Application of magnetic particles (Fe3O4) for isolation of genomic DNA from mammalian cells

Phenol/Chloroform-Free TiO2-Based miRNA Extraction from Cell Lysate

While microRNAs are considered as excellent biomarkers of various diseases, there are still several remaining challenges regarding their isolation. In this study, we aimed to design a novel RNA isolation method that would help to overcome those challenges. Therefore, we present a novel phenol/chloroform-free, low-cost method for miRNA extraction. Within this method, RNA is extracted from cell lysate with an isopropanol/water/NaCl system, followed by solid-phase extraction using TiO2 microspheres to effectively separate short RNAs from long RNA molecules. We also demonstrated the pH-dependent selectivity of TiO2 microspheres towards different sizes of RNA. We were able to regulate the size range of extracted RNAs with simple adjustments in binding conditions used during the solid-phase extraction.

Isolation of DNA from Arthrospira platensis and whole blood using magnetic nanoparticles (Fe3O4@OA and Fe3O4@OA@SiO2)

Magnetic nanoparticles (MNPs) provide a fast, cost-effective, and organic-free method for DNA isolation. In this paper, we synthesized MNP coated with oleic acid (Fe3O4@OA) and silica nanoparticles (Fe3O4@OA@SiO2), characterized the properties of MNP using TEM, VSM, and FTIR, and investigated their efficiency in DNA isolation from cyanobacteria. The yield and quality of isolated DNA were evaluated and compared with those from animal blood and those obtained by the silica column or organic solvents. The results showed the successful preparations of Fe3O4@OA and Fe3O4@OA@SiO2 with superparamagnetic behaviors and a mean diameter of 7 nm and 106 nm, respectively. The FTIR spectra of Fe3O4@OA confirmed the bonding of OA to the surface of iron oxide, while those of Fe3O4@OA@SiO2 showed the exposed silanol groups. Although MNPs yielded a lower quantity of DNA compared with phenol/chloroform extraction, they showed the potential  protection of the integrity of DNA against  centrifugal and shear forces. Fe3O4@OA@SiO2 favored more nucleic acid absorption than Fe3O4@OA, producing a 1.2 and 1.6 times greater amount of DNA from Arthrospira platensis and animal blood respectively. The purity of DNA isolated from Arthrospira platensis was also higher than that of animal blood. These findings indicate a new and simple approach for the isolation of DNA from Arthrospira genus.

Graphical Abstract

Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA

Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.

ctDNA applications and integration in colorectal cancer: an NCI Colon and Rectal-Anal Task Forces whitepaper

An increasing number of studies are describing potential uses of circulating tumour DNA (ctDNA) in the care of patients with colorectal cancer. Owing to this rapidly developing area of research, the Colon and Rectal-Anal Task Forces of the United States National Cancer Institute convened a panel of multidisciplinary experts to summarize current data on the utility of ctDNA in the management of colorectal cancer and to provide guidance in promoting the efficient development and integration of this technology into clinical care. The panel focused on four key areas in which ctDNA has the potential to change clinical practice, including the detection of minimal residual disease, the management of patients with rectal cancer, monitoring responses to therapy, and tracking clonal dynamics in response to targeted therapies and other systemic treatments. The panel also provides general guidelines with relevance for ctDNA-related research efforts, irrespective of indication.

Implementing circulating tumor DNA analysis in a clinical laboratory: A user manual

Liquid biopsy, the analysis of cell-free circulating tumor DNA (ctDNA), is becoming one of the most promising tools in oncology. It has already shown its usefulness in selecting and modulating therapy via remote analysis of the tumor genome and holds important promises in cancer therapy and management, such as assessing the success of key therapeutic steps, monitoring residual disease, early detection of relapses, and establishing prognosis. Yet, ctDNA analysis is technically challenging and its implementation in the laboratory raises multiple strategic and practical issues. As for oncology clinics, integration of this novel test in well-established therapeutic protocols can also pose numerous questions. The current review is intended as a field guide for (1) diagnostic laboratories wishing to implement, validate and possibly accredit ctDNA testing and (2) clinical oncologists interested in integrating the various applications of liquid biopsies in their daily practice. We provide advice and practical recommendations based on our own experience with the technical validations of these methods and on a review of the current literature, with a focus toward gastro-intestinal, lung and breast cancers.

DNA isolation by galactoacrylate-based nano-poly(HEMA-co-Gal-OPA) nanopolymers

Isolation of DNA is one of the important processes for biotechnological applications such as investigation of DNA structures and functions, recombinant DNA preparations, identification of genetic factors and diagnosis and treatment of genetic disorders. The aim of this study was to synthesis and characterizes the galactoacrylate based nanopolymers with high surface area and to investigate the usability of these synthesized nanopolymers for DNA isolation studies. Nanopolymers were synthesized by the surfactant free emulsion polymerization technique by using the monomers of 2-hydroxyl ethylmethacrylate and 6-O-(2^'-hydroxy-3^'-acryloyloxypropyl)-1,2:3,4-di-O-isopropylidene-α-D-galactopyranose. Galactoacrylate origin of these newly synthesized nanopolymers increased the interaction between DNA and nanopolymers. Prepared nanopolymers were characterized by SEM, FT-IR and ZETA sizer analysis. Synthesized nanopolymers were spherical, and their average particle size was about 246.8 nm. Adsorption of DNA onto galactoacrylate based nanopolymers was investigated by using different pHs, temperatures, ionic strength, DNA concentrations and desorption studies and maximum DNA adsorption was found to be as 567.12 mg/g polymer at 25 °C, in pH 5.0 acetate buffer. Reusability was investigated for 5 successive reuse and DNA adsorption capacity decreased only about 10% at the end of the 5th reuse.

Fluorescence Characterization of Gold Modified Liposomes with Antisense N-myc DNA Bound to the Magnetisable Particles with Encapsulated Anticancer Drugs (Doxorubicin, Ellipticine and Etoposide)

Liposome-based drug delivery systems hold great potential for cancer therapy. The aim of this study was to design a nanodevice for targeted anchoring of liposomes (with and without cholesterol) with encapsulated anticancer drugs and antisense N-myc gene oligonucleotide attached to its surface. To meet this main aim, liposomes with encapsulated doxorubicin, ellipticine and etoposide were prepared. They were further characterized by measuring their fluorescence intensity, whereas the encapsulation efficiency was estimated to be 16%. The hybridization process of individual oligonucleotides forming the nanoconstruct was investigated spectrophotometrically and electrochemically. The concentrations of ellipticine, doxorubicin and etoposide attached to the nanoconstruct in gold nanoparticle-modified liposomes were found to be 14, 5 and 2 µg·mL⁻¹, respectively. The study succeeded in demonstrating that liposomes are suitable for the transport of anticancer drugs and the antisense oligonucleotide, which can block the expression of the N-myc gene.

Real-time PCR to study the sequence specific magnetic purification of DNA

The performance of various molecular techniques using complex biological samples greatly depends on the efficient separation and purification of DNA targets. In recent years, magnetic separation technology making use of small magnetic beads, has gained immense popularity. Most of these methods rely on the non-specific adsorption of DNA/RNA. However, as presented here, when functionalizing the beads with complementary DNA probes, the target of interest can selectively be isolated. Such sequence specific purification was evaluated for short DNA targets by means of simple fluorescent measurements, resulting in purification efficiencies around 80%. Besides standard fluorescent techniques, a real-time PCR (qPCR) method was applied for monitoring the purification of longer DNA targets. This qPCR method was specifically optimized for directly quantifying the purification efficiency of low concentrated DNA targets bound to magnetic beads. Additionally, parameters possibly affecting the magnetic isolation, including the length of the used capture probe or the hybridization location, were investigated. Using optimized conditions in combination with qPCR, purification efficiencies between 60% and 80% were observed and this over a large concentration window. These data also show the power of a direct qPCR approach to monitor the magnetic isolation of DNA at very low concentrations.

Large-scale synthesis of single-crystalline iron oxide magnetic nanorings

We present an innovative approach to the production of single-crystal iron oxide nanorings employing a solution-based route. Single-crystal hematite (alpha-Fe2O3) nanorings were synthesized using a double anion-assisted hydrothermal method (involving phosphate and sulfate ions), which can be divided into two stages: (1) formation of capsule-shaped alpha-Fe2O3 nanoparticles and (2) preferential dissolution along the long dimension of the elongated nanoparticles (the c axis of alpha-Fe2O3) to form nanorings. The shape of the nanorings is mainly regulated by the adsorption of phosphate ions on faces parallel to c axis of alpha-Fe2O3 during the nanocrystal growth, and the hollow structure is given by the preferential dissolution of the alpha-Fe2O3 along the c axis due to the strong coordination of the sulfate ions. By varying the ratios of phosphate and sulfate ions to ferric ions, we were able to control the size, morphology, and surface architecture to produce a variety of three-dimensional hollow nanostructures. These can then be converted to magnetite (Fe3O4) and maghemite (gamma-Fe2O3) by a reduction or reduction-oxidation process while preserving the same morphology. The structures and magnetic properties of these single-crystal alpha-Fe2O3, Fe3O4, and gamma-Fe2O3 nanorings were characterized by various analytical techniques. Employing off-axis electron holography, we observed the classical single-vortex magnetic state in the thin magnetite nanorings, while the thicker rings displayed an intriguing three-dimensional magnetic configuration. This work provides an easily scaled-up method for preparing tailor-made iron oxide nanorings that could meet the demands of a variety of applications ranging from medicine to magnetoelectronics.

Direct cell entry of gold/iron-oxide magnetic nanoparticles in adenovirus mediated gene delivery

Gold/iron-oxide MAgnetic Nanoparticles (GoldMAN) imparts useful magnetic properties to various biomolecules. Gold nanoparticles immobilized on the surface of magnetic nanoparticles allow for the conjugation of biomolecules via an Au-S bond. Here, we present a practical application by utilizing GoldMAN and a magnetic field to induce intracellular transduction. This method has great potential for application of the adenovirus gene delivery vector (Ad), widely used for in vitro/in vivo gene transfer, to Ad-resistant cells. We demonstrated that Ad was easily immobilized on GoldMAN and the Ad/GoldMAN complex was introduced into the cell by the magnetic field, which increased gene expression over 1000 times that of Ad alone. The GoldMAN penetrated the plasma membrane directly, independent of the cell-surface virus receptors and endocytosis pathway. This mechanism will contribute to improve the gene expression efficiency of Ad. This technology is a useful tool for extending Ad tropism and enhancing transduction efficiency. GoldMAN also makes possible the effective use of various biomolecules within the cell because of its interesting cell-entry mechanism.

Isolation of genomic DNA using magnetic nanoparticles as a solid-phase support

In recent years, techniques employing magnetizable solid-phase supports (MSPS) have found application in numerous biological fields. This magnetic separation procedure offers several advantages in terms of subjecting the analyte to very little mechanical stress compared to other methods. Secondly, these methods are non-laborious, cheap, and often highly scalable. The current paper details a genomic DNA isolation method optimized in our laboratory using magnetic nanoparticles as a solid-phase support. The quality and yields of the isolated DNA from all the samples using magnetic nanoparticles were higher or equivalent to the traditional DNA extraction procedures. Additionally, the magnetic method takes less than 15 min to extract polymerase chain reaction (PCR) ready genomic DNA as against several hours taken by traditional phenol-chloroform extraction protocols. Moreover, the isolated DNA was found to be compatible in PCR amplification and restriction endonuclease digestion. The developed procedure is quick, inexpensive, robust, and it does not require the use of organic solvents or sophisticated instruments, which makes it more amenable to automation and miniaturization.

1, 3-dipolar cycloaddition as a general route for functionalization of Fe(3)O(4) nanoparticles

Triazole formation by 1, 3-dipolar cycloaddition reactions has been used to functionalize the surface of Fe(3)O(4) nanoparticles. Fe(3)O(4) particle samples with diameters around 22 nm were synthesized without any additional stabilizer, and were then treated with silane coupling agent to react with propargyl acid. The alkynyl group on the Fe(3)O(4) surface provides better conjugation efficiency with azide derivative molecules, which led to their attachment through the formation of a 1, 2, 3-triazole ring.