In gel electrophoresis of proteins the molecules migrate through a cross-linked polymer network that has taken up a lot of water. I would like to know the volume fraction of water inside the gel. I guess it depends on cross-linking density.
In the case of sephadex/sepharose gels the excluded volume will give the included volume . from the total column volume by subtraction but these are discrete particles. PAG gels are usually cross linked but long polymers so I wonder if the entire gel can be counted as a single moiety in which case the included buffer volume will always be 100%
Hi, for proteins you would typically use polyacrylamide gels, e.g. a 10% separation gel or a 10-15% gradient separation gel. The acrylamide/bisacrylamide stock solution is created as a w/v solution in water, so if you have the density of acrylamide/bisacrylamide and you know that their ratio is 29:1 (typical, again), you can calculate the water volume required to get to 100 mL of stock solution. When diluting for gel polymerization, the added TEMED, buffer components (and in most cases, SDS) are negligible. The acrylamide never polymerizes completely, nor is there complete crosslinking with the bisacrylamide due to inhibition of the reactions by oxygen. This is only a minor effect, mainly at the top of the gel, so in first approximation you can use what you calculated based on the polyacrylamide concentration (for example for the 10% gel, or in the gradient gel for 12.5% as the average value. For more info on all types of frequently used gels, consult the Sambrook manual "Molecular Cloning".
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