Editing Gel electrophoresis (section)

===Native===

[[File:Glucose-6-Phosphate Dehydrogenase activity stain.jpg|thumb|Specific enzyme-linked staining: [[Glucose-6-phosphate dehydrogenase deficiency|Glucose-6-Phosphate Dehydrogenase]] [[Isozyme|isoenzymes]] in ''[[Plasmodium falciparum]]'' infected [[Red blood cell]]s<ref name="pmid7012616">{{cite journal | author1=Hempelmann E | author2=Wilson RJ | title=Detection of glucose-6-phosphate dehydrogenase in malarial parasites. | journal=Mol Biochem Parasitol | year=1981 | volume=2 | issue=3–4 | pages=197–204 | pmid=7012616 | doi=10.1016/0166-6851(81)90100-6 | pmc= | url=https://pubmed.ncbi.nlm.nih.gov/7012616 | access-date=23 March 2022 | archive-date=6 July 2023 | archive-url=https://web.archive.org/web/20230706155553/https://www.sciencedirect.com/science/article/abs/pii/0166685181901006?via%3Dihub | url-status=live }}</ref>]]

Native gels are run in non-denaturing conditions so that the analyte's natural structure is maintained.  This allows the physical size of the folded or assembled complex to affect the mobility, allowing for analysis of all four levels of the biomolecular structure.  For biological samples, detergents are used only to the extent that they are necessary to [[lysis|lyse]] [[lipid bilayer|lipid membranes]] in the [[cell (biology)|cell]]. Complexes remain—for the most part—associated and folded as they would be in the cell. One downside, however, is that complexes may not separate cleanly or predictably, as it is difficult to predict how the molecule's shape and size will affect its mobility. These effects have been addressed by [[QPNC-PAGE|preparative native PAGE]].

Unlike denaturing methods, native gel electrophoresis does not use a charged [[Denaturation (biochemistry)|denaturing]] agent. The molecules being separated (usually [[proteins]] or [[nucleic acids]]) therefore differ not only in [[molecular mass]] and intrinsic charge, but also the cross-sectional area, and thus experience different electrophoretic forces dependent on the shape of the overall structure. For proteins, since they remain in the native state they may be visualized not only by general protein staining reagents but also by specific enzyme-linked staining.

A specific experiment example of an application of native gel electrophoresis is to check for enzymatic activity to verify the presence of the enzyme in the sample during protein purification. For example, for the protein alkaline phosphatase, the staining solution is a mixture of 4-chloro-2-2methylbenzenediazonium salt with 3-phospho-2-naphthoic acid-2'-4'-dimethyl aniline in Tris buffer. This stain is commercially sold as a kit for staining gels. If the protein is present, the mechanism of the reaction takes place in the following order: it starts with the de-phosphorylation of 3-phospho-2-naphthoic acid-2'-4'-dimethyl aniline by alkaline phosphatase (water is needed for the reaction). The phosphate group is released and replaced by an alcohol group from water. The electrophile 4- chloro-2-2 methylbenzenediazonium (Fast Red TR Diazonium salt) displaces the alcohol group forming the final product Red Azo dye. As its name implies, this is the final visible-red product of the reaction. In undergraduate academic experimentation of protein purification, the gel is usually run next to commercial purified samples to visualize the results and conclude whether or not purification was successful.<ref>{{Cite book|title = Fundamental Approaches to Biochemistry and Biotechnology|vauthors = Ninfa AJ, Ballou DP |publisher=Bethesda, Md: Fitzgerald Science Press|year=1998|isbn= 9781891786006}}</ref>

[[Native state|Native]] gel electrophoresis is typically used in [[proteomics]] and [[metallome|metallomics]]. However, native PAGE is also used to scan genes (DNA) for unknown mutations as in [[single-strand conformation polymorphism]].