Water for Protein Electrophoresis
Impact of Water
Organics
Acrylamide gels are formed from the polymerization of acrylamide monomer in the presence of smaller amounts of bis-acrylamide (a cross-linking agent). Organics contaminants may affect the polymerization, resulting to poor quality gels.
Ions
The migration of proteins in the gel is dependent on, among other things, ionic strength and pH of the running buffer. The ionic strength and pH of buffers used to prepare the gel and running buffer have to be maintained to assure reproducible results. The presence of high levels of ions could alter the ionic strength of the solutions and this could affect the migration rate of proteins.
Bacteria
Water that is contaminated by bacteria could contain degradation by-products such as proteases that may degrade proteins, and ions which as previously mentioned may affect alter the ionic strength of solutions.
In an experiment, total protein extract from E. coli was analyzed by 2D-PAGE. Two types of water were compared - bottled water and ultrapure water from a Milli-Q® system. They were used in the solubilization of the sample and gel and buffer preparations in the first and second dimensions of the separation. Result is shown in Figure 1. Milli-Q® water gave an over-all better gel quality, with lower background and better spot resolution.
Figure 1: 2D-PAGE of total protein extract from E. coli using two different types of water. The gel processed with Milli-Q® water gave better gel quality, with lower background and better spot resolution.
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