Adsorption, Structure, and Dynamics of DNA in Montmorillonite and Montmorillonite–Humic Acid: A Molecular-Level Insight

Extracellular DNA (eDNA) has become a focus in public health, with soil recognized as a key reservoir where eDNA's mobility and stability are primarily controlled by clay minerals and organic matter. Montmorillonite (MMT) often interacts with humic acids (HA), forming MMT-HA complexes, although the molecular mechanisms behind DNA adsorption in these complexes remain unclear. Here, molecular dynamics simulations were used to examine the adsorption, diffusion, interfacial structure, and dynamics of DNA on MMT and MMT-HA complexes, revealing critical molecular interactions. Interaction energy analysis showed that DNA adsorption is energetically more favorable on MMT than on MMT-HA, as HA reduces DNA's adsorption capacity on MMT. Diffusion coefficients indicated that DNA has lower mobility on MMT than on MMT-HA. Ca2+ cations and water molecules bridge MMT surfaces and DNA phosphate groups, enhancing DNA adsorption on MMT, while HA occupies MMT binding sites and forms limited hydrogen bonds with DNA, thereby inhibiting adsorption. These results provide insights into the adsorption, migration, and stability of eDNA on soil clay minerals.