either support itself or be enclosed in a supporting structure, like between glass plates. Simple agarose electrophoresis wouldn't benefit from enclosure into a precisely defined glass enclosure, and agarose is not strong enough to be run vertically - the slab will not support itself. Thus PAGE gels are run vertically and agarose - horizontally.

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  • $\begingroup$ To pour and run an agarose slab gel vertically the inner surface of the glass plates needs to be frosted (with microscopic imperfections). $\endgroup$ – mdperry Nov 25 '15 at 0:49

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