Size-controlled mesoporous magnetic silica beads effectively extract extracellular DNA in the absence of chaotropic solutions

Detection of extracellular antibiotic resistance genes in river water: Application of ultrafiltration-magnetic beads method

Antibiotic resistance genes (ARGs) are widespread contaminants that pose significant threats to public health. Rivers play a crucial role in the dissemination of ARGs within the aquatic environment. However, there are limitations in the current research on the differentiation of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) in river water. In this study, we developed a method combining ultrafiltration and adsorption of silica-hydroxy magnetic beads for efficient extraction of extracellular DNA (eDNA) from river water. The conditions of adsorption, washing, desorption, and pretreatment were optimized to enhance eDNA recovery. By using only 90 mL of water sample, our method could collect sufficient eDNA for subsequent detection of eARGs through qPCR analysis. The eDNA recovery rate ranged from 51.4% to 69.8%. The occurrence of five prevalent ARGs (tetC, sulI, blaTEM, ermB, qnrS) as well as integrase gene intl1 were investigated in both iDNA and eDNA extracted from river water samples collected from two tributaries of the Pearl River. Our results revealed that the absolute abundance levels of eARGs ranged from 10-1 to 105 copies/mL, which were significantly higher than those observed for iARGs ranging from 10-1 to 104 copies/mL. Moreover, there was a significant difference in contamination profiles for ARGs between two tributaries. The ultrafiltration-magnetic beads method overcomes challenges associated with low efficiency extraction when working with water samples containing low nucleic acid concentrations. This approach provides an improved technique for extracting eARGs from river water while also generating valuable data supporting assessments related to eARG contamination in such environments.

High-efficient separation of deoxyribonucleic acid from pathogenic bacteria by hedgehog-inspired magnetic nanoparticles microextraction

Efficient separation of deoxyribonucleic acid (DNA) through magnetic nanoparticles (MN) is a widely used biotechnology. Hedgehog-inspired MNs (HMN) possess a high-surface-area due to the distinct burr-like structure of hedgehog, but there is no report about the usage of HMN for DNA extraction. Herein, to improve the selection of MN and illustrate the performance of HMN for DNA separation, HMN and silica-coated Fe3O4 nanoparticles (Fe3O4@SiO2) were fabricated and compared for the high-efficient separation of pathogenic bacteria of DNA. Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) are typical Gram-negative and Gram-positive bacteria and are selected as model pathogenic bacteria. To enhance the extraction efficiency of two kinds of MNs, various parameters, including pretreatment, lysis, binding and elution conditions, have been optimized in detail. In most separation experiments, the DNA yield of HMN was higher than that of Fe3O4@SiO2. Therefore, a HMN-based magnetic solid-phase microextraction (MSPE) and quantitative real-time PCR (qPCR) were integrated and used to detect pathogenic bacteria in real samples. Interestingly, the HMN-based MSPE combined qPCR strategy exhibited high sensitivity with a limit of detection of 2.0 × 101 CFU mL-1 for E. coli and 4.0 × 101 CFU mL-1 for S. aureus in orange juice, and 2.8 × 102 CFU mL-1 for E. coli and 1.1 × 102 CFU mL-1 for S. aureus in milk, respectively. The performance of the proposed strategy was significantly better than that of commercial kit. This work could prove that the novel HMN could be applicable for the efficient separation of DNA from complex biological samples.

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.

Immobilization of Multivalent Titanium Cations on Magnetic Composite Microspheres for Highly Efficient DNA Extraction and Amplification

Magnetic-assisted DNA testing technology has attracted much attention in genetics, clinical diagnostics, environmental microbiology, and molecular biology. However, achieving satisfying DNA adsorption and desorption efficiency in real samples is still a big challenge. In this paper, a new kind of high-quality magnetic composite microsphere of MM@PGMA-PA-Ti4+ was designed and prepared for DNA extraction and detection based on the strong interaction of Ti4+ and phosphate groups. By taking the advantages of high magnetic susceptibility and high Ti4+ content, the MM@PGMA-PA-Ti4+ microspheres possessed remarkable extraction capacity for mimic biological samples (salmon sperm specimens) with saturated loadings up to 533.0 mg/g. When the DNA feeding amount was 100 μg and the MM@PGMA-PA-Ti4+ dosage was 1 mg, the adsorption and desorption efficiencies were 80 and 90%, respectively. The kinetic and equilibrium extraction data were found to fit well with the pseudo-second-order model and Freundlich isotherm model. Furthermore, the MM@PGMA-PA-Ti4+ microspheres were successfully employed for DNA extraction from mouse epithelial-like fibroblasts. The extraction ability (84 ± 4 μg/mg) and DNA purity were superior to the comparative commercial spin kits, as evaluated by electrophoresis assays and qPCR analysis. The experimental results suggest that the MM@PGMA-PA-Ti4+ microspheres possess great potential as an adsorbent for DNA purification from complex biological samples.

Adenine imprinted beads as a novel selective extracellular DNA extraction method reveals underestimated prevalence of extracellular antibiotic resistance genes in various environments

Despite severe threats of extracellular antibiotic resistance genes (eARGs) towards public health in various environments, advanced studies have been hindered mainly by ineffective extracellular DNA (exDNA) extraction methods, which is challenged by trace levels of exDNA and inference from abundant coexisting compounds. This study developed a highly selective exDNA extraction method based on molecular imprinting technology (MIT) by using adenine as the template for the first time. Results suggested that adenine imprinted beads were rough spheres at an average size of 0.39 ± 0.07 μm. They effectively adsorbed DNA in the absence of chaotropic agents, with superior capacity (796.2 mg/g), rate (0.0066/s) and regarding DNA of variable lengths, even the ultra-short DNA (<100 bp). They were also highly selective towards DNA, circumventing the interference of competitive compounds' interference. These properties contribute to efficient exDNA extraction (71 %-119 %) from various environmental samples. Specifically, adenine imprinted beads enabled significantly higher extraction rates of eARGs from river, air and vegetable samples (69 %-95 %) compared to that by commercial DNA extraction products (16 %-62 %). The adenine imprinted beads-based method reveals underestimated eARG levels in the environment and the corresponding risks, and thus will thus be a powerful tool for advanced exDNA research.

Comparative Evaluation of Different Surface Coatings of Fe3O4-Based Magnetic Nano Sorbent for Applications in the Nucleic Acids Extraction

Nucleic acid extraction and purification are crucial steps in sample preparation for multiple diagnostic procedures. Routine methodologies of DNA isolation require benchtop equipment (e.g., centrifuges) and labor-intensive steps. Magnetic nanoparticles (MNPs) as solid-phase sorbents could simplify this procedure. A wide range of surface coatings employs various molecular interactions between dsDNA and magnetic nano-sorbents. However, a reliable, comparative evaluation of their performance is complex. In this work, selected Fe3O4 modifications, i.e., polyethyleneimine, gold, silica, and graphene derivatives, were comprehensively evaluated for applications in dsDNA extraction. A family of single batch nanoparticles was compared in terms of morphology (STEM), composition (ICP-MS/MS and elemental analysis), surface coating (UV-Vis, TGA, FTIR), and MNP charge (ζ-potential). ICP-MS/MS was also used to unify MNPs concentration allowing a reliable assessment of individual coatings on DNA extraction. Moreover, studies on adsorption medium (monovalent vs. divalent ions) and extraction buffer composition were carried out. As a result, essential relationships between nanoparticle coatings and DNA adsorption efficiencies have been noticed. Fe3O4@PEI MNPs turned out to be the most efficient nano sorbents. The optimized composition of the extraction buffer (medium containing 0.1 mM EDTA) helped avoid problems with Fe3+ stripping, which improved the validity of the spectroscopic determination of DNA recovery.