N-methylimidazolium modified magnetic particles as adsorbents for solid phase extraction of genomic deoxyribonucleic acid from genetically modified soybeans

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.

Solvent-Responsive Magnetic Beads for Accurate Detection of SARS-CoV-2

Although numerous approaches were proposed for the nucleic acid (NA)-based SARS-CoV-2 detection, the nonideal NA desorption efficiency of conventional magnetic beads (MBs) limits their widespread application. In this study, we developed solvent-responsive MBs (called responsive MBs), which, in the presence of buffers, modulated the absorption and desorption capacities of NA by flipping the surface -COO-. Relative to other commercial MBs, responsive MBs exhibited similar absorption profiles and markedly enhanced desorption profiles. When applied for NA detection of complex samples, responsive MBs exhibited better performance of RNA detection than DNA, with obvious advantages in sensitivity. Specifically, the RNA and DNA desorption rates of commercial MBs were ∼85 and 82.5%, while those of responsive MBs were nearly 94 and 93.5%, respectively. Furthermore, responsive MBs exhibited remarkable extraction ability in a wide range of tissues and better performance of RNA extraction than DNA. When applied for SARS-CoV-2 detection, the responsive MBs along with the simulated digital RT-LAMP (a previously established apparatus) further improved detection efficiency, yielding a precise quantitative detection as low as 25 copies and an ultimate sensibility detection of 5 copies/mL. It was also successfully employed in numerous NA-based technologies such as polymerase chain reaction (PCR), sequencing, and so on.

Multi spectroscopic and molecular simulation studies of propyl acridone binding to calf thymus DNA in the presence of electromagnetic force

Introduction: Here, the interaction behavior between propyl acridones (PA) and calf thymus DNA (ct-DNA) has been investigated to attain the features of the binding behavior of PA with ct-DNA, which includes specific binding sites, modes, and constants. Furthermore, the effects of PA on the conformation of ct-DNA seem to be quite significant for comprehending the medicine's mechanism of action and pharmacokinetics. Methods: The project was accomplished through means of absorbance studies, fluorescence spectroscopy, circular dichroism, viscosity measurement, thermal melting, and molecular modeling techniques. Results: The intercalation of PA has been suggested by fluorescence quenching and viscosity measurements results while the thermal melting and circular dichroism studies have confirmed the thermal stabilization and conformational changes that seem to be associated with the binding. The binding constants of ct-DNA-PA complex, in the absence and presence of EMF, have been evaluated to be 6.19 × 10⁴ M^-1 and 2.95 × 10⁴ M^-1 at 298 K, respectively. In the absence of EMF, the ∆H⁰ and ∆S⁰ values that occur in the interaction process of PA with ct-DNA have been measured to be -11.81 kJ.mol^-1 and 51.01 J.mol^-1K^-1, while in the presence of EMF they were observed to be -23.34 kJ.mol^-1 and 7.49 J.mol^-1K^-1, respectively. These numbers indicate the involvement of multiple non-covalent interactions in the binding procedure. In a parallel study, DNA-PA interactions have been monitored by molecular dynamics simulations; their results have demonstrated DNA stability with increasing concentrations of PA, as well as calculated bindings of theoretical ΔG⁰. Conclusion: The complex formation between PA and ct-DNA has been investigated in the presence and absence of EMF through the multi spectroscopic techniques and MD simulation. These findings have been observed to be parallel to the results of KI and NaCl quenching studies, as well as the competitive displacement with EB and AO. According to thermodynamic parameters, electrostatic interactions stand as the main energy that binds PA to ct-DNA. Regarding the cases that involve the T_m of ct-DNA, EMF has proved to increase the stability of binding between PA and ct-DNA.

Multiplexed Profiling of Extracellular Vesicles for Biomarker Development

Extracellular vesicles (EVs) are cell-derived membranous particles that play a crucial role in molecular trafficking, intercellular transport and the egress of unwanted proteins. They have been implicated in many diseases including cancer and neurodegeneration. EVs are detected in all bodily fluids, and their protein and nucleic acid content offers a means of assessing the status of the cells from which they originated. As such, they provide opportunities in biomarker discovery for diagnosis, prognosis or the stratification of diseases as well as an objective monitoring of therapies. The simultaneous assaying of multiple EV-derived markers will be required for an impactful practical application, and multiplexing platforms have evolved with the potential to achieve this. Herein, we provide a comprehensive overview of the currently available multiplexing platforms for EV analysis, with a primary focus on miniaturized and integrated devices that offer potential step changes in analytical power, throughput and consistency.

Adsorption of DNA by using polydopamine modified magnetic nanoparticles based on solid-phase extraction

A polydopamine magnetic composite (PDA@Fe₃O₄) was prepared for the extraction of human genomic DNA and characterized by transmission electron microscopy, X-ray diffraction, FT-IR spectrometer, zeta potential and vibrating sample magnetometry. PDA@Fe₃O₄ based on magnetic solid phase extraction (MSPE) method have highly efficient capture of genomic deoxyribonucleic acid (DNA)and gene fragments ranging from about 100 bp to 200 bp. Compared with commercial beads (Shenggong, China) and spin column nucleic acid extraction kit (Tiangen, China), the PDA coated magnetic nanoparticles display superior genomic DNA extraction capacity (116 mg/g) and yield (90.2%). The isolation protocol used the solutions (composed of PEG and NaCl) with a specific pH for the binding and release of DNA. The procedure can be attributed to the charge switch of amino and hydroxyl groups on surface of the magnetic particle. The extracted DNA with high quality (A260/A280 = 1.82 ± 0.04) can be directly used as template for polymerase chain reaction (PCR) followed by agarose gel electrophoresis. The results showed the new composite to be an ideal adsorbent for separation of DNA which had the advantage of its low cost, high extraction capacity and yield.

Extraction of DNA from complex biological sample matrices using guanidinium ionic liquid modified magnetic nanocomposites

A series of guanidinium ionic liquid modified magnetic chitosan/graphene oxide (GIL-MCGO) nanocomposites have been prepared for DNA extraction via magnetic solid-phase extraction technology. These nanocomposites are of only 20 nanometers in diameter. Single stranded DNA or DNA sodium salts that were absorbed by GIL-MCGO could be quickly collected by an external magnet and extracted. The DNA extraction efficiency of 11 GIL-MCGO nanocomposites was evaluated using NanoDrop. Factors that could impact the DNA extraction process, such as pH, temperature, extraction time, and ionic strength were systematically investigated via single-factor experimental analysis. Under the optimum extraction conditions, a maximum DNA extraction capacity of 233.0 ± 0.4 mg g⁻¹ of GIL-MCGO nanocomposite was achieved. The solid phase extraction method based on GIL-MCGO nanocomposites has been demonstrated with the extraction of DNA from a series of complex sample matrices, including single stranded DNA samples, salmon sperm DNA sodium salt, human whole blood and E. coli cell lysate. The DNA extracted by using the GIL-MCGO nanocomposites are well suitable for PCR amplifications. In addition, an initial study on the interaction between GIL-MCGO and DNA was conducted: the preference of GIL-MCGO on DNA absorption with varying base composition was tested. Only a slight loss in the DNA extraction efficiency of GIL-MCGO was observed after four extraction–desorption cycles, proving excellent regeneration performance and recyclability of the GIL-MCGO nanocomposites in the DNA extraction process.

The DNA extracted from biological samples by using the GIL-MCGO nanocomposites are well suitable for PCR amplifications.

Highly Sensitive Fluorescence Methods for the Determination of Alfuzosin, Doxazosin, Terazosin and Prazosin in Pharmaceutical Formulations, Plasma and Urine

Polymeric ionic liquid-coated magnetic nanoparticles have been successfully prepared as adsorbents for the magnetic solid-phase extraction of four drugs, namely alfuzosin, doxazosin, terazosin and prazosin, from pharmaceutical preparations, urine samples and plasma samples. The four drugs were detected by fluorescence spectrophotometer. Several extraction parameters, including the pH of the solution; the type, ratio and volume of the desorbing reagent; the amount of adsorbent; the time of the extraction and desorption processes; and the addition of NaCl, were investigated and optimized. Linear responses were determined for the four drugs in the concentration range of 0.5 - 45 ng mL(-1). The limit of detection values for alfuzosin, doxazosin, terazosin and prazosin, which were defined as three times the standard deviation of a blank sample, were determined to be 0.035, 0.034, 0.027 and 0.028 ng mL(-1) (n = 11), respectively. Furthermore, this new method gave preconcentration factors of 114.5, 111.3, 111.1 and 108.5 for these four drugs.

Preparation of magnetic chitosan and graphene oxide-functional guanidinium ionic liquid composite for the solid-phase extraction of protein

A series of novel cationic functional hexaalkylguanidinium ionic liquids and anionic functional tetraalkylguanidinium ionic liquids have been synthesized, and then magnetic chitosan graphene oxide (MCGO) composite has been prepared and coated with these functional guanidinium ionic liquids to extract protein by magnetic solid-phase extraction. MCGO-functional guanidinium ionic liquid has been characterized by vibrating sample magnetometer, field emission scanning electron microscopy, X-ray diffraction spectrometer and Fourier transform infrared spectrometer. After extraction, the concentrations of protein were determined by measuring the absorbance at 278 nm using an ultra violet visible spectrophotometer. The advantages of MCGO-functional guanidinium ionic liquid in protein extraction were compared with magnetic chitosan, graphene oxide, MCGO and MCGO-ordinary imidazolium ionic liquid. The proposed method has been applied to extract trypsin, lysozyme, ovalbumin and bovine serum albumin. A comprehensive study of the adsorption conditions such as the concentration of protein, the amount of MCGO-functional guanidinium ionic liquid, the pH, the temperature and the extraction time were also presented. Moreover, the MCGO-functional guanidinium ionic liquid can be easily regenerated, and the extraction capacity was about 94% of the initial one after being used three times.

Magneto-separation of genomic deoxyribose nucleic acid using pH responsive Fe3O4@silica@chitosan nanoparticles in biological samples

Magneto-separation of genomic deoxyribose nucleic acid using pH responsive Fe₃O₄@silica@chitosan nanoparticles in biological samples.

A rhodamine-based fluorescent probe for Cu(II) determination in aqueous solution

An 'off-on' rhodamine-based fluorescence probe for the selective detection of Cu(II) has been designed, exploiting the guest-induced structure transform mechanism. This system shows a sharp Cu(II)-selective fluorescence enhancement response in an aqueous system under physiological pH, and possesses high selectivity against a background of environmentally and biologically relevant metal ions. Under optimum conditions, the fluorescence intensity enhancement of this system is linearly proportional to the Cu(II) concentration from 50 nM to 6.0 μM with a detection limit of 29 nM.

The detection of T-Nos, a genetic element present in GMOs, by cross-priming isothermal amplification with real-time fluorescence

An isothermal cross-priming amplification (CPA) assay for Agrobacterium tumefaciens nopaline synthase terminator (T-Nos) was established and investigated in this work. A set of six specific primers, recognizing eight distinct regions on the T-Nos sequence, was designed. The CPA assay was performed at a constant temperature, 63 °C, and detected by real-time fluorescence. The results indicated that real-time fluorescent CPA had high specificity, and the limit of detection was 1.06 × 10(3) copies of rice genomic DNA, which could be detected in 40 min. Comparison of real-time fluorescent CPA and conventional polymerase chain reaction (PCR) was also performed. Results revealed that real-time fluorescent CPA had a comparable sensitivity to conventional real-time PCR and had taken a shorter time. In addition, different contents of genetically modified (GM)-contaminated rice seed powder samples were detected for practical application. The result showed real-time fluorescent CPA could detect 0.5 % GM-contaminated samples at least, and the whole reaction could be finished in 35 min. Real-time fluorescent CPA is sensitive enough to monitor labeling systems and provides an attractive method for the detection of GMO.