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I'm trying to understand how exactly the binding to silica gel (in kits) step works and I cannot find any papers which provide an explanation of the physics or chemistry; especially on the way that Guanidine-HCl works.

So lets get them from the beginning.

First of all we adjust DNA binding conditions by adding a buffer which includes Guanidine-HCl and ethanol and then we centrifuge our sample. I knew that Guanidine-HCl destroys the tertiary structure of proteins but somewhere I read that also it helps the DNA to bind to a silica column. I searched to find the way that it works but I couldn't find a paper. Also what is the role of ethanol in this step? Is it just to remove proteins and polysaccharides from the sample?

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There is an excellent discussion of this in: Melzak et al. (1996) Driving forces for DNA adsorption to silica in perchlorate solutions. J. Colloid Interface Sci. 181: 635 - 644 I've skimmed the paper, and I'm beginning to understand it, but I don't feel up to actually answering the question yet. –  Alan Boyd Apr 1 at 17:40
    
So the whole story as i understood is not clear at all.Here is a abstract on what i got but i am not sure if this is the final answer. In earlier years there was the opinion that the SiO4 molecules had negative charge as the DNA too. So to achieve the binding of them you had use high conc. salt (chaotropic salt) and alkaline pH. In that way some cations from the salt will create a bridge between DNA and SiO4 molecules. In recent studies (Water interactions with silica surfaces: A big role for surface structure) seems that the things doesn't work that way. They predict that SiO4 molecules has –  F.N Apr 2 at 16:45
    
(continue from above) positive charges and the way that chaotropic agent works is by creating hydrophobic environment so to remove the water molecules from DNA and let it bind into silica membrane. As for ethanol...nothing yet. Some companies nevertheless they explain the binding mechanism as i described first. –  F.N Apr 2 at 16:54

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