Adsorption-desorption
The backbone of DNA contains negatively charged phosphodiester groups which play a key role in DNA adsorption to mineral and organic particle surfaces. At circumneutral pH, DNA is electrostatically attracted to positively charged mineral surfaces, such as those of iron (oxyhydr-)oxides and aluminium (hydr-)oxides, resulting in strong adsorption. Conversely, DNA is electrostatically repelled from negatively charged surfaces, including silicon dioxide or the basal planes of some clay minerals. Therefore, the importance of adsorbed DNA in a water sample likely increases with increasing suspended amounts of positively charged minerals. Electrostatic DNA-sorbent interactions can be modulated by solution pH for sorbents that carry a variable charge: increasing pH decreases the positive charges (and increases the negative charges), thereby weakening electrostatic attraction. Thus, increasing solution pH is expected to lower DNA adsorption and can facilitate DNA desorption from variably charged surfaces.
DNA-sorbent electrostatic interactions are also modulated by solution ionic strength and composition. Increases in solution ionic strength attenuate both DNA electrostatic attraction to and repulsion from positively and negatively charged surfaces, respectively. At very high ionic strength, electrostatic repulsion from negatively charged surfaces may be attenuated to an extent that close-contact DNA-surface attractive interactions (see below) result in DNA adsorption. The presence of divalent cations in solution may lead to increased adsorption to negatively charged sorbents via ‘cation bridging’ between the like-charged DNA and the sorbent34–37. Therefore, information on the solution ionic strength and concentrations of Ca2+ and Mg2+ is important to assess the extent of DNA adsorption. Besides electrostatic interactions, DNA-surface van der Waals interactions and H-bonding may drive adsorption. However, these energetic contributions are expected to be small in comparison to electrostatic interactions.
All of the aforementioned interactions result in ‘physisorption’ - the interaction of DNA with the sorbent surface without forming covalent bonds. However, DNA may additionally bind to some surfaces through ‘chemisorption’, which involves the formation of covalent bonds between the phosphodiester group of the DNA and hydroxyl groups on the mineral surfaces. The resulting ‘inner sphere’ complexes are very stable and may result in both DNA adsorption to mineral surfaces even at high pH (despite net negative surface charges on the minerals) as well as prevent DNA desorption from mineral surfaces even if changes in solution conditions result in DNA-sorbent electrostatic repulsion. DNA may thus be irreversibly adsorbed, which is clearly relevant for eDNA decay and detection.
Finally, co-solutes may compete with DNA for adsorption sites on particle surfaces and thereby suppress DNA adsorption. For instance, both dissolved organic matter (DOM) and phosphate are expected to adsorb to some mineral surfaces and may thus increase the fraction of eDNA present in the dissolved state24.