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Agar is a relatively cheap substance from red algae. And it contains a saccharide agarose as well as a small amount of pectin.

Agar is used for culture plates as is, but for DNA gels a grade of agarose, I guess with the pectin removed. What happens when a gel is run in agar? i.e. why remove the pectin?

If you can guess, how is the pectin removed? I know there are enzymes that might do it, but not sure what's really used.

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@dd3 has put down a great answer - esp with the figures in the answer! Would love to see an answer to what the industrial process is like. – shigeta Mar 6 '13 at 16:53
up vote 13 down vote accepted

The answer to the first part of your question can be found on Wikipedia:

Agar is a heterogeneous mixture of two classes of polysaccharide: agaropectin and agarose. Although both polysaccharide classes share the same galactose-based backbone, agaropectin is heavily modified with acidic side-groups, such as sulfate and pyruvate. The neutral charge and lower degree of chemical complexity of agarose make it less likely to interact with biomolecules, and, therefore, agarose has become the preferred matrix for work with proteins and nucleic acids.

This page compares the result of using agar gels to that of using agarose: enter image description here

The second part of your question: here's a patent, although I have no idea whether this method of agarose purification is widespread. Propylene glycol purification of agarose does seem to pop up a lot. I think people who purify their own agarose use that method, but I am not sure if biotech companies have other methods.

EDIT: it's propylene glycol, followed by ethylene glycol, that is commonly used, but PEG has been used at least once.

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thanks for doing this answer! I looked at similar patents after looking at the one you are pointing to and as late as 1987 they are precipitating agarose with glycols or PEGs... looks good! – shigeta Mar 10 '13 at 5:19
You're welcome. It was a good question, and I enjoyed finding an answer. – dd3 Mar 10 '13 at 8:24

Using DMSO (dimethyl sulfoxide), agarose can be separated. After heating and stirring around 2 hrs you will get a yellow stiff gel of agarose by filtering.

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this is cool! have a recipe? I'd like to try this! – shigeta Jun 26 '13 at 13:42
@shigeta: here is a paper – dd3 Jun 27 '13 at 1:06

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