A novel approach for the detection of DNA using immobilized peptide nucleic acid (PNA) probes and signal enhancement by real-time immuno-polymerase chain reaction (RT-iPCR)

A new approach for the detection of DNA target molecules is described, using capture probes and subsequent signal enhancement by a uniform polymerase chain reaction (PCR). Peptide nucleic acid probes were immobilized in real-time PCR-compatible microtiter plates. After hybridization of biotinylated DNA targets, detection was performed by real-time immuno-PCR, a method formerly used for protein detection. We demonstrate the feasibility of this strategy for the qualitative detection of DNA oligonucleotides with a detection limit (LOD) of 6 attomol. Furthermore, the method was applied to PCR-amplified samples from genetically modified maize DNA (Mon810). A 483-bp DNA fragment was detected in mixture with 99.9% of noncomplementary DNA with a sensitivity down to the level of attomole. Figure       

Addition of gold nanoparticles to real-time PCR: effect on PCR profile and SYBR Green I fluorescence

Real-time quantitative polymerase chain reaction (qPCR) is the industry standard technique for the quantitative analysis of nucleic acids due to its unmatched sensitivity and specificity. Optimisation and improvements of this fundamental technique over the past decade have largely consisted of attempts to allow faster and more accurate ramping between critical temperatures by improving assay reagents and the thermal geometry of the PCR chamber. Small gold nanoparticles (Au-NPs) have been reported to improve PCR yield under fast cycling conditions. In this study, we investigated the effect of Au-NPs on optimised real-time qPCR assays by amplifying DNA sequences from genetically modified canola in the presence and absence of 0.9 nM Au-NPs of diameter 12 ± 2nm. Contrary to expectations, we found that Au-NPs altered the PCR amplification profile when using a SYBR Green I detection system due to fluorescence quenching; furthermore, high-resolution melt (HRM) analysis demonstrated that Au-NPs destabilised the double-stranded PCR product. The results indicate that effects on the assay detection system must be carefully evaluated before Au-NPs are included in any qPCR assay. Figure Raw amplification profiles in the presence and absence of gold nanoparticles     

Phase-changing sacrificial layers in microfluidic devices: adding another dimension to separations

The use of polymers in microchip fabrication affords new opportunities for the development of powerful, miniaturized separation techniques. One method in particular, the use of phase-changing sacrificial layers, allows for simplified designs and many additional features to the now standard fabrication of microchips. With the possibility of adding a third dimension to the design of separation devices, various means of enhancing analysis now become possible. The application of phase-changing sacrificial layers in microchip analysis systems is discussed, both in terms of current uses and future possibilities. Figure Phase-changing sacrificial materials enable multilayer microfluidic device layouts     

Single molecule detection in nanofluidic digital array enables accurate measurement of DNA copy number

Digital polymerase chain reaction (PCR) is a promising technique for estimating target DNA copy number. PCR solution is distributed throughout numerous partitions, and following amplification, target DNA copy number is estimated based on the proportion of partitions containing amplified DNA. Here, we identify approaches for obtaining reliable digital PCR data. Single molecule amplification efficiency was significantly improved following fragmentation of total DNA and bias in copy number estimates reduced by analysis of short intact target DNA fragments. Random and independent distribution of target DNA molecules throughout partitions, which is critical to accurate digital PCR measurement, was demonstrated by spatial distribution analysis. The estimated relative uncertainty for target DNA concentration was under 6% when analyzing five digital panels comprising 765 partitions each, provided the panels contained an average of 212 to 3,365 template molecules. Partition volume was a major component of this uncertainty estimate. These findings can be applied to other digital PCR studies to improve confidence in such measurements. Figure Digital PCR amplification plot (left) and panel read out (right) of HindIII-digested pIRMM69. pIRMM69 contains one HindIII restriction enzyme site outside the hmg and transgene fragments used as targets in PCR. Red boxes with white shade denote positive hits containing one or more target DNA molecules, and white boxes with grey shade refer to no target being amplified.     

Polycation coating poly(dimethylsiloxane) capillary electrophoresis microchip for rapid separation of ascorbic acid and uric acid

A novel method for rapid separation and determination of ascorbic acid and uric acid has been developed with a polycation-modified poly(dimethylsiloxane) (PDMS) microchip under a negative-separation electric field. Just by flushing the microchip with aqueous solutions of the polycations, poly(allylamine) hydrochloride, poly(diallyldimethylammonium chloride) or chitosan could be stably coated on the PDMS microchannel surface, which resulted in a reversed electroosmotic flow and thus the rapid and efficient separation of the two substrates. Factors influencing the separation, including polycation category, buffer solution, detection potential and separation voltage, were investigated and optimized. The cheapness, rapid analysis speed and the successful analysis of human urine make this microsystem attractive for application in clinics. Figure The electropherograms of 100 μ/mL AA and UA in (1) PAH, (2) PDDA, (3) Chitosan modified PDMS microchannels and native PDMS microchip (4).     

Progress in circular dichroism laser mass spectrometry

Circular dichroism in ion yield has promising new potentials for chiral analysis. Our progress of its development is described here. Circular dichroism in ion yield is achieved by resonance-enhanced multiphoton ionization. The feasibility of circular dichroism spectroscopy and quantitative determination of circular dichroism by this method is demonstrated. Several excitation schemes have been applied using different types of lasers, which vary in wavelength and repetition rate. Progress to improve the statistical error and thus the lower limit of measurable circular dichroism is described. This is achieved by adding achiral compounds or racemic mixtures of chiral compounds to the sample gas as reference substances and ionizing them by the same laser pulse. Therefore, in the mass spectrum of every single laser pulse, ion signals of sample and reference species appear both being subject to the same kind of instrumental fluctuations (in particular of laser pulse energy). In another approach, a laser repetition rate of 200 Hz allowed averaging of large numbers of laser pulses.      

Enhanced recognition of non-complementary hybridization by single-LNA-modified oligonucleotide probes

Locked nucleic acid (LNA) is a deoxyribonucleotide analogue with an unusual ‘locked’ furanose conformation. LNA-modified oligonucleotide probes have demonstrated an enhanced binding affinity towards their complementary strands; however, their potential to discriminate non-complementary hybridization of mismatches has not been explored. In this study, we investigated the effect of the chemical nature of LNA nucleobases on the hybridization stability and the capability of LNA-modified oligonucleotides to discriminate the LNA:DNA mismatched base pairs. It was observed that LNA modification indeed improves the discrimination capability of oligonucleotides by increasing the melting temperature differences between the complementary duplexes and hybrids containing mismatches. Particularly, LNA purines offer a greater potential to recognize the mismatches than LNA pyrimidines and DNA purines. Real-time PCR experiments further confirmed that LNA modifications at the 3′-end are more effective. The results and conclusions in this study provide useful information for hybridization-based nucleic acid analysis where designing sound oligonucleotide probes is crucial to the success of the analyses.   Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Electrochemical sensors and biosensors based on heterogeneous carbon materials

Abstract  An overview of the use of electrochemical sensors made from heterogeneous carbon materials (carbon paste electrodes, screen-printed carbon electrodes) in the field of food analysis is presented. Sensors for inorganic and organic analytes as well as biosensors are summarized. Graphical abstract        

Interpretation of laser desorption mass spectra of unexpected inorganic species found in a cosmetic sample of forensic interest: fingernail polish

Monitoring of cell cultures in microbioreactors is a crucial task in cell bioassays and toxicological tests. In this work a novel tool based on a miniaturized sensor array fabricated using low-temperature cofired ceramics (LTCC) technology is presented. The developed device is applied to the monitoring of cell-culture media change, detection of the growth of various species, and in toxicological studies performed with the use of cells. Noninvasive monitoring performed with the LTCC microelectrode array can be applied for future cell-engineering purposes. Figure Microelectrode array for monitoring of cell cultures     

A viscosity-tunable polymer for DNA separation by microchip electrophoresis

A thermo-responsive separation matrix, consisting of Pluronic F127 tri-block copolymers of poly(ethylene oxide) and poly(propylene oxide), was used to separate DNA fragments by microchip electrophoresis. At low temperature, the polymer matrix was low in viscosity and allowed rapid loading into a microchannel under low pressure. With increasing temperatures above 25°C, the Pluronic F127 solution forms a liquid crystalline phase consisting of spherical micelles with diameters of 17–19 nm. The solution can be used to separate DNA fragments from 100 bp to 1500 bp on poly(methyl methacrylate) (PMMA) chips. This temperature-sensitive and viscosity-tunable polymer provided excellent resolution over a wide range of DNA sizes. Separation is based on a different mechanism compared with conventional matrices such as methylcellulose. To illustrate the separation mechanism of DNA in a Pluronic F127 solution, DNA molecular imaging was performed by fluorescence microscopy with F127 polymer as the separation matrix in microchip electrophoresis. Figure Temperature dependence of the viscosity of 20% w/w Pluronic F127 solution in 1xTBE buffer. Dotted approximates resultant curve.     

Critical evaluation of sample pretreatment techniques

Sample preparation before chromatographic separation is the most time-consuming and error-prone part of the analytical procedure. Therefore, selecting and optimizing an appropriate sample preparation scheme is a key factor in the final success of the analysis, and the judicious choice of an appropriate procedure greatly influences the reliability and accuracy of a given analysis. The main objective of this review is to critically evaluate the applicability, disadvantages, and advantages of various sample preparation techniques. Particular emphasis is placed on extraction techniques suitable for both liquid and solid samples. Figure Miniaturised extraction techniques allow sensitive analysis of also small sample volumes.     

Surface modification using a novel type I hydrophobin HGFI

Surface wettability conversion with hydrophobins is important for its applications in biodevices. In this work, the application of a type I hydrophobin HGFI in surface wettability conversion on mica, glass, and poly(dimethylsiloxane) (PDMS) was investigated. X-ray photoelectron spectroscopy (XPS) and water-contact-angle (WCA) measurements indicated that HGFI modification could efficiently change the surface wettability. Data also showed that self-assembled HGFI had better stability than type II hydrophobin HFBI. Protein patterning and the following immunoassay illustrated that surface modification with HGFI should be a feasible strategy for biosensor device fabrication. Figure A hydrophobin HGFI has been applied into surface wettability conversion for protein immobilization Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Monitoring surface-assisted biomolecular assembly by means of evanescent-field-coupled waveguide-mode nanobiosensors

Biological self-assembly is a natural process that involves various biomolecules, and finding the missing partner in these interactions is crucial for a specific biological function. Previously, we showed that evanescent-field-coupled waveguide-mode sensor in conjunction with a SiO₂ waveguide, the surfaces which contain cylindrical nanometric holes produced by atomic bombardment, allowed us to detect efficiently the biomolecular interactions. In the present studies, we showed that the assembly of biomolecules can be monitored using the evanescent-field-coupled waveguide-mode biosensor and thus provide a methodology in monitoring assembly process in macromolecular machines while they are assembling. Evanescent-field-coupled waveguide-mode sensor Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Dual-cardiac marker capillary waveguide fluoroimmunosensor based on tyramide signal amplification

The early diagnosis of acute myocardial infarction requires the determination of several markers in serum shortly after its incidence. The markers most widely employed are the isoenzyme MB of creatine kinase (CK-MB) and the cardiac troponin I (cTnI). In the present work, a capillary waveguide fluoroimmunosensor for fast and highly sensitive simultaneous determination of these markers in serum samples is demonstrated. The dual-analyte immunosensor was realized using glass capillaries internally modified with an ultrathin poly(dimethylsiloxane) film by creating discrete bands of analyte-specific antibodies. The capillary was then filled with a mixture of sample and biotinylated detection antibodies followed by reaction with streptavidin–horseradish peroxidase and incubation with a fluorescently labeled tyramide derivative to accumulate fluorescent labels onto immunoreaction bands. Upon scanning the capillary with a laser beam, part of the emitted fluorescence is trapped and waveguided through the capillary wall to a photomultiplier placed on one of its ends. The employment of tyramide signal amplification provided detection limits of 0.2 and 0.5 ng/mL for cTnI and CK-MB, respectively, in a total assay time of 30 min compared to 0.8 and 0.6 ng/mL obtained for the corresponding assays when the conventional fluorescent label R-phycoerythrin was used in a 65-min assay. In addition, the proposed immunosensor provided accurate and repeatable measurements (intra-assay and interassay coefficients of variation lower than 10%), and the values determined in serum samples were in good agreement with those obtained with commercially available enzyme immunoassays. Thus, the proposed capillary waveguide fluoroimmunosensor has all the required characteristics for fast and reliable diagnosis of acute myocardial infarction.      

Gradient HPLC separation of dehydroepiandrosterone (DHEA) from its metabolites and biological congeners: role of tetrahydrofuran in the chromatographic mechanism

A three-step gradient reversed-phase high-performance liquid chromatography (RP-HPLC) method was developed for the separation of dehydroepiandrosterone (DHEA), its sulfate ester (DHEA-S), its three C7-oxidized metabolites (7αOH-DHEA, 7βOH-DHEA, 7-keto-DHEA), and its biosynthetic congeners (androstenedione, testosterone, estradiol, pregnenolone). This new method allows the quantitative characterization of DHEA metabolism and biosynthetic transformation under given physiological, pathological, or therapeutically influenced circumstances. Tetrahydrofuran probably acts as a proton acceptor coadsorbent, while isopropanol behaves as a proton donor during the separation of testosterone, estradiol, and the stereoisomers of 7-OH-DHEA. Figure Optimized gradient RP-HPLC results in full separation of DHEA from its biosynthetic congeners and metabolites     

Amperometric sensing of hydrogen peroxide vapor for security screening

Rapid detection of the hydrogen peroxide precursor of peroxide explosives is required in numerous security screening applications. We describe a highly sensitive and selective amperometric detection of hydrogen peroxide vapor at an agarose-coated Prussian-blue (PB) modified thick-film carbon transducer. The sensor responds rapidly and reversibly to dynamic changes in the level of the peroxide vapor, with no apparent carry over and with a detection limit of 6 ppbv. The remarkable selectivity of the PB-based screen-printed electrode towards hydrogen peroxide leads to effective discrimination against common beverage samples. For example, blind tests have demonstrated the ability to selectively and non-invasively identify concealed hydrogen peroxide in drinking cups and bottles. The attractive performance of the new microfabricated PB-based amperometric peroxide vapor sensor indicates great potential for addressing a wide range of security screening and surveillance applications. Figure Experimental setup (left) with three electrode electrochemical Hydrogen Peroxide sensor hanging above container of “unknown” liquid. Schematic (right) demonstrating fundamental principles of operation of the sensor.     

Arsine and selenium hydride trapping in a novel quartz device for atomic-absorption spectrometry

A novel quartz device has been designed to trap arsine and selenium hydride and subsequently to volatilize the collected analyte and atomize it for atomic-absorption spectrometric detection. The device is actually the multiple microflame quartz-tube atomizer (multiatomizer) with inlet arm modified to serve as the trap and to accommodate the oxygen-delivery capillary used to combust hydrogen during the trapping step. The effect of relevant experimental conditions (trap temperature during trapping and hydrogen flow rate and trap temperature during volatilization) on collection and volatilization efficiency was investigated. Under the optimum conditions collection and volatilization efficiency for arsenic and selenium were 50 and 70%, respectively.      

Chemical analysis of acoustically levitated drops by Raman spectroscopy

An experimental apparatus combining Raman spectroscopy with acoustic levitation, Raman acoustic levitation spectroscopy (RALS), is investigated in the field of physical and chemical analytics. Whereas acoustic levitation enables the contactless handling of microsized samples, Raman spectroscopy offers the advantage of a noninvasive method without complex sample preparation. After carrying out some systematic tests to probe the sensitivity of the technique to drop size, shape, and position, RALS has been successfully applied in monitoring sample dilution and preconcentration, evaporation, crystallization, an acid–base reaction, and analytes in a surface-enhanced Raman spectroscopy colloidal suspension. Figure We have systematically investigated the analytical potential of Raman spectroscopy of samples in acoustically levitated drops.     

Analytical tools for the physicochemical profiling of drug candidates to predict absorption/distribution

The measurement of physicochemical properties at an early phase of drug discovery and development is crucial to reduce attrition rates due to poor biopharmaceutical properties. Among these properties, ionization, lipophilicity, solubility and permeability are mandatory to predict the pharmacokinetic behavior of NCEs (new chemical entities). Due to the high number of NCEs, the analytical tools used to measure these properties are automated and progressively adapted to high-throughput technologies. The present review is dedicated to experimental methods applied in the early drug discovery process for the determination of solubility, ionization constants, lipophilicity and permeability of small molecules. The principles and experimental conditions of the different methods are described, and important enhancements in terms of throughput are highlighted. Figure Scheme of the Drug Research Process.     

Two-dimensional electrophoresis on a microfluidic chip for quantitative amino acid analysis

Analysis of complex biological samples requires the use of high-throughput analytical tools. In this work, a microfluidic two-dimensional electrophoresis system was developed with mercury-lamp-induced fluorescence detection. Mixtures of 20 standard amino acids were used to evaluate the separation performance of the system. After fluorescent labeling with fluorescein isothiocyanate, mixtures of amino acids were separated by micellar electrokinetic chromatography in the first dimension and by capillary zone electrophoresis in the second. A double electrokinetic valve system was employed for the sample injection and the switching between separation channels. Under the optimized conditions, 20 standard amino acids were effectively separated within 20 min with high resolution and repeatability. Quantitative analysis revealed linear dynamic ranges of over three orders of magnitudes with detection limits at micromolar range. To further evaluate the reliability of the system, quantitative analysis of a commercial nutrition supplement liquid was successfully demonstrated. Figure