Fast parallel detection of feline panleukopenia virus DNA by multi‐channel microchip electrophoresis with programmed step electric field strength

A multi‐channel microchip electrophoresis using a programmed step electric field strength (PSEFS) method was investigated for fast parallel detection of feline panleukopenia virus (FPV) DNA. An expanded laser beam, a 10× objective lens, and a charge‐coupled device camera were used to simultaneously detect the separations in three parallel channels using laser‐induced fluorescence detection. The parallel separations of a 100‐bp DNA ladder were demonstrated on the system using a sieving gel matrix of 0.5% poly(ethylene oxide) (M_r = 8 000 000) in the individual channels. In addition, the PSEFS method was also applied for faster DNA separation without loss of resolving power. A DNA size marker, FPV DNA sample, and a negative control were simultaneously analyzed with single‐run and one‐step detection. The FPV DNA was clearly distinguished within 30 s, which was more than 100 times faster than with conventional slab gel electrophoresis. The proposed multi‐channel microchip electrophoresis with PSEFS was demonstrated to be a simple and powerful diagnostic method to analyze multiple disease‐related DNA fragments in parallel with high speed, throughput, and accuracy.     

A microfluidic chip‐based fluorescent biosensor for the sensitive and specific detection of label‐free single‐base mismatch via magnetic beads‐based “sandwich” hybridization strategy

A novel microfluidic chip‐based fluorescent DNA biosensor, which utilized the electrophoretic driving mode and magnetic beads‐based “sandwich” hybridization strategy, was developed for the sensitive and ultra‐specific detection of single‐base mismatch DNA in this study. In comparison with previous biosensors, the proposed DNA biosensor has much more robust resistibility to the complex matrix of real saliva and serum samples, shorter analysis time, and much higher discrimination ability for the detection of single‐base mismatch. These features, as well as its easiness of fabrication, operation convenience, stability, better reusability, and low cost, make it a promising alternative to the SNPs genotyping/detection in clinical diagnosis. By using the biosensor, we have successfully determined oral cancer‐related DNA in saliva and serum samples without sample labeling and any preseparation or dilution with a detection limit of 5.6 × 10^?11 M, a RSD (n = 5) < 5% and a discrimination factor of 3.58–4.54 for one‐base mismatch.     

Development of a ligase detection reaction/CGE method using a LIF dual‐channel detection system for direct identification of allelic composition of mutated DNA in a mixed population of excess wild‐type DNA

We developed an inexpensive LIF dual‐channel detection system and applied it to a ligase detection reaction (LDR)/CGE method to identify the allelic composition of low‐abundance point mutations in a large excess of wild‐type DNA in a single reaction with a high degree of certainty. Ligation was performed in a tube with a nonlabeled common primer and multiplex discriminating primers, each labeled with a different standard fluorophore. The discriminating primers were directed against three mutant variations in codon 12 of the K‐ras oncogene that have a high diagnostic value for colorectal cancer. LDR products generated from a particular K‐ras mutation through successful ligation events were separated from remaining discriminating primers by CGE, followed by LIF detection using the new system, which consists of two photomultiplier tubes, each with a unique optical filter. Each fluorophore label conjugated to the corresponding LDR product produced a distinct fluorescence signal intensity ratio from the two detection channels, allowing spectral discrimination of the three labels. The ability of this system to detect point mutations in a wild‐type sequence‐dominated population, and to disclose their allelic composition, was thus demonstrated successfully.     

Ultrasensitive and Signal‐on Electrochemiluminescence Aptasensor Using the Multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin Complexes

An ultrasensitive and signal‐on electrochemiluminescence (ECL) aptasensor to detect target protein (thrombin or lysozyme) was developed using the host‐guest recognition between a metallocyclodextrin complex and single‐stranded DNA (ss‐DNA). The aptasensor uses both the photoactive properties of the metallocyclodextrins named multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin complexes and their specific recognition with ss‐DNA, which amplified the ECL signal without luminophore labeling. After investigating the ECL performance of different multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin (multi‐Ru‐β‐CD) complexes, tris‐tris(bipyridine)‐ruthenium(II)‐β‐cyclodextrin (tris(bpyRu)‐β‐CD) was selected as a suitable host molecule to construct an atasensor. First, double‐stranded DNA (ds‐DNA) formed by hybridization of the aptamer and its target DNA was attached to a glassy carbon electrode via coupling interaction, which showed low ECL intensity with 2‐(dibutylamino) ethanol (DBAE) as coreactant, because of the weak recognition between ds‐DNA and tris(bpyRu)‐β‐CD. Upon addition of the corresponding protein, the ECL intensity increased when target ss‐DNA was released because of the higher stability of the aptamer‐protein complex than the aptamer‐DNA one. A linear relationship was observed in the range of 0.01 pmol/L to 100 pmol/L between ECL intensity and the logarithm of thrombin concentrations with a limited detection of 8.5 fmol/L (S/N=3). Meanwhile, the measured concentration of lysozyme was from 0.05 pmol/L to 500 pmol/L and the detection limit was 33 fmol/L (S/N=3). The investigations of proteins in human serum samples were also performed to demonstrate the validity of detection in real clinical samples. The simplicity, high sensitivity and specificity of this aptasensor show great promise for practical applications in protein monitoring and disease diagnosis.     

Rapid Electrochemical Assessment of Tumor Suppressor Gene Methylations in Raw Human Serum and Tumor Cells and Tissues Using Immunomagnetic Beads and Selective DNA Hybridization

We report a rapid and sensitive electrochemical strategy for the detection of gene‐specific 5‐methylcytosine DNA methylation. Magnetic beads (MBs) modified with an antibody for 5‐methylcytosines (5‐mC) are used for the capture of any 5‐mC methylated single‐stranded (ss)DNA sequence. A flanking region next to the 5‐mCs of the captured methylated ssDNA is recognized by hybridization with a synthetic biotinylated DNA sequence. Amperometric transduction at disposable screen‐printed carbon electrodes (SPCEs) is employed. The developed biosensor has a dynamic range from 3.9 to 500 pm and a limit of detection of 1.2 pm for the methylated synthetic sequence of the tumor suppressor gene O‐6‐methylguanine‐DNA methyltransferase (MGMT) promoter region. The method is applied in the 45‐min analysis of specific methylation in the MGMT promoter region directly in raw spiked human serum samples and in genomic DNA extracted from U‐87 glioblastoma cells and paraffin‐embedded brain tumor tissues without any amplification and pretreatment step.     

Fabrication of a Sensitive Electrochemical Biosensor for Detection of DNA Hybridization Based on Gold Nanoparticles/CuO Nanospindles Modified Glassy Carbon Electrode

In this work, a sensitive electrochemical DNA biosensor for the detection of sequence‐specific target DNA was reported. Firstly, CuO nanospindles (CuO NS) were immobilized on the surface of a glassy carbon electrode (GCE). Subsequently, gold nanoparticles (Au NPs) were introduced to the surface of CuO NS by the electrochemical deposition mode. Probe DNA with SH (HS‐DNA) at the 5′‐phosphate end was covalently immobilized on the surface of the Au NPs through Au? S bond. Scanning electron microscopy (SEM) was used to elucidate the morphology of the assembled film, and electrochemical impedance spectroscopy technique (EIS) was used to investigate the DNA sensor assembly process. Hybridization detection of DNA was performed with differential pulse voltammetry (DPV) and the methylene blue (MB) was hybridization indicator. Under the optimal conditions, the decline of reduction peak current of MB (ΔI) was linear with the logarithm of the concentration of complementary DNA from 1.0×10^?13 to 1.0×10^?6 mol·L^?1 with a detection limit of 3.5×10^?14 mol·L^?1 (S/N=3). In addition, this DNA biosensor has good selectivity, and even can distinguish single‐mismatched target DNA.     

Rapid and sensitive DNA target detection using enzyme amplified electrochemical detection based on microchip

A rapid and sensitive DNA targets detection using enzyme amplified electrochemical detection (ED) based on microchip was described. We employed a biotin‐modified DNA, which reacted with avidin‐conjugated horseradish peroxidase (avidin–HRP) to obtain the HRP‐labeled DNA probe and hybridized with its complementary target. After hybridization, the mixture containing dsDNA‐HRP, excess ssDNA‐HRP, and remaining avidin–HRP was separated by MCE. The separations were performed at a separation voltage of +1.6 kV and were completed in less than 100 s. The HRP was used as catalytic labels to catalyze H₂O₂/o‐aminophenol reaction. Target DNA could be detected by the HRP‐catalyzed reduction with ED. With this protocol, the limits of quantification for the hybridization assay of 21‐ and 39‐mer DNA fragments were of 8×10^?12 M and 1.2×10^?11 M, respectively. The proposed method has been applied satisfactorily in the analysis of Escherichia coli genomic DNA. We selected the detection of PCR amplifications from the gene of E. coli to test the real applicability of our method. By using an asymmetric PCR protocol, we obtained ssDNA targets of 148 bp that could be directly hybridized by the single‐stranded probe and detected with ED.     

Impact of Single Basepair Mismatches on Electron‐Transfer Processes at Fc‐PNA⋅DNA Modified Gold Surfaces

Gold‐surface grafted peptide nucleic acid (PNA) strands, which carry a redox‐active ferrocene tag, present unique tools to electrochemically investigate their mechanical bending elasticity based on the kinetics of electron‐transfer (ET) processes. A comparative study of the mechanical bending properties and the thermodynamic stability of a series of 12‐mer Fc‐PNA?DNA duplexes was carried out. A single basepair mismatch was integrated at all possible strand positions to provide nanoscopic insights into the physicochemical changes provoked by the presence of a single basepair mismatch with regard to its position within the strand. The ET processes at single mismatch Fc‐PNA?DNA modified surfaces were found to proceed with increasing diffusion limitation and decreasing standard ET rate constants k⁰ when the single basepair mismatch was dislocated along the strand towards its free‐dangling Fc‐modified end. The observed ET characteristics are considered to be due to a punctual increase in the strand elasticity at the mismatch position. The kinetic mismatch discrimination with respect to the fully‐complementary duplex presents a basis for an electrochemical DNA sensing strategy based on the Fc‐PNA?DNA bending dynamics for loosely packed monolayers. In a general sense, the strand elasticity presents a further physicochemical property which is affected by a single basepair mismatch which may possibly be used as a basis for future DNA sensing concepts for the specific detection of single basepair mismatches.     

Direct Detection of DNA and DNA‐Ligand Interaction by Impedance Spectroscopy

In this work we present an impedimetric detection system for DNA‐ligand interactions. The sensor system consists of thiol‐modified single‐stranded DNA chemisorbed to gold. Impedance measurements in the presence of the redox system ferri‐/ferrocyanide show an increase in charge transfer resistance (R_ct) after hybridisation of a complementary target. Different amounts of capture strands, used for gold electrode modification, result in surface coverages between 3 and 15 pmol/cm² ssDNA. The relative change in R_ct upon hybridisation increases with increasing amount of capture probe on the electrode from 1.5‐ to 4.5‐fold. Impedimetric detection of binding events of a metal‐intercalator ([Ru(phen)₃]²⁺) and a groove binder (spermine) to double‐stranded DNA is demonstrated. Binding of [Ru(phen)₃]²⁺ and spermine exhibits a decrease in charge transfer resistance. Here, the ligand’s interaction leads to electrostatic shielding of the negatively charged DNA backbone. The impedance changes have been evaluated in dependence on the concentration of both DNA binders. Furthermore, the association of a single‐stranded binding protein (SSBP) is found to cause an increase in charge transfer resistance only when incubated with single‐stranded DNA. The specific binding of an anti‐dsDNA antibody to the dsDNA‐modified electrode surface decreases in contrast the interfacial impedance.     

MALDI‐MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single‐stranded DNA‐binding protein

The Escherichia coli single‐stranded DNA binding protein (SSB) selectively binds single‐stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB?ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross‐linking, combined with high‐mass matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB?ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19 100) can be detected with standard MALDI‐MS. With chemical cross‐linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79 500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB?ssDNA complex at m/z 94 200 even in the absence of chemical cross‐linking. The stability of the SSB?ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB?ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB?ssDNA complex is how ssDNA binds to SSB, rather than the protein‐to‐DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non‐specific aggregation in the MALDI plume. Copyright © 2012 John Wiley & Sons, Ltd.     

Electrochemical Detection of DNA Hybridization Based on the Probe Labeled with Carbon‐Nanotubes Loaded with Silver Nanoparticles

A sensitive electrochemical method for the detection of DNA hybridization based on the probe labeled with multiwall carbon‐nanotubes (MWNTs) loaded with silver nanoparticles (Ag‐MWNTs) has been developed. MWNTs were electroless‐plated with a large number of silver nanoparticles to form Ag‐MWNTs. Probe single strand DNA (ss‐DNA) with a thiol group at the 3′‐terminal labeled with Ag‐MWNTs by self‐assembled monolayer (SAM) technique was employed as an electrochemical probe. Target ss‐DNA with a thiol group was immobilized on a gold electrode by SAM technique and then hybridized with the electrochemical probe. Binding events were monitored by differential pulse voltammetric (DPV) signal of silver nanoparticles. The signal difference permitted to distinguish the match of two perfectly complementary DNA strands from the near perfect match where just three base pairs were mismatched. There was a linear relation between the peak current at +120 mV (vs. SCE) and complementary target ss‐DNA concentration over the range from 3.1×10^?14 to 1.0×10^?11 mol/L with a detection limit of 10 fmol/L of complementary target ss‐DNA. The proposed method has been successfully applied to detection of the DNA sequence related to cystic fibrosis. This work demonstrated that the MWNTs loaded with silver nanoparticles offers a great promising approach for sensitive detection of DNA hybridization.     

Development of a targeted adductomic method for the determination of polycyclic aromatic hydrocarbon DNA adducts using online column‐switching liquid chromatography/tandem mass spectrometry

Human exposure to polycyclic aromatic hydrocarbons (PAHs) from sources such as industrial or urban air pollution, tobacco smoke and cooked food is not confined to a single compound, but instead to mixtures of different PAHs. The interaction of different PAHs may lead to additive, synergistic or antagonistic effects in terms of DNA adduct formation and carcinogenic activity resulting from changes in metabolic activation to reactive intermediates and DNA repair. The development of a targeted DNA adductomic approach using liquid chromatography/tandem mass spectrometry (LC/MS/MS) incorporating software‐based peak picking and integration for the assessment of exposure to mixtures of PAHs is described. For method development PAH‐modified DNA samples were obtained by reaction of the anti‐dihydrodiol epoxide metabolites of benzo[a]pyrene, benzo[b]fluoranthene, dibenzo[a,l]pyrene (DB[a,l]P) and dibenz[a,h]anthracene with calf thymus DNA in vitro and enzymatically hydrolysed to 2′‐deoxynucleosides. Positive LC/electrospray ionisation (ESI)‐MS/MS collision‐induced dissociation product ion spectra data showed that the majority of adducts displayed a common fragmentation for the neutral loss of 116 u (2′‐deoxyribose) resulting in a major product ion derived from the adducted base. The exception was the DB[a,l]P dihydrodiol epoxide adduct of 2′‐deoxyadenosine which resulted in major product ions derived from the PAH moiety being detected. Specific detection of mixtures of PAH‐adducted 2′‐deoxynucleosides was achieved using online column‐switching LC/MS/MS in conjunction with selected reaction monitoring (SRM) of the [M+H]⁺ to [M+H–116]⁺ transition plus product ions derived from the PAH moiety for improved sensitivity of detection and a comparison was made to detection by constant neutral loss scanning. In conclusion, different PAH DNA adducts were detected by employing SRM [M+H–116]⁺ transitions or constant neutral loss scanning. However, for improved sensitivity of detection optimised SRM transitions relating to the PAH moiety product ions are required for certain PAH DNA adducts for the development of targeted DNA adductomic methods. Copyright © 2010 John Wiley & Sons, Ltd.     

Electrochemical DNA Biosensor Based on Magnetite/Multiwalled Carbon Nanotubes/Chitosan Nanocomposite for Bacillus Cereus Detection of Potential Marker for Gold Prospecting

A label‐free DNA biosensor based on magnetite/multiwalled carbon nanotubes/chitosan (Fe₃O₄/MWCNTs‐COOH/CS) nanomaterial for detection of Bacillus cereus DNA sequences was fabricated. Negatively charged DNA was electrostatically adsorbed onto materials by protonation of positively charged chitosan under acidic conditions. The electrode surface and hybridization process were carried out by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). Under optimal conditions, the biosensor showed a good linear relationship between peak currents difference (ΔI) and logarithm of the target DNA concentration (Log C) ranging from 2.0×10⁻¹³ to 2.0×10⁻⁶ M with a detection limit of 2.0×10⁻¹⁵ M (signal/noise ratio of 3). The biosensor also revealed an excellent selectivity to three‐base, completely mismatched and completely matched DNA. This is a simple, fast and friendly method with a low detection limit for the detection of Bacillus cereus specific DNA compared with previously reported electrochemical DNA biosensor. Furthermore, the DNA biosensor may lead to the development of a technology for gold prospecting in the wild.     

New Electroactive Hybridization Indicators 2‐Phthalimido‐N‐Substitutedphenylethanesulfonamide Derivatives for Biosensor Applications: Ring Substituent Effect on Interaction between Compound and DNA

In this work, an electrochemical DNA‐based sensor was developed for the detection of the interaction between the anticonvulsant compounds 2‐phthalimido‐N‐substituted phenylethanesulfonamides (PMPES‐derivatives) and 24‐mer short DNA sequences by using differential pulse voltammetry (DPV) based on both compound and guanine oxidation signals at the renewable carbon graphite electrode (CGE) surface. The influence of compounds on DNA showed differences depending on the nature and position of the substituent on the N‐phenyl ring. Compounds bearing 3‐methoxy, 4‐chloro and 2,6‐dimethyl substituents bind to single stranded probe DNA more strongly than the other derivatives of PMPES. Thus, these compounds were evaluated for use as an electrochemical hybridization label (indicator).     

Quantitative Detection of G‐Quadruplex DNA in Live Cells Based on Photon Counts and Complex Structure Discrimination

G‐quadruplex DNA show structural polymorphism, leading to challenges in the use of selective recognition probes for the accurate detection of G‐quadruplexes in vivo. Herein, we present a tripodal cationic fluorescent probe, NBTE , which showed distinguishable fluorescence lifetime responses between G‐quadruplexes and other DNA topologies, and fluorescence quantum yield (Φ_f) enhancement upon G‐quadruplex binding. We determined two NBTE ‐G‐quadruplex complex structures with high Φ_f values by NMR spectroscopy. The structures indicated NBTE interacted with G‐quadruplexes using three arms through π–π stacking, differing from that with duplex DNA using two arms, which rationalized the higher Φ_f values and lifetime response of NBTE upon G‐quadruplex binding. Based on photon counts of FLIM, we detected the percentage of G‐quadruplex DNA in live cells with NBTE and found G‐quadruplex DNA content in cancer cells is 4‐fold that in normal cells, suggesting the potential applications of this probe in cancer cell detection.     

Duplex‐Selective Ruthenium‐Based DNA Intercalators

We report the design and synthesis of small molecules that exhibit enhanced luminescence in the presence of duplex rather than single‐stranded DNA. The local environment presented by a well‐known [Ru(dipyrido[3,2‐a:2′,3′‐c]phenazine)L₂]²⁺‐based DNA intercalator was modified by functionalizing the bipyridine ligands with esters and carboxylic acids. By systematically varying the number and charge of the pendant groups, it was determined that decreasing the electrostatic interaction between the intercalator and the anionic DNA backbone reduced single‐strand interactions and translated to better duplex specificity. In studying this class of complexes, a single Ru^II complex emerged that selectively luminesces in the presence of duplex DNA with little to no background from interacting with single‐stranded DNA. This complex shows promise as a new dye capable of selectively staining double‐ versus single‐stranded DNA in gel electrophoresis, which cannot be done with conventional SYBR dyes.     

Single‐gap Microelectrode Functionalized with Single‐walled Carbon Nanotubes and Pbzyme for the Determination of Pb2+

Lead is a highly toxic metal, which can persist in the natural environment and enrich in biological bodies. It can cause many severe diseases in the human body even at extremely low concentration. Here, we developed a new biosensor using single‐walled carbon nanotubes (SWNTs) modified with a specific Pbzyme (Pbzyme/SWNTs/FET) to detect lead ion (Pb²⁺), which can monitor the lead pollution. This biosensor used 3‐aminopropyltriethoxysilane to immobilize SWNTs on the area between the source and the drain of single‐gap microelectrode (FET), and the duplex DNA (Pbzyme) consisted of DNAzyme (GR‐5) and complementary DNA (CS‐DNA) was functionalized with the SWNTs’ surface through a peptide bond. The use of GR‐5 DANzyme and Pb²⁺ to form a stable complex structure to cleave the CS‐DNA can change radically the Pbzyme's structure on the SWNTs’ surface, which will further affect the number of carriers in SNWTs and the conductivity of the Pbzyme/SWNTs/FET. The change in conductivity can be used to evaluate the Pb²⁺ concentration. Under the optimal conditions, the relative resistances presented a positive correlation with the Pb²⁺ concentrations, showing a good linear relationship in the range of 10 pM to 50 nM, where the linear regression equation was y=10.104log [C_Pb]+5.8656, and the detection limit was 7.4 pM. Finally, the biosensor was applied to measure the Pb²⁺ contents in the soil collected from the forest grass green belt and paint, and the results were compared with the results of atomic fluorescence spectrometry.     

Electrochemical Detection of Activated Protein C Using an Aptasensor Based on PAMAM Dendrimer Modified Pencil Graphite Electrodes

Electrochemical aptasensing of APC was carried out using PAMAM dendrimer modified pencil graphite electrodes (PGEs) for the first time herein. Poly(amidoamine) dendrimer having 16 succinamic acid surface groups (generation 2, G2‐PS) modified PGEs were developed, and then were utilized for APC monitoring using differential pulse voltammetry, electrochemical impedance spectroscopy and cyclic voltammetry. The selectivity of single‐use aptasensor was tested against to other proteins; BSA and THR as well as to the affinity of APC binding to different DNA aptamer, or oligonucleotide. Voltammetric APC detection was also explored in a diluted fetal bovine serum resulting with a detection limit DL as 1.5 µg/mL.     

Synthesis of bis-indole carboxamides as G-quadruplex stabilizing and inducing ligands

The design and synthesis of a series of bis‐indole carboxamides with varying amine containing side chains as G‐quadruplex DNA stabilising small molecules are reported. Their interactions with quadruplexes have been evaluated by means of Förster resonance energy transfer (FRET) melting analysis, UV/Vis spectroscopy, circular dichroism spectroscopy and molecular modelling studies. FRET analysis indicates that these ligands exhibit significant selectivity for quadruplex over duplex DNA, and the position of the carboxamide side chains is of paramount importance in G‐quadruplex stabilisation. UV/Vis titration studies reveal that bis‐indole ligands bind tightly to quadruplexes and show a three‐ to fivefold preference for c‐kit2 over h‐telo quadruplex DNA. CD studies revealed that bis‐indole carboxamide with a central pyridine ring induces the formation of a single, antiparallel, conformation of the h‐telo quadruplex in the presence and absence of added salt. The chirality of h‐telo quadruplex was transferred to the achiral ligand (induced CD) and the formation of a preferred atropisomer was observed.