Solid-phase Extraction Of DNA Research Articles

Solid-phase extraction of DNA by using a composite prepared from multiwalled carbon nanotubes, chitosan, Fe3O4 and a poly(ethylene glycol)-based deep eutectic solvent

A magnetically responsive composite was prepared for improved solid-phase extraction of salmon sperm DNA sodium salt. It consists of chitosan-modified Fe3O4-magnetized multi-walled carbon nanotubes coated with a poly(ethylene glycol) based deep eutectic solvent. The sorbent was characterized by X-ray diffraction, vibrating sample magnetometry, Fourier transform infrared spectrometry, thermogravimetric analysis and transmission electron microscopy. The effects of the concentration of DNA, ionic strength, pH value, temperature and extraction time on extraction performance were optimized. Compared to plain Fe3O4, the new sorbent displays a superior DNA extraction capacity of 178 mg·g−1. It also displays favorable selectivity for DNA over bovine hemoglobin. Regeneration studies show that (a) 79% of DNA can be eluted from loaded sorbent by using 1 M NaCl, and that (b) the conformation of DNA remains unchanged as evidenced by CD spectra. The sorbent can be recycled six times without significant loss of extraction capacity. It was applied to the extraction of DNA from bovine whole blood prior to DNA quantitation by agarose gel electrophoresis. The results show this new sorbent to be a viable material for separation of DNA that excels by its low cost, high loading capacity and ease of regeneration.

P156: Detection adducts DNA in human blood and lung cancer tissue by a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer

Background Identification of DNA-based biomarkers of cancer cells is highly promising and rapidly developing direction that can advance early detection and therapy of malignancies. DNA adducts are felicitous markers of cancer, because their chemical structure is significantly different from that of mutated or methylated DNA, that allows to determine them with high precision using mass spectrometry. The aim of this work is to develop the methodology of sample preparation and its mass spectrometric analysis. Samples were prepared from the blood plasma and from the tumor tissue from lung cancer patients and from blood of healthy individuals. Materials and methods DNA was isolated from the blood plasma and tissue by using column method (BioSilica, Russia) The final yield from 1 ml of blood was 100 ng. DNA samples were subjected to acid hydrolysis (1 M HCl) at 70 °C. After 3 h, the hydrolysis was stopped by cooling on ice for 5 min and later on adding an equivalent amount of an alkali and a phosphate buffer solution (pH 7). To assess the extent of hydrolysis of the samples they were analysed by electrophoresis on a 1.2% agarose gel in Tris-acetate buffer. The samples were extracted at cartridge HF Bond Elut-C18 100 mg, 1 ml (Agilent Technologies, USA) and eluted in several fractions with a gradual increase of methanol in the eluent. Stream of nitrogen was applied to dry the extract. The samples were subjected to mass spectrometric analysis after pre-separation by UHLC Ultimate 3000 RS (Dionex, USA) in a column Dionex Acclaim RSLC 120 C18 (2.1 × 50 mm 120 A, 0.2 μm) flow rate of 0.5 ml/min using as eluents 0.1% solution of formic acid in water (A) and 0.1% solution of formic acid in atsetontrile (B). Elution was carried out in gradient mode: (%B): 0–3min (5%), 3–28min (5–95%), 28–30 min (95%), 30–31 min (95–5%), 31–35 min (5%). Mass spectrometry was carried out on ESI-qTOF ultrahigh resolution Maxis 4G (Bruker, Germany) in the positive ion detection mode range 50–1000 m/z, 2 Hz with the following settings electrospray ion source: CV 3800 V, Nebulizer gas 1 bar, Dry Gas 8 l/min, Dry Temp: 200 °C. Results It was found that the DNA which was cleaved with acid hydrolysis in the result contained single DNA bases. The samples were stable at 4 °C for at least 7 days. The optimal eluent for solid phase extraction of DNA is 80% solution of methanol in water. The number of DNA adducts was evaluated by the integrated value of the mass spectrometric response detector. It was shown that most amount of adducts 4-hydroxy-1-(3-pyridyl)-1- butanone and N3-(2-carbamoyl-2-hydroxyethyl)adenine was found in DNA samples derived from tumor tissue. The adduct N7-(2-carbamoyl-2-hydroxyethyl)guanine was found in tumor tissue samples and DNA derived from plasma, as well as in all samples of healthy tissue. Conclusion The established protocol of DNA sample preparation followed by analysis using a mass spectrometer high resolution allows to detect the content of the DNA adducts in small DNA probes (100 ng). We found, that acid hydrolysis is cheaper and more practical in comparison to enzymatic digestion in order to generated samples containing single DNA bases without damaging the structure of adducts. This research was supported by Federal Targeted Programme for Research and Development in Priority Areas of Development of the Russian Scientific and Technological Complex for 2014–2020, “Development of molecular signatures for early detection of lung cancer” (No. 14.575.21.0064 from 05.08.2014, RFMEFI57514X0064) and supported by Tomsk State University, Competitiveness Improvement Program”. Work was conducted with the application of the Tomsk regional common use center technical equipment acquired thanks to a grant of the Russian Ministry of the Agreement No.14.594.21.0001 (RFMEFI59414X0001).

A surface topography assisted droplet manipulation platform for biomarker detection and pathogen identification

This paper reports a droplet microfluidic, sample-to-answer platform for the detection of disease biomarkers and infectious pathogens using crude biosamples. The platform exploited the dual functionality of silica superparamagnetic particles (SSP) for solid phase extraction of DNA and magnetic actuation. This enabled the integration of sample preparation and genetic analysis within discrete droplets, including the steps of cell lysis, DNA binding, washing, elution, amplification and detection. The microfluidic device was self contained, with all reagents stored in droplets, thereby eliminating the need for fluidic coupling to external reagent reservoirs. The device incorporated unique surface topographic features to assist droplet manipulation. Pairs of micro-elevations were created to form slits that facilitated efficient splitting of SSP from droplets. In addition, a compact sample handling stage, which integrated the magnet manipulator, the droplet microfluidic device and a Peltier thermal cycler, was built for convenient droplet manipulation and real-time detection. The feasibility of the platform was demonstrated by analysing ovarian cancer biomarker Rsf-1 and detecting Escherichia coli with real time polymerase chain reaction and real time helicase dependent amplification.

Solid phase extraction of DNA from biological samples in a post-based, high surface area poly(methyl methacrylate) (PMMA) microdevice

This work describes the performance of poly(methyl methacrylate) (PMMA) microfluidic DNA purification devices with embedded microfabricated posts, functionalized with chitosan. PMMA is attractive as a substrate for creating high surface area (SA) posts for DNA capture because X-ray lithography can be exploited for extremely reproducible fabrication of high SA structures. However, this advantage is offset by the delicate nature of the posts when attempting bonding to create a closed system, and by the challenge of functionalizing the PMMA surface with a group that invokes DNA binding. Methods are described for covalent functionalization of the post surfaces with chitosan that binds DNA in a pH-dependent manner, as well as for bonding methods that avoid damaging the underlying post structure. A number of geometric posts designs are explored, with the goal of identifying post structures that provide the requisite surface area without a concurrent rise in fluidic resistance that promotes device failure. Initial proof-of-principle is shown by recovery of prepurified human genomic DNA (hgDNA), with real-world utility illustrated by purifying hgDNA from whole blood and demonstrating it to be PCR-amplifiable.

Volume reduction solid phase extraction of DNA from dilute, large-volume biological samples

Microdevices are often designed to process sample volumes on the order of tens of microliters and cannot typically accommodate larger volume samples without adversely affecting efficiency and greatly increasing analysis time. However, dilute, large-volume biological samples are frequently encountered, especially in forensic or clinical laboratories. A microdevice, capable of efficiently processing 0.5–1 mL samples has been developed for solid phase extraction (SPE) of DNA. SPE was carried out on a microdevice utilizing magnetic silica particles and an optimized volumetric flow rate and elution buffer, resulting in a 50-fold decrease in volume and a 15-fold increase in DNA concentration. Device characterization studies showed DNA extraction efficiencies comparable with previously reported silica-based purification methods, with robust performance demonstrated by the successful amplification of a fragment from the gelsolin gene extracted from dilute whole blood. In addition, the microchip-based method for SPE of large volume, dilute samples was also used to demonstrate the first successful on-chip purification of mitochondrial DNA (mtDNA) from both dilute whole blood and a degraded blood stain.