Came across this prestained protein marker and the bands indicates different molecular weights in different buffers. How is that? Are these supposed to be made by proteins of constant molecular weights? Is this because of the prestain that associated with different protein?
In protein markers, the proteins are bound to a dye molecule that has a charge on it. This covalent interaction changes the overall charge on the protein making the molecular weights you observe ‘approximate’. In addition, the charge on these protein molecule will change depending on the buffer (of variable ionic strength and pH) used. Therefore you see different MWs when you run them in different gels made with different buffers.
Ionic strenght is diferect among electrophoresis buffers. This parameters affects protein mobility within an electric field
While gels are suitable for Mw estimates, there are pitfalls as mentioned above. For true firs principle measurements of Mw, you'd want to use a multi-angle static light scattering detector, such as those made by Wyatt Technology.
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