What happens to DNA in the presence of a chaotropic salt?

Answer 1

The term "chaotropic" means chaos-forming, a term which in biochemistry usually refers to a compound's ability to disrupt the regular hydrogen bond structures in water. Hydrogen bonding profoundly affects the secondary structure of polymers such as DNA, RNA, and proteins, as well as how water-soluble a molecule is. Under native conditions, nucleic acids are covered by a hydrate shell consisting of water molecules that maintain the solubility of DNA in aqueous solutions. With the addition of chaotropic ions to the nucleic acid, this relatively ordered structure of water molecules of the hydrate shell is destroyed. The chaotropic salts create a hydrophobic environment. Under these hydrophobic conditions, the silica membrane of the NucleoSpin columns is the most suitable binding partner for the nucleic acids. Proteins, metabolites, and other contaminants do not bind to the membrane and therefore are washed away during the subsequent washing steps. As a further feature of the chaotropic salts, the respective cations saturate the silica membrane with positive charges, which still improves the binding of nucleic acids under hydrophobic conditions. Chaotropic salts increase the solubility of nonpolar substances in water. They denature proteins because they have the ability to disrupt hydrophobic interactions. They do not denature DNA or RNA. Their function in the NucleoSpin Extraction Kit is to denature cellular proteins (such as DNase and RNase). The high concentration of salt also facilitates binding of the nucleic acids DNA and RNA to the silica membrane in the column.

Answer 2

Chaotropic salts disrupt the structure of DNA by weakening the hydrogen bonds that hold the double helix together. This can cause the DNA to denature or unfold.