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Agarose gels (hydrogels) are commonly used in molecular biology for electrophoresis of DNA.

When a solution of hot agarose is poured, the material is clear: enter preformatted text here When a gel forms, the material becomes partially opaque: enter image description here

This phenomenon is NOT observed in acrylamide gels used for electrophoresis of protein. Unpolymerized and polymerized acrylamide both appear clear.

I assume that what we are observing here is light scattering. I am not sure if the scattering is Rayleigh or Mie, and I am not sure why it occurs upon agarose gel formation. I am not sure why it doesn't happen with acrylamide, another gel.

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  • $\begingroup$ I agree with your hunch that it most likely has to do with light scattering, but why the two gels would look different even though they seem to have roughly similar pore sizes around 100 nm is unclear (pardon the pun). Maybe it is due to the density of the pores? $\endgroup$
    – pentane
    May 6, 2016 at 20:07
  • $\begingroup$ A very popular reference (for apparently an explanation) seems to be Doi E. 1993. Gels and gelling of globular proteins. Trends Food Sci Tech 4:1-5. I just can't yet find the original. For free I mean. Otherwise: sciencedirect.com/science/article/pii/S0924224405800032 $\endgroup$
    – Řídící
    May 6, 2016 at 20:32

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Agarose is a polysaccharide, and like all polysaccharides it is bristling with polar hydroxyl groups. This means the agarose chains interact very strongly with each other by hydrogen bonding. If the solution is heated to a high enough temperature to break the hydrogen bonds (around 90-100ºC) then the agarose molecules behave pretty much like any other soluble polymer i.e. a randomly oriented chain with no long range order. In this state the solution of agarose is clear.

However as the temperature falls and hydrogen bonds start to form the agarose molecules pair up into double helices, then these double helices themselves aggregate with other double helices to form thicker fibres. A Google search found this nice picture showing what happens:

enter image description here

(image from this site)

The gel is due to this network of super-helices linked at their ends. However for the purposes of this question the key fact is that the diameter of the super-helix bundles is around 20nm or about a half to a third of the wavelength of visible light. This puts them at the upper size limit for Rayleigh scattering or the lower end for Mie scattering. So you get the usual Rayleigh effects e.g. the gel looks blue in reflected light and orange in scattered light, but you also get a slight milkiness as associated with Mie scattering.

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