Molecular-Scale Investigations Reveal Noncovalent Bonding Underlying the Adsorption of Environmental DNA on Mica.

Abstract

Mineral-soil organic matter (SOM including DNA, proteins, and polysaccharides) associations formed through various interactions, play a key role in regulating long-term SOM preservation. The mechanisms underlying DNA-mineral and DNA-protein/polysaccharide interactions at nanometer and molecular scales in environmentally relevant solutions remain uncertain. Here, we present a model mineral-SOM system consisting of mineral (mica)-nucleic acid (environmental DNA, eDNA)/protein (bovine serum albumin)/polysaccharide (alginate), and combine atomic force microscopy (AFM)-based dynamic force spectroscopy and PeakForce quantitative nanomechanical mapping using DNA-decorated tips. Single-molecule binding and adhesion force of eDNA to mineral and to mineral adsorbed by protein/polysaccharide reveal the noncovalent bonds and that systematically changing ion compositions, ionic strength, and pH result in significant differences in organic-organic and organic-mineral binding energies. Consistent with the bond-strength measurements, protein, rather than polysaccharide, promotes mineral-bound DNA molecules by ex situ AFM deposition observations in relatively high concentrations of divalent cation-containing acidic solutions. These molecular-scale determinations and nanoscale observations should substantially improve our understanding of how environmental factors influence the organic-mineral interfacial interactions through the synergy of collective noncovalent and/or covalent bonds in mineral-organic associations.