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

The Influence of Ionic Environment on Nucleosome-Mica Interactions Revealed via Molecular Dynamics Simulations

Mica serves as a crucial substrate in Atomic Force Microscopy (AFM) studies for visualizing and characterizing nucleosomes. Nucleosomes interact with the negatively charged mica surface via adsorbed cations. However, the specific influences of monovalent and divalent cations on nucleosome adsorption to the mica surface remain unclear. In this study, we investigated the binding of nucleosomes to the mica surface in the presence of monovalent potassium ions and divalent magnesium ions using molecular dynamics simulations. We also explored the impact of pre-treated mica surfaces on nucleosome binding and structure. Our findings reveal that nucleosome-mica interactions vary depending on the cations present, resulting in distinct effects on nucleosome structure. Notably, nucleosomes bind effectively to a mica surface in the presence of potassium ions with minimal structural perturbations.

Magnetic composite microspheres with a controlled mesoporous shell for highly efficient DNA extraction and fragment screening

Rapid extraction and screening of high-purity DNA fragments is an indispensable technology in advanced molecular biology. In this article, mesoporous magnetic composite microspheres (MSP@mTiO2) with tunable pore sizes were successfully fabricated for high-purity DNA extraction and fragment screening. Owing to the strong complexation ability of Ti ions with DNA phosphate groups and the high specific surface area of mesoporous microspheres, the MSP@mTiO2 microspheres possess excellent adsorption performance, where the saturated loading capacity of MSP@mTiO2 with a specific surface area of 122 m2 g-1 is as high as 575 μg mg-1 for a salmon sperm specimen. ITC experiments demonstrated that DNA adsorption on MSP@mTiO2 microspheres is mainly driven by entropy, which gives us more potential ways to regulate the balance of adsorption and desorption. Meanwhile, the mesoporous MSP@mTiO2 microspheres exhibit a much higher extraction efficiency compared with non-porous MSP@TiO2 for whole genome DNA from Arabidopsis thaliana plants. Interestingly, DNA fragments with different lengths could be screened by simply regulating the pore size of MSP@mTiO2 or the concentration of Na3PO4 in the eluent. A small pore size and low phosphate concentration are advantageous for the extraction of short-stranded DNA fragments, and DNA fragments (≤1000 bp) can be efficiently extracted when the mesopore size of MSP@mTiO2 is lower than 7.6 nm. The extraction results from the mesoporous composite microspheres provide new promising insights into the purification and screening of DNA from complex biological samples.

Plasmid size determines adsorption to clay and breakthrough in a saturated sand column

Horizontal gene transfer (HGT) is a major factor in the spread of antibiotic resistant genes (ARG). Transformation, one mode of HGT, involves the acquisition and expression of extracellular DNA (eDNA). eDNA in soils is degraded rapidly by extracellular nucleases. However, if bound to a clay particle, eDNA can persist for long periods of time without losing its transformation ability. To better understand the mechanism of eDNA persistence in soil, this experiment assessed the effects of 1) clay mineralogy, 2) mixed salt solution, 3) plasmid size on DNA adsorption to clay and 4) breakthrough behavior of three differently sized plasmids in an environmentally relevant solution. Batch test methods were used to determine adsorption trends of three differently sized DNA plasmids, pUC19, pBR322, and pTYB21, to several pure clay minerals, goethite (α-FeOOH), illite, and kaolinite, and one environmental soil sample. Results show not all sorbents have equal adsorption capacity based on surface area with adsorption capacities decreasing from goethite > illite = kaolinite > bulk soil, and low ionic strength solutions will likely not significantly alter sorption trends. Additionally, plasmid DNA size (i.e., length) was shown to be a significant predictor of adsorption efficiency and that size affects DNA breakthrough, with breakthroughs occurring later with larger plasmids. Given that DNA persistence is linked to its adsorption to soil constituents and breakthrough, eDNA size is likely an important contributor to the spread of ARG within natural microbial communities.

Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type

Ion-mediated attraction between DNA and mica plays a crucial role in biotechnological applications and molecular imaging. Here, we combine molecular dynamics simulations and single-molecule atomic force microscopy experiments to characterize the detachment forces of single-stranded DNA at mica surfaces mediated by the metal cations Li+, Na+, K+, Cs+, Mg2+, and Ca2+. Ion-specific adsorption at the mica/water interface compensates (Li+ and Na+) or overcompensates (K+, Cs+, Mg2+, and Ca2+) the bare negative surface charge of mica. In addition, direct and water-mediated contacts are formed between the ions, the phosphate oxygens of DNA, and mica. The different contact types give rise to low- and high-force pathways and a broad distribution of detachment forces. Weakly hydrated ions, such as Cs+ and water-mediated contacts, lead to low detachment forces and high mobility of the DNA on the surface. Direct ion-DNA or ion-surface contacts lead to significantly higher forces. The comprehensive view gained from our combined approach allows us to highlight the most promising cations for imaging in physiological conditions: K+, which overcompensates the negative mica charge and induces long-ranged attractions. Mg2+ and Ca2+, which form a few specific and long-lived contacts to bind DNA with high affinity.

Adsorption effects and mechanisms of phosphorus by nanosized laponite

Phosphorus (P), an important macroelement for crops, may be lost into water systems by human activities and subsequently cause serious environmental problems such as eutrophication. Thus, the recovery of P from wastewater is essential. P can be adsorbed and recovered from wastewater using many natural, environmentally friendly clay minerals, however the adsorption ability is limited. Here we applied a synthesis nanosized clay mineral, laponite, to evaluate the P adsorption ability and molecular mechanisms of the adsorption process. We apply X-ray Photoelectron Spectroscopy (XPS) to observe the adsorption of inorganic phosphate onto laponite, and then measure the adsorption content of phosphate by laponite via batch experiments in different solution conditions, including pH, ionic species and concentrations. Then the molecular mechanisms of adsorption are analyzed by Transmission Electron Microscopy (TEM) and molecular modeling using Density Functional Theory (DFT). The results show that phosphate adsorbs to the surface and interlayer of laponite via hydrogen bonding, and the adsorption energies of the interlayer are greater than those of the surface. These bulk solution and molecular-scale results in a model system may provide new insights into the recovery of phosphorus by nanosized clay, with possible environmental engineering applications for P-pollution control and sustainable utilization of P sources.

A Tale of Two Foulants: The Coupling of Organic Fouling and Mineral Scaling in Membrane Desalination

Membrane desalination that enables the harvesting of purified water from unconventional sources such as seawater, brackish groundwater, and wastewater has become indispensable to ensure sustainable freshwater supply in the context of a changing climate. However, the efficiency of membrane desalination is greatly constrained by organic fouling and mineral scaling. Although extensive studies have focused on understanding membrane fouling or scaling separately, organic foulants commonly coexist with inorganic scalants in the feedwaters of membrane desalination. Compared to individual fouling or scaling, combined fouling and scaling often exhibits different behaviors and is governed by foulant-scalant interactions, resembling more complex but practical scenarios than using feedwaters containing only organic foulants or inorganic scalants. In this critical review, we first summarize the performance of membrane desalination under combined fouling and scaling, involving mineral scales formed via both crystallization and polymerization. We then provide the state-of-the-art knowledge and characterization techniques pertaining to the molecular interactions between organic foulants and inorganic scalants, which alter the kinetics and thermodynamics of mineral nucleation as well as the deposition of mineral scales onto membrane surfaces. We further review the current efforts of mitigating combined fouling and scaling via membrane materials development and pretreatment. Finally, we provide prospects for future research needs that guide the design of more effective control strategies for combined fouling and scaling to improve the efficiency and resilience of membrane desalination for the treatment of feedwaters with complex compositions.

Visualization the fixation of cadmium on manganese dioxide in sulfur reduction environments

Manganese oxides as common soil components were considered as an important sink for the cadmium pollution, which, however, would be affected by the reductive sulfide introduced during the flooding period of paddy soil. In this study, the phase transitions caused by the reactions among S^2-, MnO₂ and Cd²⁺ were visualized by atomic force microscopy (AFM). The dissolution of MnO₂ was in-situ studied by AFM in the S^2-containing environments. Moreover, in the ternary system (S^2-, MnO₂ and Cd²⁺), the pre-adsorption of Cd²⁺ by the MnO₂ nanosheets would promote the subsequent precipitation of CdS on the surface of MnO₂, while the pre-formed CdS nanoparticles in the aquatic phase would tend to suspense rather than precipitating on MnO₂. The kinetic study results indicated that the CdS crystallite generation rate was faster than the MnO₂ dissolution rate in the aquatic environments with different sulfide contents. In the macroscopic Cd²⁺ fixation test, the introduction of S^2- dramatically improved the fixation of the pre-adsorbed Cd²⁺ on the MnO₂ nanosheets by forming the CdS precipitate. This study provided a fundamental understanding of the interactions among the S^2-, MnO₂ and Cd²⁺ ternary system and shed light on the development of Cd pollution remediation methods for paddy soils.

Role of Cel5H protein surface amino acids in binding with clay minerals and measurements of its forces

Our previous study on the binding activity between Cel5H and clay minerals showed highest binding efficiency among other cellulase enzymes cloned. Here, based on previous studies, we hypothesized that the positive amino acids on the surface of Cel5H protein may play an important role in binding to clay surfaces. To examine this, protein sequences of Bacillus licheniformis Cel5H (BlCel5H) and Paenibacillus polymyxa Cel5A (PpCel5A) were analyzed and then selected amino acids were mutated. These mutated proteins were investigated for binding activity and force measurement via atomic force microscopy (AFM). A total of seven amino acids which are only present in BlCel5H but not in PpCel5A were selected for mutational studies and the positive residues which are present in both were omitted. Of the seven selected surface lysine residues, only three mutants K196A(M2), K54A(M3) and K157T(M4) showed 12%, 7% and 8% less clay mineral binding ability, respectively compared with wild-type. The probable reason why other mutants did not show altered binding efficiency might be due to relative location of amino acids on the protein surface. Meanwhile, measurement of adhesion forces on mica sheets showed a well-defined maximum at 69 ± 19 pN for wild-type, 58 ± 19 pN for M2, 53 ± 19 pN for M3, and 49 ± 19 pN for M4 proteins. Hence, our results demonstrated that relative location of surface amino acids of Cel5H protein especially positive charged amino acids are important in the process of clay mineral-protein binding interaction through electrostatic exchange of charges.

DNA Binding to the Silica: Cooperative Adsorption in Action

The adsorption and desorption of nucleic acid to a solid surface is ubiquitous in various research areas like pharmaceutics, nanotechnology, molecular biology, and molecular electronics. In spite of this widespread importance, it is still not well understood how the negatively charged deoxyribonucleic acid (DNA) binds to the negatively charged silica surface in an aqueous solution. In this article, we study the adsorption of DNA to the silica surface using both modeling and experiments and shed light on the complicated binding (DNA to silica) process. The binding agent mediated DNA adsorption was elegantly captured by cooperative Langmuir model. Bulk-depletion experiments were performed to conclude the necessity of a positively charged binding agent for efficient DNA binding, which complements the findings from the model. A profound understanding of DNA binding will help to tune various processes for efficient nucleic acid extraction and purification. However, this work goes beyond the DNA binding and can shed light on other binding agent mediated surface-surface, surface-molecule, molecule-molecule interaction.

Sorption Mechanisms of Chemicals in Soils

Sorption of chemicals onto soil particle surfaces is an important process controlling their availability for uptake by organisms and loss from soils to ground and surface waters. The mechanisms of chemical sorption are inner- and outer-sphere adsorption and precipitation onto mineral surfaces. Factors that determine the sorption behavior are properties of soil mineral and organic matter surfaces and properties of the sorbing chemicals (including valence, electron configuration, and hydrophobicity). Because soils are complex heterogeneous mixtures, measuring sorption mechanisms is challenging; however, advancements analytical methods have made direct determination of sorption mechanisms possible. In this review, historical and modern research that supports the mechanistic understanding of sorption mechanisms in soils is discussed. Sorption mechanisms covered include cation exchange, outer-sphere adsorption, inner-sphere adsorption, surface precipitation, and ternary adsorption complexes.

Dynamic force spectroscopy for quantifying single-molecule organo–mineral interactions

Organo–mineral interactions have long been the focus in the fields of biomineralization and geomineralization, since such interactions not only modulate the dynamics of crystal nucleation and growth but may also change crystal phases, morphologies, and structures.

Molecular dynamics simulation of the adsorption of per- and polyfluoroalkyl substances (PFASs) on smectite clay

Molecular dynamics (MD) simulations are used to predict the partitioning of per- and polyfluoroalkyl substances (PFASs) to smectite clay, a high surface area adsorbent ubiquitous in temperate soils. Simulated systems model a stack of flexible smectite lamellae in contact with a bulk aqueous reservoir containing PFAS molecules. Perfluorobutanesulfonic acid (PFBS), perfluorohexanesulfonic acid (PFHxS), and perfluorooctanesulfonic acid (PFOS) are simulated at various aqueous chemistry conditions to examine the effect of PFAS size, salinity, and coordinating cation type (K⁺, Na⁺, and Ca²⁺) on adsorption. The metadynamics technique is employed to facilitate the exploration of the simulation cell and to reconstruct the underlying free energy landscape. Adsorption is favorable on the hydrophobic domains of the external basal surfaces with the fluorinated chain adopting a flat orientation on the surface. Analysis of the adsorption energetics reveals large favorable entropic contributions to adsorption. The enthalpy of adsorption is unfavorable, though much less so in the presence of Ca²⁺ due to stabilizing 'lateral cation bridging' interactions between divalent cations and PFAS sulfonate head groups. Overall, this research advances the mechanistic understanding of PFAS-smectite interactions and provides new insights that could help inform fate and transport models and the development of adsorbents and remediation techniques.

Struvite crystallization induced the discrepant transports of antibiotics and antibiotic resistance genes in phosphorus recovery from swine wastewater

Struvite (MgNH₄PO₃·6H₂O) crystallization is one of important methods of phosphorus recovery from wastewater. As to livestock wastewater, the high-strength occurrence of antibiotics and antibiotic resistance genes might induce struvite recovery to spread antibiotic resistance to the environment. However, limited information has been reported on the simultaneous transport of antibiotics and ARGs in struvite recovery. In the present study, tetracyclines (TCs) and tetracyclines antibiotic resistance genes (ARGs) were selected as the targeted pollutants, and their discrepant residues in struvite recovery from swine wastewater were investigated. TCs and ARGs were obviously detected, with their contents of 4.88-79.5 mg/kg and 6.99 × 10⁷-2.14 × 10¹¹ copies/g, notably higher than those of TCs 0.550-1.94 mg/kg and ARGs 3.98 × 10⁴-5.66 × 10⁷ copies/g obtained from synthetic wastewater. The correlational relationship revealed that predominant factors affecting TCs and ARGs transports were different. Results from network analyses indicated that among the total edges, the negative correlations between TCs and ARGs predominately occupied 18.0%. The redundancy analysis revealed that mineral components in the recovered products, including struvite, K-struvite and amorphous calcium phosphate, coupling with organic contents, displayed insignificant roles on TCs residues, where heavy metals exerted positive and remarkable functions to boost TCs migration. Unexpectedly, mineral components and heavy metals did not displayed significant promotion on ARGs transport as a whole.

Molecular insight into the interfacial chemical functionalities regulating heterogeneous calcium-arsenate nucleation

Heterogeneous nucleation induced by natural organic matter (NOM) can lower the energy barrier for calcium arsenate (Ca-As) precipitation, which aids in immobilizing arsenate (As^Ⅴ). However, it remains unclear how certain chemical functionalities of NOM affect Ca-As nucleation at the molecular scale. By analyzing changes in the local supersaturation and/or interfacial energy, the present work investigates the Ca-As heterogeneous nucleation kinetics and mechanisms on functional-group-modified model surfaces. Mica surfaces modified by functional groups of amine (NH₂), hydroxyl (OH), or carboxyl (COOH) through self-assembled monolayers were used to investigate how chemical functionalities affect the Ca-As heterogeneous nucleation, in which the distributions of formation kinetics and size (as measured by the change in particle height) of nucleated Ca-As particles were measured by using in situ atomic force microscopy. In a parallel analysis, a quartz-crystal microbalance with dissipation was used to detect the buildup of Ca²⁺ and/or HAsO₄^2- ions at the solid-fluid interface. PeakForce quantitative nanomechanical mapping and dynamic force spectroscopy using functional-group-modified tips made it possible to calculate the binding energies holding functional groups to Ca-As particles. Nucleated Ca-As particles were characterized by using Raman spectroscopy and high-resolution transmission electron microscopy. The results indicate that the height of amorphous Ca-As particles formed on a modified mica surface may be ranked in descending order as NH₂ > OH > bare mica > COOH, as determined by the buildup of Ca²⁺ and HAsO₄^2- ions at the solid-fluid interface and the decrease of interfacial energy due to the functional groups. These nanoscale observations and molecular-scale determinations improve our understanding of the roles played by chemical functionalities on NOM in immobilizing dissolved As through heterogeneous nucleation in soil and water.

Dissolution and Precipitation Dynamics at Environmental Mineral Interfaces Imaged by In Situ Atomic Force Microscopy

Chemical reactions at the mineral-solution interface control important interfacial processes, such as geochemical element cycling, nutrient recovery from eutrophicated waters, sequestration of toxic contaminants, and geological carbon storage by mineral carbonation. By time-resolved in situ imaging of nanoscale mineral interfacial reactions, it is possible to clarify the mechanisms governing mineral-fluid reactions.In this Account, we present a concise summary of this topic that addresses a current challenge at the frontier of understanding mineral interfaces and their importance to a wide range of mineral re-equilibration processes in the presence of a fluid aqueous phase. We have used real-time nanoscale imaging of liquid-cell atomic force microscopy (AFM) to observe the in situ coupling of the dissolution-precipitation process, whereby the dissolution of a parent mineral phase is coupled at mineral interfaces with the precipitation of another product phase, chemically different from the parent. These nanoscale observations allow for the identification of dissolution and growth rates through systematically investigating various minerals, including calcite (CaCO₃), siderite (FeCO₃), cerussite (PbCO₃), magnesite (MgCO₃), dolomite (CaMg(CO₃)₂), brushite (CaHPO₄·2H₂O), brucite (Mg(OH)₂), portlandite (Ca(OH)₂), and goethite (α-FeOOH), in various reacting aqueous fluids containing solution species, such as arsenic, phosphate, organo- or pyrophosphate, CO₂, selenium, lead, cadmium, iron, chromium, and antimony. We detected the in situ replacement of these parent mineral phases by product phases, identified through a variety of analytical methods such as Raman spectroscopy, high-resolution transmission electron microscopy, and various X-ray techniques, as well as modeling by geochemical simulation using PHREEQC. As a consequence of the coupled processes, sequestration of toxic elements and hazardous species and inorganic and organic carbon, and limiting or promoting recovery of nutrients can be achieved at nano- and macroscopic scales.We also used in situ AFM to quantitatively measure the retreat rates of molecular steps and directly observe the morphology changes of dissolution etch pits on calcium phosphates in organic acid solutions present in most rhizosphere environments. By molecular modeling using density functional theory (DFT), we explain the origin of dissolution etch pit evolution through specific stereochemistry and molecular recognition and provide an energetic basis by calculating the binding energies of chemical functionalities on organic acids to direction-specific steps on mineral surfaces. In addition, we further quantified precipitation kinetics of calcium phosphates (Ca-P's) on typical mineral surfaces at the nanoscale in environmentally relevant solutions with various organic molecules, by measurements obtained from sequential images obtained by liquid-cell AFM. In situ dynamic force spectroscopy (DFS) was used to determine binding energies of single-molecules with different chemical functionalities found in natural organic matter at mineral-fluid interfaces. Quantifying molecular organo-mineral bonding or binding energies mechanistically explains phosphate precipitation and transformation. From DFS measurements, molecular-scale interactions of mineral-natural organic matter (DNA, proteins, and polysaccharides) associations were determined. With this powerful tool, single-molecule determinations of polysaccharide-amorphous iron oxide or hematite interactions provided the mechanistic origin of the phase- or facet-dependent adsorption. These systematic investigations and findings significantly contribute to a more quantitative prediction of the fate of nutrients and contaminants, chemical element cycling, and potential geological carbon capture and nuclear waste storage in aqueous environments.