Just as the agarose had to be weighed out precisely, so does the solvent used to dissolve the agarose. Rather than just use water, we use buffered solutions which allow the DNA to run smoothly through the gel. These solutions optimize the pH and ion concentration of the gel and will also bathe the gel as it is subjected to the electric current which actually moves the DNA through the gel.

Perhaps you have seen the terms TBE or TAE. These are names of two commonly used buffers in electrophoresis. In fact, you can see the "E" in "TBE" on the label of the bottle to the left of the flask in the photo. The "T" stands for Tris, a chemical which helps maintain a consistent pH of the solution. The "E" stands for EDTA, which itself is another anacronym. EDTA chelates (gobbles up) divalent cations like magnesium. This is important because most nucleases require divalent cations for activity, and you certainly wouldn't want any stray nucleases degrading your sample while it's running through the gel, would you? Finally, the "B" or "A" stand for Boric acid or Acetic acid, which provide the proper ion concentration for the buffer.

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