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.

Sorption Mechanisms of Chemicals in Soils

“…The change in the height of the tip as it moves across the surface is related to the surface morphology. Zhai et al [77] studied DNA adsorption on mica mineral surfaces by attaching a DNA fragment to an AFM tip. They concluded that the DNA adsorbs on the surface as an outer-sphere complex.…”

Nano‐atomic scale hydrophobic/philic confinement of peptides on mineral surfaces by cross‐correlated SPM and quantum mechanical DFT analysis

“…Some phyllosilicates showed a remarkable capability of catalysis of biomolecules and condensation, organization of biopolymers and even cells (Heinz, 2012; Tavanaee et al ., 2017; Pietrement et al ., 2018). Within this kind of studies, scanning probe microscopy (SPM) methods provide unique information and a clear picture at the micro and nanoscale of the system under consideration showing features related to the adsorption process and conformation of the objects onto the surface (Moro et al ., 2015; Math et al ., 2019; Zhai et al ., 2019), even in the case of particular, complex‐to‐treat and tricky specimens, such as single biomolecule behaviour. However, when dealing with small objects (molecules or small biopolymers), and when imaging information at the subnanometre level is recorded, to strengthen the interpretation of the results, it is necessary to couple the imaging methods with atomic‐scale simulations, either of molecular dynamics or quantum‐mechanics type.…”

An experimental assessment of the distribution of environmental DNA along the water column

“…This can lead to accumulation in certain parts of the water column, or changing speed of diffusion (Cai et al 2006a;Cai et al 2006b). When bound particles are too dense, it can also promote deposition and accumulation of eDNA in the substrate (Zhai et al 2019). Size of suspended particles also influences this dynamic, as finer substrates tend to capture more eDNA due to smaller pores (Shogren et al 2016).…”