An RNA‐Guided Cas9 Nickase‐Based Method for Universal Isothermal DNA Amplification

We have developed an ingenious method, termed Cas9 nickase‐based amplification reaction (Cas9nAR), to amplify a target fragment from genomic DNA at a constant temperature of 37 °C. Cas9nAR employs a sgRNA:Cas9n complex with a single‐strand nicking property, a strand‐displacing DNA polymerase, and two primers bearing the cleavage sequence of Cas9n, to promote cycles of DNA replication through priming, extension, nicking, and displacement reaction steps. Cas9nAR exhibits a zeptomolar limit of detection (2 copies in 20 μL of reaction system) within 60 min and a single‐base discrimination capability. More importantly, the underlying principle of Cas9nAR offers simplicity in primer design and universality in application. Considering the superior sensitivity and specificity, as well as the simple‐to‐implement, rapid, and isothermal features, Cas9nAR holds great potential to become a routine assay for the quantitative detection of nucleic acids in basic and applied studies.     

Photothermal Detection of Individual Gold Nanoparticles: Perspectives for High‐Throughput Screening

We use photothermal microscopy to detect and image individual gold nanoparticles that are either embedded in a polymer film or immobilized in an aqueous environment. Reducing the numerical aperture of the detection optics allows us to achieve a 200‐fold‐enlarged detection volume while still retaining sufficient detectivity. We characterize the capabilities of this approach for the detection of gold colloids with a diameter of 20 nm, with emphasis on practical aspects that are important for high‐throughput‐screening applications. The extended detection volume in combination with the stability of the photothermal signal are major advantages compared to fluorescence‐based approaches, which are limited by photoblinking and photobleaching. Careful consideration is given to the trade‐off between the maximum increase in local temperature that can be tolerated by a biological specimen and the minimum integration time needed to reliably determine whether a given volume contains a target species. We find that our approach has the potential to increase the detection‐limited flow rate (i.e. the limit given by the detection volume divided by the minimum detection time) by two to three orders of magnitude.     

Adsorptive Stripping Voltammetric Detection of Single‐Stranded DNA at Electrochemically Modified Glassy Carbon Electrode

Electrochemically modified glassy carbon electrode (GCE) was used to study the electrochemical oxidation and detection of denatured single‐stranded (ss) DNA by means of adsorptive stripping voltammetry. The modification of GCE, by electrochemical oxidation at +1.75 V (vs.SCE) for 10 min and cyclic sweep between +0.3 V and ?1.3 V for 20 cycles in pH 5.0 phosphate buffer, results in 100‐fold improvement in sensitivity for ssDNA detection. We speculated that the modified GCE has a high affinity to single‐stranded DNA through hydrogen bond (specific static adsorption). Single‐stranded DNA can accumulate at the GCE surface at open circuit and produce a well‐defined oxidation peak corresponding to the guanine residues at about +0.80 V in pH 5.0 phosphate buffer, while the native DNA gives no signal under the same condition. The peak currents are proportional to the ssDNA concentration in the range of 0–18.0 μg mL^?1. The detection limit of denatured ssDNA is ca. 0.2 μg mL^?1 when the accumulation time is 8 min at open circuit. The accumulation mechanism of ssDNA on the modified GCE was discussed.     

Single Microbead‐Anchored Fluorescent Immunoassay (SMFIA): A Facile and Versatile Platform Allowing Simultaneous Detection of Multiple Antigens

A new concept of single microbead (MB)‐anchored fluorescent immunoassay (SMFIA) is proposed with greatly improved sensitivity. In the SMFIA, a single MB is manipulated as the reaction carrier so that the target‐tethered fluorescent immunocomplexes will be highly concentrated on one MB. By monitoring the enriched fluorescence signal on the single MB through imaging, highly sensitive target quantification can be realized just by employing the most common sandwich immunoreactions without requirement of further signal amplification routes. The high sensitivity of the SMFIA can fully meet the demand of current medical diagnosis. Furthermore, we have further advanced a fluorescence‐encoding mechanism for the proposed SMFIA which allows the simultaneous detection of multiple antigens in a single reaction. Sharing the distinct advantages of simple operation, high sensitivity and multiplexed detection capability, the SMFIA provides a general platform for the detection of various biomarkers.     

Concentration cascade of leading electrolyte using bidirectional isotachophoresis

We present a novel method of creating concentration cascade of leading electrolyte (LE) in isotachophoresis (ITP) by using bidirectional ITP. ITP establishes ion-concentration shock waves between high-mobility LE and low-mobility trailing electrolyte (TE) ions. In bidirectional ITP, we set up simultaneous shock waves between anions and cations such that these waves approach each other and interact. The shock interaction causes a sudden decrease in LE concentration ahead of the focused anions and a corresponding decrease in analyte zone concentrations. This readjustment of analyte zone concentrations is accompanied by a corresponding increase in their zone lengths, in accordance to conservation laws. The method generates in situ gradient in the LE concentration, and therefore can be achieved in a single, straight channel simply by establishing the initial electrolyte chemistry. We have developed an analytical model useful in designing the process for maximum sensitivity and estimating increase in sample zone length due to shock interaction. We also illustrate the technique and evaluate its effectiveness in increasing detection sensitivity using transient simulations of species transport equations. We validated the theoretical predictions using experimental visualizations of bidirectional ITP zones for various electrolyte chemistries. Lastly, we use our technique to demonstrate a factor of 20 increase in the sensitivity of ITP-based detection of 2,4,6-trichlorophenol.     

Electrokinetic supercharging preconcentration prior to CGE analysis of DNA: Sensitivity depends on buffer viscosity and electrode configuration

Aiming to high sensitivity DNA analysis by CGE, electrokinetic supercharging (EKS) approach was adopted in this article. EKS is known as an online preconcentration technique that combines electrokinetic sample injection (EKI) with transient ITP (tITP). Herein, two factors of buffer viscosity and electrode configuration were studied to further improve EKS performance. An ultralow‐viscosity Tris‐Boric acid‐EDTA (TBE) buffer solution, consisted of 2% low‐molecular‐weight hydroxypropyl methyl cellulose (HPMC) and 6% mannitol and with pH 8.0 adjusted by boric acid, was applied. The boric acid would make a complex with mannitol and generates borate polyanion, which acts as the leading ion for tITP process. The new electrode configuration, a Pt ring around capillary, was modified on Agilent CE system to lead large amount sample introduction during EKS. The standard DNA sample of φX174/HaeIII digest was used to evaluate the qualitative and quantitative abilities of the proposed strategy. The 170 000‐fold highly diluted sample at concentration of 3.0 ng/mL was enriched by EKS and detected by normal UV detection method. The obtained LOD of the weakest peak of 72 bp fragment was around 7.7 pg/mL, apparently improved more than 10 000‐fold in comparison with conventional CGE with UV detection.     

Highly sensitive analysis of catecholamines by counter‐flow electrokinetic supercharging in the constant voltage mode

Electrokinetic supercharging is one of the most powerful sample‐stacking methods that combines field amplified sample injection and transient ITP. In counter‐flow electrokinetic supercharging, a constant counter pressure is applied during sample injection in order to counterbalance the movement of the injected sample zone. As a result, there will be a pronounced increase in the amount of sample injected and the portion of the capillary available for electrophoresis. In this report, counter‐flow electrokinetic supercharging optimization factors such as the electric field application in the constant voltage and constant current modes, the magnitude of counter pressure, and the terminating electrolyte concentrations were investigated. The enrichments obtained with a 30 min injection of 10 nM catecholamines in 5 mM terminating electrolyte solution in the constant voltage mode applying a counter pressure of 1.3 psi were 41000‐fold for dopamine, 50 000‐fold for norepinephrine, and 32 000‐fold for epinephrine, yielding detection limits of 1.3, 1.4, and 1.2 nM, respectively, with absorbance detection at 200 nm.     

Pre-binding dynamic range and sensitivity enhancement for immuno-sensors using nanofluidic preconcentrator

Almost all immuno-biosensors are inherently limited by the quality of antibodies available for the target molecule, and obtaining a highly sensitive antibody for a given target molecule is a challenge. We describe a highly efficient and flexible way to enhance immunoassay detection sensitivity and binding kinetics using a nanofluidic based electrokinetic preconcentrator. The device is a microfluidic integration of charge-based biomolecule concentrator and a bead-based immunoassay. Because the preconcentrator can increase the local biomolecule concentration by many orders of magnitude, it gives the immuno-sensor better sensitivity and faster binding kinetics. With a 30 min preconcentration, we were able to enhance the immunoassay sensitivity (with molecular background) by more than 500 fold from higher 50 pM to the sub 100 fM range. Moreover, by adjusting the preconcentration time, we can switch the detection range of the given bead-based assay (from 10-10 000 ng ml(-1) to 0.01-10 000 ng ml(-1)) to have a broader dynamic range of detection. As the system can enhance both detection sensitivity and dynamic range, it can be used to address the most critical detection issues in the detection of common disease biomarkers.     

Online preconcentration and two‐dimensional separation of cationic compounds via hyphenation of capillary zone electrophoresis with cyclodextrin‐modified micellar electrokinetic capillary chromatography

A novel preconcentration/separation approach, which online combined CZE with CD‐modified MEKC, was developed for simultaneous enhancing resolving power and detection sensitivity. CZE with cation‐selective exhaustive injection and transient ITP preconcentration was used as the first dimension, from which the effluent fractions were further analyzed by CD‐modified MEKC acting as the second dimension. As the key to successful integration of CZE with MEKC, a new interface was designed and electroaccumulation focusing strategy was employed to avoid analyte band diffusion at the interface. The comprehensive 2‐D system was successfully established with only one high voltage and four electrodes. The grouping of two orthogonal separation techniques, together with analytes preconcentration techniques, significantly enhanced resolution and sensitivity for 2‐D separation of cationic compounds. The resulting electrophoregram was quite different from that of either single CZE or MEKC. Up to 14 000‐ to 35 000‐fold improvement in sensitivity was obtained relative to conventional electrokinetic injection method. The limits of detection (S/N=3) were in the range of 0.03–0.1 μg/L. The number of theoretical plates was in the range of 103 000–184 000. This method was successfully applied to the analysis of trace cationic cardiovascular drugs in wastewater.     

Immunobinding‐induced alteration in the electrophoretic mobility of proteins: An approach to studying the preconcentration of an acidic protein under cationic isotachophoresis

The objective of this study is to explore an approach for analyzing negatively charged proteins using paper‐based cationic ITP. The rationale of electrophoretic focusing the target protein with negative charges under unfavorable cationic ITP condition is to modify the electrophoretic mobility of the target protein through antigen‐antibody immunobinding. Cationic ITP was performed on a paper‐based analytical device that was fabricated using fiberglass paper. The paper matrix was modified with (3‐aminopropyl)trimethoxysilane to minimize sample attraction to the surface for cationic ITP. Negatively charged BSA was used as the model target protein for the cationic ITP experiments. No electrophoretic mobility was observed for BSA‐only samples during cationic ITP experimental condition. However, the presence of a primary antibody to BSA significantly improved the electrokinetic behavior of the target protein. Adding a secondary antibody conjugated with amine‐rich quantum dots to the sample further facilitated the concentrating effect of ITP, reduced experiment time, and elevated the stacking ratio. Under our optimized experimental conditions, the cationic ITP‐based paper device electrophoretically stacked 94% of loaded BSA in less than 7 min. Our results demonstrate that the technique has a broad potential for rapid and cost‐effective isotachphoretic analysis of multiplex protein biomarkers in serum samples at the point of care.     

Coupling porous sheathless interface MS with transient‐ITP in neutral capillaries for improved sensitivity in glycopeptide analysis

IgG antibodies are modulated in their function by the specific structure of the N‐glycans attached to their Fc (fragment crystallizable) portions. However, the glycosylation analysis of antigen‐specific IgGs is a challenging task as antibody levels to a given antigen only represent a fraction of the total IgG levels. Here, we investigated the use of a transient‐ITP (t‐ITP)—MS method for highly sensitive IgG1 glycosylation profiling as a complementary method to a high‐throughput nano‐RPLC‐MS method. It was found that t‐ITP‐CZE using neutrally coated separation capillaries with a large volume injection (37% of capillary volume) and interfaced to MS with a sheathless porous sprayer yielded a 40‐fold increase in sensitivity for IgG1 Fc glycopeptide analysis when compared to the conventional strategy. Furthermore, the glycoform profiles found with the t‐ITP‐CZE strategy were comparable to those from nano‐RPLC‐MS. In conclusion, the use of the highly sensitive t‐ITP‐CZE‐MS method will provide information on IgG Fc glycosylation for those samples with IgG1 concentrations below the LODs of the conventional method.     

Preconcentration and separation of double-stranded DNA fragments by electrophoresis in plastic microfluidic devices

We have evaluated double-stranded DNA separations in microfluidic devices which were designed to couple a sample preconcentration step based on isotachophoresis (ITP) with a zone electrophoretic (ZE) separation step as a method to increase the concentration limit of detection in microfluidic devices. Developed at ACLARA BioSciences, these LabCard trade mark devices are plastic 32 channel chips, designed with a long sample injection channel segment to increase the sample loading. These chips were designed to allow stacking of the sample into a narrow band using discontinuous ITP buffers, and subsequent separation in the ZE mode in sieving polymer solutions. Compared to chip ZE, the sensitivity was increased by 40-fold and we showed baseline resolution of all fragments in the PhiX174/HaeIII DNA digest. The total analysis time was 3 min/sample, or less than 100 min per LabCard device. The resolution for multiplexed PCR samples was the same as obtained in chip ZE. The limit of detection was 9 fg/microL of DNA in 0.1xpolymerase chain reaction (PCR) buffers using confocal fluorescence detection following 488 nm laser excitation with thiazole orange as the fluorescent intercalating dye.     

Electrokinetic supercharging focusing in capillary zone electrophoresis of weakly ionizable analytes in environmental and biological samples

Five non‐steroidal anti‐inflammatory drugs, naproxen, fenoprofen, ketoprofen, diclofenac and piroxicam, were separated and analyzed by electrokinetic supercharging in CZE. Three different setups of the ITP technique were assayed for the separation and preconcentration of these five non‐steroidal anti‐inflammatory drugs. For the setup that gave the best results, we evaluated the influence of different parameters on separation and preconcentration efficiency such as sample pH, concentration of the leading stacker, BGE composition, electrokinetic injection time, composition and hydrodynamic injection of the solvent plug and of the terminating stacker. In the selected setup, the BGE (10 mM Na₂B₄O₇ + 50 mM NaCl in 10% of MeOH aqueous solution) contained the leading electrolyte while the terminating electrolyte, hydrodynamically injected after the sample (50 mbar×12 s), was 50 mM of CHES. Prior to sample injection at (700 s at −2 kV) a short plug of MeOH (50 mbar ×3 s) was hydrodynamically injected. The results show that this strategy enhanced detection sensitivity 2000‐fold compared with normal hydrodynamic injection, providing detection limits of 0.08 μg/L for standard samples with good repeatability (values of relative standard deviation, %RSD < 1.03%). Method validation with river water samples and human plasma demonstrated good linearity, with detection limits of 0.9 and 2 μg/L for river water samples and human plasma samples, respectively (as well as satisfactory precision in terms of repeatability and reproducibility).     

Improved conditions for silver–ammonia staining of DNA in polyacrylamide gel

An improved silver–ammonia staining method for DNA on polyacrylamide gels is described. In this method, staining of DNA using silver–ammonia complex allows high sensitivity, low cost, low toxicity, and simple protocol without requiring fixation and sensitization steps. The protocol takes less than 40 min to complete, with a detection limit of 1.5 pg of single DNA band on polyacrylamide gels, approximately 30‐fold higher than that of original silver–ammonia staining method. Furthermore, this novel technique not only exhibits high sensitivity for large DNA fragment, but also shows a better trend to detect low‐base‐pair DNA compared with other silver staining methods.     

On‐line coupled capillary isotachophoresis‐capillary zone electrophoresis in hydrodynamically closed separation system hyphenated with laser induced fluorescence detection

An analytical method, based on a column coupling capillary ITP and CZE in a hydrodynamically closed separation mode hyphenated with the detection in the modular arrangement, was developed in this work. Analytical possibilities of this approach are demonstrated on the direct and ultrasensitive quantitative determination of quinine (QUI) in diluted real multicomponent ionic matrices (beverages, urine). The detection cell interface, with the rectangular arrangement of the optical channels inside, connected the separation capillary with the LIF detector via optical fibers in the on‐column detection arrangement. ITP enabled the direct large volume (30 μL) injections of the diluted real matrices with an on‐line sample pretreatment (preseparation, preconcentration) so that no external sample preparation (except for the dilution) was necessary for the separation of the analyte in the multicomponent ionic matrices. Due to the ITP sample preconcentration and intrinsic sensitivity of the LIF detection, very low concentration LOD (as low as 77 pg/mL), were reached at the same time. This was ca. two orders lower than the corresponding LOD achieved by the same 2D separation system with UV absorbance detection. Compared to the single column CE‐LIF methods applied for this model analyte and matrix, this method was found to be superior in terms of concentration LOD, with acceptable selectivity and benefits of the on‐line sample preparation. A food control and bioanalytical application clearly illustrates great practical possibilities and routine use of the proposed modular ITP–CZE–LIF technique.     

Fast quantification of cyclophosfamide and its N‐dechloroethylated metabolite 2‐dechloroethylcyclophosphamide in human plasma by UHPLC‐MS/MS

A rapid, novel and reliable UHPLC‐MS/MS method was developed and validated for simultaneous determination of cyclophosphamide (CP) and its dechloroethylated metabolite, 2‐dechloroethylcyclosphamide (2‐DCECP) in human plasma. The plasma samples were conducted by protein precipitation with 3‐fold acetonitrile, containing 0.1% formic acid. Mass spectrometric detection was performed using electrospray positive ionization with multiple reaction monitoring mode, using tinidazole as internal standard (IS). Chromatographic separation was performed on an Agilent poroshell 120 SB‐C₁₈ column (2.1 × 75 mm, 2.7 µm) using gradient elution of acetonitrile and 0.1% formic acid at a flow rate of 0.5 mL/min, the total run time was 2.5 min. The limit of quantification (LOQ) was 20 ng/mL for both CP and 2‐DCECP. Accuracies and precisions were <15% at LOQ and below 10% at quality control concentration levels. This UHPLC‐MS/MS method was successfully applied for the estimation of CP and 2‐DCECP in human plasma, which was also useful for clinical toxicology studies and therapeutic drug monitoring of CP. Copyright © 2014 John Wiley & Sons, Ltd.     

Isotachophoresis with counterflow in an open capillary: Computer simulation and experimental validation

The purpose of applying a countercurrent flow to isotachophoretic migration is to increase the effective separation channel length during ITP. However, severe dispersion induced by applying a counterflow can be detrimental to ITP. This paper uses numerical simulations in a 2D axisymmetric domain to investigate the dispersion caused by a parabolic counterflow in open‐capillary ITP. Counterflow in these simulations was generated by applying a back pressure to stop the isotachophoretic stack, i.e., forming stationary ITP zones. It is found that dispersion is strongly related to analyte molecular diffusivity: R‐phycoerythrin, due to its small diffusivity, showed ～20‐fold increase in zone width in stationary counterflow ITP, compared to ITP in the absence of counterflow, while fluorescein only had ～10% increase in zone width under similar operating conditions. Applying the Taylor–Aris dispersion formula in counterflow ITP simulations provided only a rough estimate of the dispersion, e.g., overestimation of analyte zone widths. Experiments on counterflow ITP were conducted in a silica capillary that was covalently and dynamically coated to exclude electroosmosis effect. The counterflow was generated by adjusting the relative height of the fluids in the two reservoirs at the capillary ends. Good qualitative agreement between simulations and experiments was found.     

Electropolymerized o‐Phenylenediamine on Graphite Promoting the Electrochemical Detection of Nafcillin

By combining molecular modelling and electrochemistry we envision the creation of modified electrodes tailored for a more sensitive and selective detection of a single analyte. In this study we report on a graphite screen printed electrode modified with electropolymerized o‐phenylenediamine, selected by rational design, which promotes the detection of nafcillin (NAF), an antibiotic. Parameters such as monomer concentration, pH and number of electropolymerization cycles were optimized to obtain the highest current signal for the target upon amperometric detection. NAF identification was based on the redox process at +1.1 V (vs pseudo Ag), ascribed to the oxidation of the C‐7 side chain. With the optimized modification protocol, a two‐fold increase in nafcillin signal could be obtained: the calibration plot in 0.1 M Britton‐Robinson buffer pH 4 showed a limit of detection of 80 nM with improved sensitivity and reproducibility (RSD<5 %) compared to the detection at non‐modified electrodes.     

Framework-Hotspot Enhanced Trans Cleavage of CRISPR-Cas12a for Clinical Samples Detection

The trans-cleavage property of CRISPR-Cas12a system makes it an excellent tool for disease diagnosis. Nevertheless, most methods based on CRISPR-Cas system still require pre-amplification of the target to achieve the desired detection sensitivity. Here we generate Framework-Hotspot reporters (FHRs) with different local densities to investigate their effect on trans-cleavage activity of Cas12a. We find that the cleavage efficiency increases and the cleavage rate accelerates with increasing reporter density. We further construct a modular sensing platform with CRISPR-Cas12a-based target recognition and FHR-based signal transduction. Encouragingly, this modular platform enables sensitive (100 fM) and rapid (<15 min) detection of pathogen nucleic acids without pre-amplification, as well as detection of tumor protein markers in clinical samples. The design provides a facile strategy for enhanced trans cleavage of Cas12a, which accelerates and broadens its applications in biosensing.     

An Electrochemical DNA Biosensor for the Detection of the Apa I Polymorphism in the Vitamin D Receptor Gene Using Meldola's Blue as a Hybridization Indicator

Electrochemical detection of nucleic acid base mismatches related to Apa I single nucleotide polymorphism (SNP) in the vitamin D receptor gene was performed successfully using 7‐dimethyl‐amino‐1,2‐benzophenoxazinium salt (Meldola's blue, MDB) with 10.9 pmol/100 μL of detection limit. MDB reduction signals obtained from probe, mismatch(probe‐SNP containing target) and hybrid(probe‐target) modified pencil graphite electrode(PGE) increased respectively. The sensor was able to clearly distinguish perfect match from mismatch DNA in a 30 min. detection time. Several factors affecting on the hybridization and indicator response are studied to maximize sensitivity and selectivity. The advantages of the biosensor are discussed in comparison with previous electrochemical assays for DNA hybridization.