Why is it always we run our DNA samples in horizontal manner and not horizontal like one employed for proteins.
Background:
Gel electrophoresis is a technique used for the separation of deoxyribonucleic acid, ribonucleic acid, or protein molecules using an electric current applied to a gel matrix.In most cases the gel is a crosslinked polymer whose composition and porosity is chosen based on the specific weight and composition of the target to be analyzed. When separating proteins or small nucleic acids (DNA, RNA, or oligonucleotides) the gel is usually composed of different concentrations of acrylamide and a cross-linker, producing different sized mesh networks of polyacrylamide. Agarose is the material of choice when nucleic acids of larger lengths are to be separated.
Now coming to the main issue of this topic: Why a DNA gel is mostly run horizontal and Protein gel’s vertical? The simple answer to this is the ease in doing the popular way-meaning migrating DNA gels in horizontal manner and Protein vertically. In fact proteins can be migrated in a horizontal manner also and many DNA gels are run using PAGE vertically. Another reason for popularity of vertical protein gels could be that most of the apparatus available support gels running this way.
There are several reasons for proteins gels to be run mostly vertically:
1) The use of the combination of stacking and resolving gel.
2) Molecular oxygen inhibits polymerization by reacting with the free radical SO4- ions {Ammonium persulfate (APS) is rather unstable and decays to produce free radical SO4- ions, which react with the acrylamide molecules and initiates their polymerizationin presence of Tetramethylethylenediamine (TEMED) catatalyze the polymerization of acrylamide}, which is actually the reason why PAGE gels are poured in between plates and not in open top horizontal apparatuses, as can be done with agarose.
3) Another advantage with the vertical set-up is that it allows for a much smaller gel volume, which is useful when making a denaturing gel which includes several toxic and expensive ingredients than a simple agarose gel for DNA.
Generally things which are easy to perform and with great efficiency , works in long run and becomes immensely popular (vertical migration of proteins).
External links for details on PAGE :
A nice article on ENCOR Biotechnoly Inc