Native PAGE electrophoresis conditions

In native gel electrophoresis and CZE, the sample components are resolved by their differences in electrophoretic mobility or mass-to-charge ratios. Electrophoretic analysis under native conditions in gel electrophoresis is not as widely used as SDS-PAGE. In gels, disadvantages of native analysis are the low field... 

Because conformational changes in RNA or short DNAs typically cause small changes in electrophoretic mobility, analysis of nucleic acid folding requires careful optimization of electrophoresis conditions. By contrast, protein—nucleic acid interactions are typically easier to analyze by native PAGE because the molecular weight and positive charge of the protein produces a relatively large shift in gel mobility. 

The conditions of electrophoresis are most important for success of the SSCP technique. Separation of ssDNA by nondenaturating (native) electrophoresis may be performed either in slab gels (native PAGE) or in capillaries (CE). The decision for one of these methods may depend on the equipment available and the number of samples to be analyzed. 

Electrophoresis is only partly helpful here. If the dimer is held together by covalent bonds ( S-S bridges, for example, under nonreducing conditions), then SDS-PAGE would show a protein band at around 30,000. However, non-covalent dimerization of the native state would be disrupted by SDS. and only monomer bands would be seen. 

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