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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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    $\begingroup$ 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. $\endgroup$ – Alan Boyd Apr 1 '14 at 17:40
  • $\begingroup$ 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 $\endgroup$ – F.N Apr 2 '14 at 16:45
  • $\begingroup$ (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. $\endgroup$ – F.N Apr 2 '14 at 16:54
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    $\begingroup$ As far as I know, the ethanol is just a wash in which DNA is insoluble to remove contaminants $\endgroup$ – Luigi Jan 6 '15 at 18:54
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Guanidine HCL is a chaotropic salt. Chaotropic salts are critical for cell lysis and binding to the silica resin. Specifically, Chaotropes have two important roles in nucleic acid extraction

  1. Destabilize hydrogen bonds, van der Waals forces and hydrophobic interactions.

    • Leading to destabilization of proteins (including nucleases).

      Macromolecular structure and function is dependent on the net effect of these forces (see protein folding), therefore it follows that an increase in chaotropic solutes in a biological system will denature macromolecules, reduce enzymatic activity and induce stress on a cell (i.e., a cell will have to synthesize stress protectants). Tertiary protein folding is dependent on hydrophobic forces from amino acids throughout the sequence of the protein. Chaotropic solutes decrease the net hydrophobic effect of hydrophobic regions because of a disordering of water molecules adjacent to the protein. This solubilises the hydrophobic region in the solution, thereby denaturing the protein. This is also directly applicable to the hydrophobic region in lipid bilayers; if a critical concentration of a chaotropic solute is reached (in the hydrophobic region of the bilayer) then membrane integrity will be compromised, and the cell will lyse. [Source]

  2. Disrupt the association of nucleic acids with water.

    • Thereby providing optimal conditions for their transfer to silica.

      Salts can have chaotropic properties by shielding charges and preventing the stabilization of salt bridges. Hydrogen bonding is stronger in non-polar media, so salts, which increase the chemical polarity of the solvent, can also destabilize hydrogen bonding. Mechanistically this is because there are insufficient water molecules to effectively solvate the ions. This can result in ion-dipole interactions between the salts and hydrogen bonding species which are more favorable than normal hydrogen bonds. [Source]

Ethanol, like Guanidine HCL, is a chaotopic agent. Ethanol is added for 2 reasons:

  1. Enhance and influence the binding of nucleic acids to the silica.

    • Interfere with non-covalent intramolecular forces as outlined above.

    • Reduce association of nucleic acids with water. From Melzak et al. (1996):

      Decreaing the water activity in solution through addition of either a chaotropic salt or an alcohol changes the helical structureof B-DNA either continuously to C-DNA or through a sharp cooperative transition to A-DNA (28). Either transition is accompanied by a decrease in solvent-accessible surface area.

  2. The correct concentration allows for washing of the salts from the membrane. [Source].


Citations

  • Melzak et al. (1996) Driving forces for DNA adsorption to silica in perchlorate solutions. J. Colloid Interface Sci. 181: 635 - 644.
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