DNA and RNA molecules that are analyzed by gel electrophoresis have to stay intact. The presence of unwanted nucleases would degrade the nucleic acids in the sample, and the molecules of interest will not be detected. (For more information, please refer to a separate section on RNase-free water).
Ions/Metals The ionic strength and pH of buffers used to prepare the gel and running buffer have to be maintained. The presence of high levels of ions could alter the ionic strength of the solutions.
Bacteria Water that is contaminated by bacteria could contain degradation by-products such as nucleases and ions which as previously mentioned, affect gel electrophoresis of nucleic acids.
In an experiment, rRNA from E.coli was loaded onto an agarose gel. The gels and buffers were prepared with two types of water - pure (Type 2) and ultrapure (Type 1). Result is shown in Figure 1. Higher signal/band intensities were obtained in gels prepared and run with ultrapure water.
Figure 1: Agarose gel electrophoresis of rRNA. Gels and buffers were prepared using pure and ultrapure water. The band intensities were higher with ultrapure water.
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