Extraction,amplification and detection of DNA in microfluidic chip-based assays

This review covers three aspects of PCR-based microfluidic chip assays: sample preparation, target amplification, and product detection. We also discuss the challenges related to the miniaturization and integration of each assay and make a comparison between conventional and microfluidic schemes. In order to accomplish these essential assays without human intervention between individual steps, the micro-components for fluid manipulation become critical. We therefore summarize and discuss components such as microvalves (for fluid regulation), pumps (for fluid driving) and mixers (for blending fluids). By combining the above assays and microcomponents, DNA testing of multi-step bio-reactions in microfluidic chips may be achieved with minimal external control. The combination of assay schemes with the use of micro-components also leads to rapid methods for DNA testing via multi-step bioreactions. Contains 259 references. Figure

A graphical presentation of main PCR assays: DNA extraction from raw sample, target amplification by PCR and final product detection in conventional bench-top lab and miniaturized microfluidic chip.     

Rapid extraction and preservation of genomic DNA from human samples

Simple and rapid extraction of human genomic DNA remains a bottleneck for genome analysis and disease diagnosis. Current methods using microfilters require cumbersome, multiple handling steps in part because salt conditions must be controlled for attraction and elution of DNA in porous silica. We report a novel extraction method of human genomic DNA from buccal swab and saliva samples. DNA is attracted onto a gold-coated microchip by an electric field and capillary action while the captured DNA is eluted by thermal heating at 70 °C. A prototype device was designed to handle four microchips, and a compatible protocol was developed. The extracted DNA using microchips was characterized by qPCR for different sample volumes, using different lengths of PCR amplicon, and nuclear and mitochondrial genes. In comparison with a commercial kit, an equivalent yield of DNA extraction was achieved with fewer steps. Room-temperature preservation for 1 month was demonstrated for captured DNA, facilitating straightforward collection, delivery, and handling of genomic DNA in an environment-friendly protocol.

Comparative evaluation of extraction methods for simultaneous mass-spectrometric analysis of complex lipids and primary metabolites from human blood plasma

Metabolomic results on human blood plasma largely depend on the sample preparation protocols employed for protein precipitation and metabolite extraction. Five different extraction methods were examined, which can be grouped into two categories, liquid-liquid extraction and protein precipitation methods, including long-standing protocols such as the Folch extraction and Bligh-Dyer extraction in comparison to modern methods such as the Matyash protocol and two global metabolite extraction methods. Extracts were subjected to analysis of blood plasma lipids and primary metabolites by using chip-based direct infusion nanoelectrospray tandem mass spectrometry and gas chromatography coupled to time-of-flight mass spectrometry, respectively. Optimal extraction schemes were evaluated based on the number of identified metabolites, extraction efficiency, compound diversity, reproducibility, and convenience for high-throughput sample preparations. Results showed that Folch and Matyash methods were equally valid and robust for lipidomic assessments while primary metabolites were better assessed by the protein precipitation methods with organic solvent mixtures. Graphical Abstract

Schematic workflow of five extraction methods and subsequent mass spectrometry analysis using GC-TOF MS and nanoelectrospray direct-infusion ion trap MS/MS?     

Magnetic molecularly imprinted polymer nanoparticles for the solid-phase extraction of paracetamol from plasma samples,followed its determination by HPLC

We are presenting magnetic molecularly imprinted polymer nanoparticles (m-MIPs) for solid-phase extraction and sample clean-up of paracetamol. The m-MIPs were prepared from magnetite (Fe₃O₄) as the magnetic component, paracetamol as the template, methacrylic acid as a functional monomer, and 2-(methacrylamido) ethyl methacrylate as a cross-linker. The m-MIPs were then characterized by transmission electron microscopy, FT-IR spectroscopy, X-ray diffraction and vibrating sample magnetometry. The m-MIPs were applied to the extraction of paracetamol from human blood plasma samples. Following its elution from the column loaded with the m-MIPs with an acetonitrile-buffer (9:1) mixture, it was submitted to HPLC analysis. Paracetamol can be quantified by this method in the 1 μg L^?1 to 300 μg L^?1 concentration range. The limit of detection and limit of quantification in plasma samples are 0.17 and 0.4 μg L^?1. The preconcentration factor of the m-MIPs is 40. The HPLC method shows good precision (4.5 % at 50 μg L^?1 levels) and recoveries (between 83 and 91 %) from spiked plasma samples. Figure

We are presenting magnetic molecularly imprinted polymer nanoparticles (m-MIPs) for solid-phase extraction and sample clean-up of paracetamol. The m-MIPs were applied to the extraction of paracetamol from human blood plasma samples     

Evaluation of a commercial enzymatic test kit regarding the quantitative analysis of different free fatty acids

The quantitative determination of the total free fatty acids (FFAs) is an important analytical task because FFAs exhibit important physiological effects and are also relevant in many other fields, for instance, in food research. Our aim was to investigate whether a commercially available enzymatic test kit developed for the determination of FFAs in human serum is also suitable to determine different physiological and nonphysiological FFAs and to which extent the impact on the sensitivities (i.e., the accuracy by which a given FFA can be determined) differ. It will be shown that the chain length as well as the double bond content has a significant impact on the sensitivity by which a given FFA can be determined. For instance, palmitic acid (16:0) is determined with an approximately 20 times higher sensitivity in comparison to docosahexaenoic acid (22:6n-3). All data were obtained by measuring the concentrations of the FFAs by gas chromatography, and selected FFAs were also determined in a complex matrix of human serum. It is concluded that this kit is not useful if major alterations of the FFA composition of a complex mixture are expected because the individual FFAs are not detected with the same sensitivities: the concentrations of polyunsaturated FFA determined by this kit are wrong. Figure

The used enzymatic kit detects different free fatty acids with significantly different sensitivities: the number of carbon atoms and the number of double bonds massively contribute to these differences     

N-Methyl-4-hydrazino-7-nitrobenzofurazan: a fluorogenic substrate for peroxidase-like DNAzyme,and its potential application

Characterization and optimization studies of N-methyl-4-hydrazino-7-nitrobenzofurazan (MNBDH) as a new fluorogenic substrate in the peroxidation reaction catalyzed by DNAzyme are reported. The effects of pH, H₂O₂ concentration, metal-cation type, and the concentration and type of surfactant on the fluorescence intensity were investigated. The optimized reaction was subsequently used for the development of an assay for DNA detection based on a molecular-beacon probe. The use of a fluorogenic substrate enabled the detection of a single-stranded DNA target with a 1 nmol L^?1 detection limit. Graphical Abstract

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Label-free and rapid colorimetric detection of DNA damage based on self-assembly of a hemin-graphene nanocomposite

Hemin-graphene nanosheets (H-GNs) can be controllably assembled by target DNA via a hybridization process. This results in a color change from dark blue-green to light blue-green. The degree of aggregation is dependent on DNA concentration and very sensitive to base mismatch. The formation of the blue-green color can be detected with bare eyes or a spectrometer. The method is simple, rapid, and works over the concentration range from 1.0 to 100 nM. The detection limit for target DNA is 0.2 nM. Excellent selectivity is also found in that a DNA with a single base mismatch can be discriminated. This was exploited to detect DNA damage as induced by styrene oxide, sodium arsenite, Fenton’s reagent, or UV radiation. We presume that this method represents a promising tool for evaluating genotoxicity. Figure

Detection of DNA damage based on DNA-directed self-assembly of H-GNs     

Polymer-based devices for the label-free detection of DNA in solution: low DNA concentrations yield large signals

Poly (N-isopropylacrylamide-co-N-(3-aminopropyl) methacrylamide hydrochloride) microgel-based optical devices (etalons) have been shown to change their optical properties in the presence of single-stranded DNA. We hypothesize that this is due to the negatively charged DNA penetrating through the Au overlayer of the etalon, resulting in cross-linking and collapse of the positively charged microgels. We have shown that this technology is capable of detecting micromolar concentrations of target DNA in solutions containing two and four base pair mismatch sequences without the use of labels. Furthermore, the device’s response increases as the concentration of DNA decreases, which is unique for sensing strategies. We point out that coupling this transduction mechanism to DNA amplification strategies could result in extremely low detection limits.

Integration of sample pretreatment, μPCR,and detection for a total genetic analysis microsystem

Since the emergence of lab-on-a-chip technology, a variety of chemical and biochemical assays were successfully implemented on microdevice platforms. Among the chip-based applications, genetic analysis based on the polymerase chain reaction (PCR) has been extensively developed in order to accomplish the goal of cheap, rapid, high-throughput, and point-of-care DNA testing. We are summarizing here several formats of the miniaturized PCR systems including the integration of units for sample pretreatment and downstream analytical detection. The various sections cover (a) miniaturized PCR systems, (b) integrated sample pretreatment-PCR microsystems, (c) integrated PCR-detection microsystems, and (d) integrated sample pretreatment-PCR-detection microsystems. Respective microdevices were successfully introduced recently in the form of a fully integrated microsystem for genetic analysis with sample-in-answer-out capability. Contains 120 references. Figure

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A novel electrochemical DNA biosensor construction based on layered CuS–graphene composite and Au nanoparticles

A novel CuS–graphene (CuS-Gr) composite was synthesized to achieve excellent electrochemical properties for application as a DNA electrochemical biosensor. CuS-Gr composite was prepared by a hydrothermal method, in which two-dimensional graphene served as a two-dimensional conductive skeleton to support CuS nanoparticles. A sensitive electrochemical DNA biosensor was fabricated by immobilizing single-stranded DNA (ss-DNA) labeled at the 5′ end using 6-mercapto-1-hexane (HS-ssDNA) on the surface of Au nanoparticles (AuNPs) to form ssDNA-S–AuNPs/CuS-Gr, and hybridization sensing was done in phosphate buffer. Cyclic voltammetry and electrochemical impedance spectroscopy were performed for the characterization of the modified electrodes. Differential pulse voltammetry was applied to monitor the DNA hybridization using an [Fe(CN)₆]^3?/4? solution as a probe. Under optimum conditions, the biosensor developed exhibited a good linear relationship between the current and the logarithm of the target DNA concentration ranging from 0.001 to 1 nM, with a low detection limit of 0.1 pM (3σ/S). The biosensor exhibited high selectivity to differentiate one-base-mismatched DNA and three-base-mismatched DNA. The results indicated that the sensing platform based on CuS-Gr provides a stable and conductive interface for electrochemical detection of DNA hybridization, and could easily be extended to the detection of other nucleic acids. Graphical abstracts

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A nanocomposite consisting of plasma-polymerized propargylamine and graphene for use in DNA sensing

We report on a novel graphene-based nanoarchitecture modified with plasma-polymerized propargylamine (G-PpPG) and its application in electrochemical sensors for DNA. Films of G-PpPG were characterized by X-ray photoelectron spectroscopy and electrochemical impedance spectroscopy. The presence of graphene enhances the electrochemical activity of the films, and the high density of amino groups (deposited at a low plasma input power) on their surface assists in the immobilization of probe DNA on the water-swollen polymeric network. By contrast, the degree of hybridization of the total complementary target DNA to the probe DNA remains unchanged when G-PpPG nanofilms prepared at higher input power. No substantial non-specific adsorption of totally mismatched target DNA on the polymer films is observed because of the complete coverage of the probe DNA. The detection limit for total complementary target DNA is approximately 1.84 nmol?·?L^?1. The dynamic range extends from 0.1 to 1,000 nmol?·?L^?1. The new nanocomposite may also be used to immobilize other probe DNA sequences, and this makes the approach potentially applicable to the detection of other oligomers. Figure

Preparing the DNA sensor made from the graphene-based nanoarchitecture modified by using PpPG (G-PpPG) includes the following processes: (a) Modifying the Au electrode with the graphene nanosheet, (b) depositing the PpPG film onto the Au electrode coated with graphene, (c) immobilizing the probe DNA onto the G-PpPG film, and (d) hybridizing the MM0 target with the G-PpPG film immobilized with P1     

Quantitative determination of memantine in human plasma by GC using negative ion chemical ionization MS detection after derivatization with a new reagent, o-(pentafluorobenzyloxycarbonyl)-2,3,4,5-tetrafluorobenzoyl chloride

A method is presented for the quantitative determination of memantine in plasma by use of the derivatization reagent o-(pentafluorobenzyloxycarbonyl)-2,3,4,5-tetrafluorobenzoyl chloride. Memantine can be quantitatively analyzed down to 49?pg per mL of plasma using a 250?μL sample and negative ion chemical ionisation mass spectrometry (GC-NICI-MS). Plasma samples were made alkaline with carbonate buffer and extracted with n-hexane. The extracts were treated with reagent solution for 20?min, concentrated, and submitted to GC-NICI-MS. The method is rapid because extraction and derivatization occur in one single step. Amantadine is used as an internal standard. The utility and robustness of the assay is demonstrated by giving data on specificity, linearity, accuracy and precision, benchtop stability, freeze-thaw stability, autosampler stability, aliquot analysis, and prospective analytical batch size accuracy.

Sensitive detection of enteropathogenic E. coli using a bfpA gene-based electrochemical sensor

We have developed a sensitive assay for enteropathogenic E. coli (EPEC) by integrating DNA extraction, specific polymerase chain reaction (PCR) and DNA detection using an electrode modified with the bundle-forming pilus (bfpA) structural gene. The PCR amplified products are captured on the electrode and hybridized with biotinylated detection probes to form a sandwich hybrid containing two biotinylated detection probes. The sandwich hybridization structure significantly combined the numerous streptavidin alkaline phosphatase on the electrode by biotin-streptavidin connectors. Electrochemical readout is based on dual signal amplification by both the sandwich hybridization structure and the enzyme. The electrode can satisfactorily discriminate complementary and mismatched oligonucleotides. Under optimal conditions, synthetic target DNA can be detected in the 1 pM to 10 nM concentration range, with a detection limit of 0.3 pM. EPEC can be quantified in the 10 to 10⁷ CFU mL^?1 levels within 3.5 h. The method also is believed to present a powerful platform for the screening of pathogenic microorganisms in clinical diagnostics, food safety and environmental monitoring.

Identification and quantification of cannabinoids in Cannabis sativa L. plants by high performance liquid chromatography-mass spectrometry

High performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) has been successfully applied to cannabis plant extracts in order to identify cannabinoid compounds after their quantitative isolation by means of supercritical fluid extraction (SFE). MS conditions were optimized by means of a central composite design (CCD) approach, and the analysis method was fully validated. Six major cannabinoids [tetrahydrocannabinolic acid (THCA), tetrahydrocannabinol (THC), cannabidiol (CBD), tetrahydrocannabivarin (THCV), cannabigerol (CBG), and cannabinol (CBN)] were quantified (RSD < 10%), and seven more cannabinoids were identified and verified by means of a liquid chromatograph coupled to a quadrupole-time-of-flight (Q-ToF) detector. Finally, based on the distribution of the analyzed cannabinoids in 30 Cannabis sativa L. plant varieties and the principal component analysis (PCA) of the resulting data, a clear difference was observed between outdoor and indoor grown plants, which was attributed to a higher concentration of THC, CBN, and CBD in outdoor grown plants. Graphical Abstract

Representative figure of the identification and quantification process of cannabinoids     

Comparison of Three Plasma Sources for Ambient Desorption/Ionization Mass Spectrometry

Plasma-based desorption/ionization sources are an important ionization technique for ambient surface analysis mass spectrometry. In this paper, we compare and contrast three competing plasma based desorption/ionization sources: a radio-frequency (rf) plasma needle, a dielectric barrier plasma jet, and a low-temperature plasma probe. The ambient composition of the three sources and their effectiveness at analyzing a range of pharmaceuticals and polymers were assessed. Results show that the background mass spectrum of each source was dominated by air species, with the rf needle producing a richer ion spectrum consisting mainly of ionized water clusters. It was also seen that each source produced different ion fragments of the analytes under investigation: this is thought to be due to different substrate heating, different ion transport mechanisms, and different electric field orientations. The rf needle was found to fragment the analytes least and as a result it was able to detect larger polymer ions than the other sources. Figure

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Dispersive solid phase extraction of lead(II) using a silica nanoparticle-based ionic liquid ferrofluid

We demonstrate the application of an ionic liquid-based ferrofluid to the dispersive solid phase extraction of lead(II) using PAN as the chelator. The ionic liquid contains silica nanoparticles with a magnetic core as the dispersion medium, and its use results in improved stability of the colloidal dispersion and a complete extraction of lead(II) within a few seconds. In addition, there is no need for centrifugation. Specifically, the effect of different variables on the extraction of lead(II) was studied using an experimental design. Lead(II) was quantified by AAS. Under optimized conditions, the calibration graph for lead(II) is linear in the range from 5 to 372 μg L^?1, the relative standard deviation is 1.34 % (for n?=?7), the limit of detection is 1.66 μg L^?1, and the enrichment factor is 200. The maximum adsorption capacity of sorbent was calculated to be 10.7 mg g^?1, and adsorption follows a Langmuir isotherm. Figure

A schematic view of D-SPE experimental set up. We demonstrate the application of an ionic liquid-based ferrofluid to the dispersive solid phase extraction of lead(II) using PAN as the chelator. The ionic liquid contains silica nanoparticles with a magnetic core as the dispersion medium     

A lanthanide nanoparticle-based luminescent probe for folic acid

We report on a novel luminescent method for the detection of folic acid (FA), a member of the vitamin B family. Y₂O₃ nanoparticles were doped with europium(III) ions and surface-modified with captopril. Their fluorescence is quenched by FA, and intensity is a function of folic acid concentration in the 0.1 – 40 μM concentration range. The detection limit is 83 nM of FA at pH 7 and room temperature.

Electrochemical detection of DNA binding by tumor suppressor p53 protein using osmium-labeled oligonucleotide probes and catalytic hydrogen evolution at the mercury electrode

In this paper, we present an electrochemical DNA–protein interaction assay based on a combination of protein-specific immunoprecipitation at magnetic beads (MBIP) with application of oligonucleotide (ON) probes labeled with an electroactive oxoosmium complex (Os,bipy). We show that double-stranded ONs bearing a dT₂₀ tail labeled with Os,bipy are specifically recognized by the tumor suppressor p53 protein according to the presence or absence of a specific binding site (p53CON) in the double-stranded segment. We demonstrate the applicability of the Os,bipy-labeled probes in titration as well as competition MBIP assays to evaluate p53 relative affinity to various sequence-specific or structurally distinct unlabeled DNA substrates upon modulation of the p53-DNA binding by monoclonal antibodies used for the immunoprecipitation. To detect the p53-bound osmium-labeled probes, we took advantage of a catalytic peak yielded by Os,bipy-modified DNA at the mercury-based electrodes, allowing facile determination of subnanogram quantities of the labeled oligonucleotides. Versatility of the electrochemical MBIP technique and its general applicability in studies of any DNA-binding protein is discussed. Figure

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Progress in stacking techniques based on field amplification of capillary electrophoresis

Numerous strategies have been developed to mitigate the intrinsic low detection sensitivity that is a limitation of capillary electrophoresis. Among them, in-line stacking is an effective strategy to address the sensitivity challenge, and among the different stacking techniques, stacking based on field amplification is the most effective and simplest method of achieving high sensitivity without special complicated mechanisms or operations. This review introduces several stacking techniques based on field amplification. Field-amplified sample stacking, large-volume sample stacking, matrix field-amplified stacking injection (FASI), head-column FASI, matrix FASI combined with head-column FASI, FASI coupled with extraction and clean-up methods, electrokinetic supercharging, cation–anion selective exhaustive injection-sweeping-micellar electrokinetic chromatography, and newly developed techniques based on field amplification combined with other methods are included, and examples of straightforward methods for solving the sensitivity problem are provided. We also present a brief overview of the advantages, limitations, and future developments of these techniques. Graphical Abstract

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Zundel-Type H-Bonding in Biomolecular Ions

Using quantum chemical calculations and infrared multiphoton dissociation (IRMPD) spectroscopy in the fingerprint and X-H stretching regions, we demonstrate here that the all-Ala b ₆ fragment ion features a macrocyclic structure with C₂ symmetry. For this structure, the ionizing proton is equally shared by the Ala(1) and Ala(4) amide oxygens in a Zundel-type symmetric (X…H⁺…X) H-bond. Figure

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