Native Gel Electrophoresis

Native gelelectrophoresis uses native or non-denaturing gels for the analysis of proteins in their folded, native state. The electrophoretic mobility of an intact protein is depended on its charge-to-mass ratio as well as on its physical shape and size. Chemically, proteins are structurally very complex and functionally sophisticated molecules that are known to man. The nature and position of each amino acid located within the long string of amino acid sequence that forms a protein determines its three-dimensional shape and function and therefore its migration behavior in a gel during an electrophoresis experiment. Agarose gel electrophoresis is a method of choice for large molecule separation over 1 million Da. Acrylamide cannot be used for this purpose, because it remains liquid at the concentration required for the appropriate separation of high-molecular-weight analytes. The movement of molecules through an agarose gel is dependent on the size and charge of separated particles, as well as the pore size present in the gel. The observed migration is also affected by the type of electrophoresis buffer, especially its ionic strength. The electrical conductance of the gel is dependent on the presence of various ions, including those present in the sample. Undoubtedly, major advantages of this particular technique are easy and rapid preparation of the gels and the possibility of high-molecular-weight species fractionation. The combination of agarose gel with polyacrylamide gel electrophoresis enabled creation of the genome maps and facilitated the Human Genome Project. At present, there are three different geometrical forms in which gel electrophoresis can be carried out: horizontal slabs, vertical slabs, or vertical cylinders (rods) of gel, often also referred to as tube gels. Slab gels in thinner layers are preferred to thicker slab or tube gels, as they offer faster separation, sharper zones, and more rapid and efficient cooling and subsequent staining. In PAG electrophoresis, there is a clear preference for the horizontal system utilizing ultrathin gel layers polymerized on to carrier foils. The advantages of horizontal versus vertical systems are easier handling, use of premanufactured gels, more efficient cooling, reduced material costs, availability of fully automated systems, and flexibility towards other forms of electrophoresis such as isoelectric focusing. In the stacking gel of a multiphasic system, sample components are separated in the isotachophoresis mode with no molecular sieving effect. After passing the boundary between stacking and separating gel, the sample components are then separated by size and charge in the usual way. The very high resolving power of this method, which is often referred to as disc PAGE, is due to the formation of very sharp zones produced by the gel and buffer discontinuities. The production of thin starting zones makes disc PAGE very suitable for use with dilute sample solutions. Nondenaturing gel electrophoresis is used to separate proteins by retaining their higher-order structure and their interactions with other polypeptides; this is achieved by avoiding the use of denaturing agents in the gel. Unlike SDS-PAGE, in nondenaturing gel electrophoresis, the migration of proteins depends on their global shape and charge, implying that the mobility of a protein complex can vary according to the nature of its conformation. In this kind of approach, one must remember that the electric charge of a protein, or a protein complex, depends on the composition of the electrophoresis buffer.