A method based on amino-modified magnetic nanoparticles to extract DNA for PCR-based analysis

The non-negligible non-specific adsorption of oligonucleotides in target-immobilized Mag-SELEX

Target-immobilized magnetic beads-based Systematic Evolution of Ligands by Exponential Enrichment (target-immobilized Mag-SELEX) has emerged as a powerful tool for aptamer selection owing to its convenience, efficiency, and versatility. However, in this study we systematically investigated non-specific adsorption in target-immobilized Mag-SELEX and found that the non-specific adsorption of the oligonucleotides to target-labeled magnetic beads was comparable to that of the screening libraries, indicating a substantial portion of captured sequences likely stem from non-specific adsorption. Longer nucleic acid sequences (80 nt and above, such as polyA80 and yeast tRNA) were found to attenuate this non-specific adsorption, with more complex higher-order structures demonstrating greater efficacy, while dNTP and short sequences such as primer sequences (20 nt), polyT(59), or polyA(59), did not possess this capability. Various evidence suggested that hydrophobic interactions and other weak interactions may be the primary underlying cause of non-specific adsorption. Additionally, surface modification of magnetic beads with polar molecule polyethylene glycol (PEG) also yielded a significant reduction in non-specific adsorption. In conclusion, our research underscores the critical importance of closely monitoring non-specific adsorption in target-immobilized Mag-SELEX.

The Recent Applications of Magnetic Nanoparticles in Biomedical Fields

Magnetic nanoparticles (MNPs) have found extensive application in the biomedical domain due to their enhanced biocompatibility, minimal toxicity, and strong magnetic responsiveness. MNPs exhibit great potential as nanomaterials in various biomedical applications, including disease detection and cancer therapy. Typically, MNPs consist of a magnetic core surrounded by surface modification coatings, such as inorganic materials, organic molecules, and polymers, forming a nucleoshell structure that mitigates nanoparticle agglomeration and enhances targeting capabilities. Consequently, MNPs exhibit magnetic responsiveness in vivo for transportation and therapeutic effects, such as enhancing medical imaging resolution and localized heating at the site of injury. MNPs are utilized for specimen purification through targeted binding and magnetic separation in vitro, thereby optimizing efficiency and expediting the process. This review delves into the distinctive functional characteristics of MNPs as well as the diverse bioactive molecules employed in their surface coatings and their corresponding functionalities. Additionally, the advancement of MNPs in various applications is outlined. Additionally, we discuss the advancements of magnetic nanoparticles in medical imaging, disease treatment, and in vitro assays, and we anticipate the future development prospects and obstacles in this field. The objective is to furnish readers with a thorough comprehension of the recent practical utilization of MNPs in biomedical disciplines.

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.

Cooperative dynamics of DNA-grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami

Magnetic nanoparticles (MNPs) provide new opportunities for enzyme-free biosensing of nucleic acid biomarkers and magnetic actuation by patterning on DNA origami, yet how the DNA grafting density affects their dynamics and accessibility remains poorly understood. Here, we performed surface functionalization of MNPs with single-stranded DNA (ssDNA) via click chemistry with a tunable grafting density, which enables the encapsulation of single MNPs inside a functional polymeric layer. We used several complementary methods to show that particle translational and rotational dynamics exhibit a sigmoidal dependence on the ssDNA grafting density. At low densities, ssDNA strands adopt a coiled conformation that results in minor alterations to particle dynamics, while at high densities, they organize into polymer brushes that collectively influence particle dynamics. Intermediate ssDNA densities, where the dynamics are most sensitive to changes, show the highest magnetic biosensing sensitivity for the detection of target nucleic acids. Finally, we demonstrate that MNPs with high ssDNA grafting densities are required to efficiently couple to DNA origami. Our results establish ssDNA grafting density as a critical parameter for the functionalization of MNPs for magnetic biosensing and functionalization of DNA nanostructures.

Cytosine-rich mismatched DNA aptamer combined with superparamagnetic photonic crystal sensing material for the specific visual detection of silver ions

DNA aptamer superparamagnetic photonic crystals (DSPCs), enriched with a highly selective cytosine-rich mismatched single-stranded DNA aptamer (CRDA), were successfully employed in a novel visual detection strategy for the detection of silver ions (Ag+). The technologies of superparamagnetic colloidal nanospheres (SCNs), DNA aptamer, and photonic crystals were combined to fabricate DPSCs. The aptamer was immobilized via electrostatic adsorption with amino groups that were chemically introduced on the surface of the SCNs, forming D-NH-SCNs. The detection is achieved by forming an Ag+ complex (C-Ag+-C) between Ag+ and D-NH-SCN. The DSPCs assembled under a magnetic field by D-NH-SCNs effectively detected Ag+ in the range of 1 μg/L to 5 mg/L, corresponding to the critical concentration range for heavy metals in drinking water. During the detection, the DSPC exhibited a wavelength blueshift from 652.8 nm to 626.4 nm (26.4 nm), as well as changes in reflection intensity. Notably, when detecting Ag+, a change in DSPC color from orange to yellow was observed. In summary, the developed visual detection material facilitates direct Ag + sensing. In the future, different DNA aptamers will be modified further to detect various targets in the fields of medicine, environmental monitoring, and food safety.

Integrated nucleic acid purification technology based on amino-modified centrifugal microfluidic chip

Nucleic acid detection is an important tool for clinical diagnosis. The purification of the sample is the most time-consuming step in the nucleic acid testing process and will affect the results of the assay. Here, we developed a surface modification-based nucleic acid purification method and designed an accompanying set of centrifugation equipment and chips to integrate the steps of nucleic acid purification on a single platform. The results of experiments with HeLa cells and HPV type 16 as samples showed that the mentioned method had good nucleic acid purification capability and the accompanying equipment greatly simplified the operation of the experimenters in the whole process. Overall, our equipment can improve the efficiency of nucleic acid purification and is suitable for application in larger-scale clinical assays.

Integrated Three-Dimensional Microdevice with a Modified Surface for Enhanced DNA Separation from Biological Samples

Functional interfaces and devices for rapid adsorption and immobilization of nucleic acids (NAs) are significant for relevant bioengineering applications. Herein, a microdevice with poly(acrylic acid) (PAA) photosensitive resin was integrated by three-dimensional (3D) printing, named DPAA for short. Precise microscale structures and abundant surface carboxyl functional groups were fabricated for fast and high-throughput deoxyribonucleic acid (DNA) separation. Surface modification was then done using polydopamine (PDA) and poly(ethylene glycol) (PEG) to obtain modified poly(acrylic acid) (PAA)-based devices DPDA-PAA and DPEG-PAA rich in amino and hydroxyl groups, respectively. The fabricated device DPAA possessed superior printing accuracy (40-50 μm). Functionalization of amino and hydroxyl was successful, and the modified devices DPDA-PAA and DPEG-PAA maintained a high thermal stability like DPAA. Surface potential analysis and molecular dynamics simulation indicated that the affinity for DNA was in the order of DPDA-PAA > DPEG-PAA > DPAA. Further DNA separation experiments confirmed the high throughput and high selectivity of DNA separation performance, consistent with the predicted affinity results. DPDA-PAA showed relatively the highest DNA extraction yield, while DPEG-PAA was the worst. An acidic binding system is more favorable for DNA separation and recovery. DPDA-PAA showed significantly better DNA extraction performance than DPAA in a weakly acidic environment (pH 5.0-7.0), and the average DNA yield of the first elution was 2.16 times that of DPAA. This work validates the possibility of modification on integrated 3D microdevices to improve their DNA separation efficiency effectively. It also provides a new direction for the rational design and functionalization of bioengineering separators based on nonmagnetic methods. It may pave a new path for the highly efficient polymerase chain reaction diagnosis.

An efficient extraction method for short single-stranded DNA from agarose gels in aptamer screening

With the rapid advancements in aptamer screening, the efficient extraction of short single-stranded DNA (ssDNA) from agarose gel has become a new requirement. However, the currently available products are primarily designed for double-stranded DNA (dsDNA) and exhibit limited efficacy when applied to the extraction of short ssDNA. In this study, we successfully developed a novel method based on amino-modified silica-coated magnetic particles (ASMPs) for the extraction of short ssDNA from agarose gel. The gel slices containing short ssDNA were subjected to centrifugation in a spin column/centrifugation tube assembly with silica wool, followed by the adsorption using ASMPs. Subsequently, reagents containing phosphate groups were employed to desorb ssDNA from the surface of ASMPs. Through optimization of each step, we realized remarkable efficiency in the extraction of short ssDNA. To assess the efficacy of our method, we utilized it in aptamer screening. The results demonstrated that our method outperformed three commercially available DNA gel extraction products (Q-kit, S-kit, and V-kit). The relative recovery rates of all methods were as follows: M-dNTP (100.00 %) > M-BB (63.38 %) > Q-kit (46.64 %) > S-kit (15.98 %) > V-kit (0.38 %). The results strongly suggest that the developed method holds promise for short ssDNA extraction from agarose gel.

Simplified Synthesis of the Amine-Functionalized Magnesium Ferrite Magnetic Nanoparticles and Their Application in DNA Purification Method

For pathogens identification, the PCR test is a widely used method, which requires the isolation of nucleic acids from different samples. This extraction can be based on the principle of magnetic separation. In our work, amine-functionalized magnesium ferrite nanoparticles were synthesized for this application by the coprecipitation of ethanolamine in ethylene glycol from Mg(II) and Fe(II) precursors. The conventional synthesis method involves a reaction time of 12 h (MgFe2O4-H&R MNP); however, in our modified method, the reaction time could be significantly reduced to only 4 min by microwave-assisted synthesis (MgFe2O4-MW MNP). A comparison was made between the amine-functionalized MgFe2O4 samples prepared by two methods in terms of the DNA-binding capacity. The experimental results showed that the two types of amine-functionalized magnesium ferrite magnetic nanoparticles (MNPs) were equally effective in terms of their DNA extraction yield. Moreover, by using a few minutes-long microwave synthesis, we obtained the same quality magnesium ferrite particles as those made through the long and energy-intensive 12-h production method. This advancement has the potential to improve and expedite pathogen identification processes, helping to better prevent the spread of epidemics.

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.

Efficient capture of recombinant SARS-CoV-2 receptor-binding domain (RBD) with citrate-coated magnetic iron oxide nanoparticles

Several vaccines against COVID-19 use a recombinant SARS-CoV-2 receptor-binding domain (RBD) as antigen, making the purification of this protein a key step in their production. In this work, citrate-coated magnetic iron oxide nanoparticles were evaluated as nano adsorbents in the first step (capture) of the purification of recombinant RBD. The nanoparticles were isolated through coprecipitation and subsequently coated with sodium citrate. The citrate-coated nanoparticles exhibited a diameter of 10 ± 2 nm, a hydrodynamic diameter of 160 ± 3 nm, and contained 1.9 wt% of citrate. The presence of citrate on the nanoparticles' surface was confirmed through FT-IR spectra and thermogravimetric analysis. The crystallite size (10.1 nm) and the lattice parameter (8.3646 Å) were determined by X-ray diffraction. In parallel, RBD-containing supernatant extracted from cell culture was exchanged through ultrafiltration and diafiltration into the adsorption buffer. The magnetic capture was then optimized using different concentrations of nanoparticles in the purified supernatant, and we found 40 mg mL^-1 to be optimal. The ideal amount of nanoparticles was assessed by varying the RBD concentration in the supernatant (between 0.113 mg mL^-1 and 0.98 mg mL^-1), which resulted in good capture yields (between 83 ± 5% and 94 ± 4%). The improvement of RBD purity after desorption was demonstrated by SDS-PAGE and RP-HPLC. Furthermore, the magnetic capture was scaled up 100 times, and the desorption was subjected to chromatographic purifications. The obtained products recognized anti-RBD antibodies and bound the ACE2 receptor, proving their functionality after the developed procedure.

Amino-modified silica membrane capable of DNA extraction and enrichment for facilitated isothermal amplification detection of Mycoplasma pneumoniae

Herein, we developed a facile integrated Mycoplasma pneumoniae diagnosis platform by combining amino-modified silica membrane (AMSM)-based nucleic acids fast extraction and enrichment with colorimetric isothermal amplification detection. AMSM demonstrates a strong ability to capture and enrich nucleic acids in complicated biological matrices, and the purified AMSM/nucleic acids composite could be directly used to perform isothermal amplification including denaturation bubble-mediated strand exchange amplification (SEA) and loop-mediated isothermal amplification (LAMP) reactions. Through comparing clinical specimens, excellent performance of AMSM-based SEA assay with 93.33% sensitivity and 100% specificity relative to real-time PCR was observed, and for AMSM-based LAMP was 96.67% and 100%, respectively. The diagnostic procedure could be completed within 55 min, and the colorimetric-based visual result further alleviates the use of sophisticated equipment. The proposed approach possesses great potential as a simple and time-saving alternative for point-of-care testing (POCT) of M. pneumoniae in resource-limited regions.

Solvent-sensitive nanoparticle-enhanced PCR assay for the detection of enterotoxigenic Escherichia coli

Stimulus-responsive nanoparticles are among the most utilized nanoscale materials in biomedical applications. As these nanoparticles exhibit a manipulable response to a particular stimulus, such as pH, heat, and organic solvent, they are potential signalling units in diagnostic assays. This study aims to enhance the limit of detection and reduce the turnaround time of magnetic nanoparticle polymerase chain reaction (PCR) enzyme-linked gene assay (MELGA), an advanced PCR-based technique termed the solvent-sensitive nanoparticle (SSNP)-enhanced PCR assay. This technique was proposed to detect pathogenic enterotoxigenic Escherichia coli (ETEC) through applying stimulus-responsive nanoparticles. The SSNPs were elaborated with three main components, including mesoporous silica nanoparticles as a structural unit, organic dye (Nile red) as a payload, and the corresponding organic solvent-sensitive polymer shell as "gatekeeper" (poly(maleic anhydride-alt-methyl vinyl ether, PMAMVE). A suitable organic solvent capable of inducing polymer swelling and dye dissolution was investigated by considering a solubility parameter. Using ethanol, the encapsulated Nile red can diffuse out of the SSNPs faster than other solvents and reach a constant concentration within 15 min. For the PCR inhibition study, various SSNPs concentrations (10-30 μg/reaction) were mixed with the ETEC gene and PCR reagent. The results showed that the particles in this concentration range did not inhibit PCR. By comparing the efficacy of conventional PCR, MELGA, and SSNP-enhanced PCR assay, the proposed technique showed a better detection limit than that of PCR, whereas that of MELGA was the lowest. Moreover, compared to MELGA or conventional PCR, this technique provided remarkably faster results in the postamplification process.

Sugar based cationic magnetic core-shell silica nanoparticles for nucleic acid extraction

Nucleic acid (NA) extraction is an essential step in molecular testing for a wide range of applications. Conventional extraction protocols usually suffer from time consuming removal of non-nucleic acid impurities. In this study, a new magnetic nanoparticle (MNP) is presented to simplify the NA extraction. A core–shell design, comprising of a ferromagnetic core coated with mesoporous silica, forms the basis of the functional nanoparticle. Chemical functionalization of the silica coating includes a multistep synthesis, in which an activated nanoparticle is coupled with a triethylene glycol spaced glycosyl imidazole. The molecular design aims for charge interactions between the imidazolium-based positive nanoparticle surface and nucleic acids, with specific hydrogen bonding between the surface bonded carbohydrate and nucleic acid targets to ensure nucleic acid selectivity and avoid protein contamination. Two different carbohydrates, differing in molecular size, were selected to compare the efficiency in terms of NA extraction. A triethylene glycol spacer provides sufficient flexibility to remove particle surface constraints for the interaction. The Brunauer–Emmett–Teller (BET) analysis shows a significantly larger surface area for the disaccharide-based particles NpFeSiImMalt (∼181 m² g⁻¹) compared to the monosaccharide analogue NpFeSiImGlc (∼116 m² g⁻¹) at small particles sizes (range ∼ 15 nm) and sufficient magnetization (29 emu g⁻¹) for easy isolation by an external magnetic field. The particles enabled a high DNA particle loading ratio of 30–45 wt% (MNP/DNA ratio), reflecting an efficient extraction process. A high desorption rate (7 min) with more than 86% of unchanged DNA loading was recorded, indicating low damage to the target extract.

New design of cationic magnetic core–shell nanoparticles fabricated with a large hydrophilic group (carbohydrate molecules) enabled high adsorption of a nucleic acid, easy isolation and controlled the movement by applying an external magnetic field.

Solid-phase extraction methods for nucleic acid separation. A review

The separation and purification of biomacromolecules such as nucleic acid is a perpetual topic in separation processes and bioengineering (fine chemicals, biopharmaceutical engineering, diagnostics, and biological characterization). In principle, the solid-phase extraction for nucleic acid exhibits efficient phase separation, low pollution risk, and small sample demand, compared to the conventional liquid-phase extraction. Herein, solid-phase extraction methods are systematically reviewed to outline research progress and explore additional solid-phase sorbents and devices for novel, flexible, and high-efficiency nucleic acid separation processes. The functional materials capture nucleic acid, magnetic and magnetic-free solid-phase extraction methods, separation device design and optimization, and high-throughput automatable applications based on high-performance solid-phase extraction are summarized. Finally, the current challenges and promising topics are discussed.

Spherical Nucleic Acid Mediated Functionalization of Polydopamine-Coated Nanoparticles for Selective DNA Extraction and Detection

Magnetic nanoparticles have been widely used for the separation of biomolecules for biological applications due to the mild and efficient separation process. In previous studies, core-shell magnetic nanoparticles (NPs) were designed for DNA extraction without much sequence specificity. In this work, to achieve highly selective DNA extraction, we designed a core-shell magnetic structure by coating polydopamine (PDA) on Fe₃O₄ NPs. Without divalent metal ions, PDA does not adsorb DNA at neutral pH. The Fe₃O₄@PDA NPs were then functionalized with spherical nucleic acids (SNA) to provide a high density of probe DNA. Fe₃O₄@PDA@SNA was also compared with when a linear SH-DNA was covalently attached to the NPs surface, showing a higher density of the probe SNA than SH-DNA can be loaded on the NPs in a remarkably shorter time. Nonspecific DNA extraction was thoroughly inhibited by both probes. DNA extraction by the Fe₃O₄@PDA@SNA was more effective as well as 5-fold faster than by the Fe₃O₄@PDA@SH-DNA, probably due to the favorable standing conformation of DNA strands in SNA. Moreover, extraction by Fe₃O₄@PDA@SNA showed high robustness in fetal bovine serum, and the same design can be used for selective detection of DNA. Finally, the method was also demonstrated on silica NPs and WS₂ nanosheets for coating with PDA and SNA. Altogether, our findings revealed an interesting and general surface modification strategy using PDA@SNA conjugates for sequence-specific DNA extraction.

A one step method for isolation of genomic DNA using multi-amino modified magnetic nanoparticles

A simple and efficient approach for the rapid extraction of genomic DNA from blood using various amino-modified magnetic nanoparticles (AMNPs) has been described. The salmon sperm DNA was isolated from aqueous solution based on electrostatic interaction between the positively charged amino-groups of AMNPs and the negatively charged phosphate groups of the DNA. The results of ultraviolet-visible (UV-Vis) spectrometry showed that increasing number of amino groups on the AMNPs surface resulted in an improvement in DNA adsorption efficiency. Several variables including the extraction pH, adsorption time, ionic strength and quantity of AMNPs were optimized to achieve the best extraction efficiency with the proposed method. Acceptable adsorption efficiency of 92% and recovery of 91% were achieved using multi-amino modified MNPs (mAMNPs) with an extraction time of 10 min and an overall processing time of 30 min. The mAMNPs enabled genomic DNA capture from human whole blood, and the resulting mAMNP/DNA complexes could be directly used as templates for PCR amplification without the need for complex and time-consuming DNA elution and purification steps. Our results imply that this method can be used as an effective strategy for genomic DNA extraction and may be extended to other types of biological samples.

Schematic procedure of DNA isolation using mAMNPs.