The principle of this method is based on the nucleic acid-binding properties of silica particles or diatoms in the presence of a chaotropic agent, which follows the chaotropic effect.
Put simply, the chaotropic effect is where a chaotropic anion in an aqueous solution disturbs the structure of water, and weakens the hydrophobic interaction.
According to the chaotropic effect,
in the presence of the chaotropic agent, hydration water of nucleic acids are taken from the phosphodiester bond of the phosphate group of the backbone of a nucleic acid. Thus, the phosphate group becomes "exposed" and hydrophobic interaction between silica and exposed phosphate group are formed.