Polyvalent Metal Ion Promoted Adsorption of DNA Oligonucleotides by Montmorillonite

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.

Neglected contributors to the transmission of bacterial antibiotic resistance in drinking water: Extracellular antibiotic resistance genes and the natural transformation

Antibiotic resistance genes (ARGs) have increasingly gained recognition as an "emerging contaminant" that poses a threat to the biosafety of drinking water. However, previous researches have primarily focused on the intracellular state of ARGs and rarely investigated the ecological characteristics (e.g., distribution and origin), environmental behavior (spread), and risks of extracellular form (eARGs) within drinking water systems. Therefore, this review evaluated isolation strategies and extraction methods for recovering eARGs from drinking water, elucidated the distribution characteristics of eARGs, and examined their impact on the antibiotic resistome from source water to tap water. We emphasized that chlorination and biological treatments significantly contribute to the prevalence and persistence of eARGs in drinking water. Moreover, we highlighted the role of biological reactors (e.g., biofilter, biological activated carbon) and drinking water distribution systems in facilitating the natural transformation of eARGs while significantly contributing to bacterial antibiotic resistance (BAR) propagation. Finally, we summarized the current risk assessment systems for ARGs and critically address remaining challenging questions necessary for better forecasting health risks associated with eARGs in drinking water environments. Collectively, this review enhances the understanding of ecological characteristics and environmental behavior of eARGs in drinking water while providing important implications for controlling and reducing BAR contamination not only in drinking water but also in other aquatic environments.

A comprehensive adsorption and desorption study on the interaction of DNA oligonucleotides with TiO2 nanolayers

The utilization of TiO2 nanolayers that possess excellent biocompatibility and physical properties in DNA sensing and sequencing remains largely to be explored. To examine their applicability in gene sequencing, a comprehensive study on the interaction of DNA oligonucleotides with TiO2 nanolayers was performed through adsorption and desorption experiments. TiO2 nanolayers with 10 nm thickness were fabricated via magnetron sputtering onto a 6-inch silicon wafer. A simple chip block method, validated via quartz crystal microbalance experiments with dissipation monitoring (QCM-D), was proposed to study the adsorption behaviors and interaction mechanisms under a variety of critical influencing factors, including DNA concentration, length, and type, adsorption time, pH, and metal ions. It is determined that the adsorption takes 2 h to reach saturation in the MES solution and the adsorption capacity is significantly enhanced by lowering the pH due to the isoelectric point being pH = 6 for TiO2. The adsorption percentages of nucleobases are largely similar in the MES solution while following 5T = 5G > 5C > 5A in HEPES buffer for an adsorption duration of 2.5 h. Through pre-adsorption experiments, it is deduced that DNA oligonucleotides are horizontally adsorbed on the nanolayer. This further demonstrates that mono-, di-, and tri-valent metal ions promote the adsorption, whereas Zn2+ has strong adsorption by inducing DNA condensation. Based on the desorption experiments, it is revealed that electrostatic force dominates the adsorption over van der Waals force and hydrogen bonds. The phosphate group is the main functional group for adsorption, and the adsorption strength increases with the length of the oligonucleotide. This study provides comprehensive data on the adsorption of DNA oligonucleotides onto TiO2 nanolayers and clarifies the interaction mechanisms therein, which will be valuable for applications of TiO2 in DNA-related applications.

Adsorption of DNA and Aptamers to Sodium Urate Crystals and Inhibition of Crystal Growth

An elevated level of blood uric acid (UA) can cause the formation of kidney stones, gout, and other diseases. We recently isolated a few DNA aptamers that can selectively bind to UA. In this work, we investigated the adsorption of a UA aptamer and random sequence DNA onto sodium urate crystals. Both DNA strands adsorbed similarly to urate crystals. In addition, both the UA aptamer and random DNA can inhibit the growth of urate crystals, suggesting a nonspecific adsorption mechanism rather than specific aptamer binding. In the presence of 500 nM DNA, the growth of needle-like sodium urate crystals was inhibited, and the crystals appeared granular after 6 h. To understand the mechanism of DNA adsorption, a few chemicals were added to desorb DNA. DNA bases contributed more to the adsorption than the phosphate backbone. Surfactants induced significant DNA desorption. Finally, DNA could also be adsorbed onto real UA kidney stones. This study provides essential insights into the interactions between DNA oligonucleotides and urate crystals, including the inhibition of growth and interface effects of DNA on sodium urate crystals.

Revealing the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation

It has been recently demonstrated that free DNA tracers have the potential in tracing water flow and contaminant transport through the vadose zone. However, whether the free DNA tracer can be used in flood irrigation area to track water flow and solute/contaminant transport is still unclear. To reveal the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation, we tested the fate and transport behavior of surface applied free DNA tracers through packed saturated sandy soil columns with a 10 cm water head mimicking flood irrigation. From the experimental breakthrough curves and by fitting a two-site kinetic sorption model (R2 = 0.83-0.91 and NSE = 0.79-0.89), adsorption/desorption rates could be obtained and tracer retention profiles could be simulated. Together these results revealed that 1) the adsorption of free DNA was dominantly to clay particles in the soil, which took up 1.96 % by volume, but took up >97.5 % by surface area and densely cover the surface of sand particles; and 2) at a pore water pH of 8.0, excluding the 4.9 % passing through and 3.1 % degradation amount, the main retention mechanisms in the experimental soil were ligand exchange (42.0 %), Van der Waals interactions (mainly hydrogen bonds), electrostatic forces and straining (together 44.7 %), and cation bridge (5.3 %). To our knowledge, this study is the first to quantify the contribution of each of the main retention mechanisms of free synthetic DNA tracers passing through soil. Our findings could facilitate the application of free DNA tracer to trace vadose zone water flow and solute/contaminant transport under flood irrigation and other infiltration conditions.

Graphene Oxide-Assisted Aptamer-Based Fluorescent Detection of Tetracycline Antibiotics

Tetracyclines are a group of common antibiotics, but owing to their toxicity, most of them are only used in animal husbandry and veterinary medicine. A DNA aptamer for tetracyclines has recently been reported. Upon aptamer binding, the fluorescence of tetracyclines was enhanced. This unique fluorescence enhancement was used to selectively detect the tetracyclines. The purpose of this study was to use graphene oxide (GO) to suppress the background fluorescence for enhanced detection. First, the adsorption of doxycycline on GO was studied. At pH 8.0, 82.7% of doxycycline was adsorbed by GO, and adding 2 µM aptamer desorbed 55.4% of doxycycline. With GO, the signal increase was comparable from pH 6 to 8, whereas without GO, the increase was significantly lower at pH 8. Under optimized condition, a detection limit of 1.6 nM doxycycline was achieved at pH 8.0 in the presence of GO, whereas without GO, the detection limit was 18.9 nM. This is an interesting example of the use of nanomaterials to enhance the performance of aptamer-based biosensors.

Preparation of Montmorillonite Nanosheets with a High Aspect Ratio through Heating/Rehydrating and Gas-Pushing Exfoliation

Montmorillonite (MMT) is an abundant silicate mineral with ultrahigh stability. The exfoliation of stacked MMT into high-aspect-ratio nanosheets is of crucial importance for various applications such as toxic gas suppression, barrier property enhancement, flame retardancy, and ion conduction. In this work, we develop a new heating/rehydrating and gas-pushing method that can successfully exfoliate MMT into nanosheets with aspect ratios (600-5000) far higher than the currently reported values (1-120). The MMT first goes through a "starvation pretreatment" under different heating temperatures to improve its hydrophilicity and is then rehydrated in a hydrogen peroxide solution. The hydrogen peroxide in the MMT interlayer space can decompose into water and oxygen bubbles, thus finally leading to the exfoliation via gas-pushing while preserving the large lateral size (mainly in the range of 1-6 μm) of the nanosheets. By changing the pretreatment temperature and pH value of the hydrogen peroxide solution, the exfoliation performance can be tuned. This simple and low-cost exfoliation method is promising to achieve the mass production of MMT nanosheets with a high aspect ratio and may promote its application in various fields such as energy conversion, drug delivery, and photocatalysis.

Clays as Vehicles for Drug Photostability

Clay minerals are often used due to their high adsorption capacity, which has sparked interest in their biological applications to stabilize drugs and pharmaceutical products. This research aims to summarize information about the stability of drugs, cosmetics, dermocosmetics, and pharmaceutical compounds incorporated in the structure of different clay minerals. The databases used to search the articles were Web of Science, Scopus, PubMed, and Science Direct. Photostabilization of these compounds is reviewed and its importance demonstrated. For biological applications, the increase in solubility and bioavailability of clay minerals has proven useful for them as drug carriers. While their natural abundance, low toxicity, and accessible cost have contributed to classical applications of clay minerals, a wide range of interesting new applications may be facilitated, mainly through incorporating different organic molecules. The search for new functional materials is promising to challenge research on clay minerals in biological or biotechnological approaches.

Adsorption of DNA Oligonucleotides by Self-Assembled Metalloporphyrin Nanomaterials

Porphyrin assemblies have controllable morphology, high biocompatibility, and good optical properties and were widely used in biomedical diagnosis and treatment. With the development of DNA biotechnology, combining DNA with porphyrin assemblies can broaden the biological applications of porphyrins. Porphyrin assemblies can serve as nanocarriers for DNA, although the fundamental interactions between them are not well understood. In this work, zinc meso-tetra(4-pyridyl)porphyrin (ZnTPyP) assemblies were prepared in the presence of various surfactants and at different pH values, yielding a variety of aggregation forms. Among them, the hexagonal stacking form exposes more pyridine substituents, and the hydrogen bonding force between the substituents and the DNA bases allows the DNA to be quickly adsorbed on the surface of the assemblies. The effects of DNA sequence and length were systematically tested. In particular, the adsorption of duplex DNA was less efficient compared to the adsorption of single-stranded DNA. This fundamental study is useful for the further combination of DNA and porphyrin assemblies to prepare new functional hybrid nanomaterials.

A sensor array based on DNA-wrapped bimetallic zeolitic imidazolate frameworks for detection of ATP hydrolysis products

Most current biosensors were designed for the detection of individual analytes, or a group of chemically similar analytes. We reason that sensors designed to track both reactants and products might be useful for following chemical reactions. Adenosine triphosphate (ATP) is a key biomolecule that participates in various biochemical reactions, and its hydrolysis plays a fundamental role in life. ATP can be converted to adenosine diphosphate (ADP) and inorganic phosphate (Pi) via the dephosphorylation process. ATP can also be hydrolyzed to adenosine monophosphate (AMP) and pyrophosphate (PPi) through depyrophosphorylation, depending on where the bond is cleaved. The detection of ATP-related hydrolysates would enable a better understanding of the different reaction pathways with a high level of robustness and confidence. Herein, we prepared a fluorescent sensor array based on a series of bimetallic zeolite imidazole frameworks M/ZIF-8 (M = Ni, Mn, Cu) and ZIF-67 to discriminate ATP hydrolysis and detect ATP hydrolysis related analytes. A fluorescently-labeled DNA oligonucleotide was used for signaling. Interestingly, Cu/ZIF-8 exhibited an ultrahigh selectivity for recognizing pyrophosphate with a detection limit of 2.5 μM. Moreover, the practicality of this sensor array was demonstrated in fetal bovine serum, clearly discriminating ATP hydrolysis products.

Metal-Doped Polydopamine Nanoparticles for Highly Robust and Efficient DNA Adsorption and Sensing

Controlling DNA adsorption on nanomaterials is crucial for a wide range of applications in analytical and biomedical sciences. Polydopamine (PDA) is a versatile material that can be coated on nearly any surface, and thus adsorbing DNA onto PDA can be a general method for indirect DNA functionalization of surfaces. Polyvalent metal ions were reported to promote DNA adsorption on PDA nanoparticles (NPs), but previous works added the metal ions after the formation of PDA. Herein, we compared the effect of polyvalent metal ions added during the synthesis of PDA NPs (called metal-doped) with the effect of polyvalent metal ions added after the synthesis (metal-adsorbed). A series of metal ions including Ca²⁺, Zn²⁺, Ni²⁺, Fe³⁺, and Gd³⁺ were tested, and Zn²⁺ was studied in detail due to its excellent ability for promoting DNA adsorption. With 100 μM Zn²⁺, metal-doped NPs were ∼30% more efficient than metal-adsorbed NPs for DNA adsorption in buffer attributable to a higher metal loading on the surface of the metal-doped NPs. Metal leaching was negligible from the metal-doped NPs, and they showed a remarkably higher robustness than the metal-adsorbed NPs, resulting in a 20-fold higher DNA extraction efficiency from serum. Based on the desorption studies, a higher adsorption affinity for the metal-doped NPs was confirmed. Finally, the Zn²⁺-doped PDA NPs were used for sensitive DNA detection with a limit of detection of 0.45 nM, and the sensor was highly resistant to nonspecific protein and phosphate displacement.