Sandwich Hybridization Assay Research Articles

Panton-Valentine leukocidin and biofilm production of Staphylococcus aureus isolated from respiratory tract

Staphylococcus aureus is one of the first bacteria colonizing in cystic fibrosis (CF) respiratory tract and different virulence factors are responsible for disease progression. It is not clear if CF S. aureus strains are more virulent than strains isolated from non-CF patients. Biofilm production was detected by a modified tissue culture plate method, presence of genes encoding for Panton-Valentine leukocidin (PVL) was investigated by a signal amplified sandwich hybridization assay and antimicrobial susceptibility patterns were detected by disk diffusion method. Staphylococcus aureus clinical isolates (n = 88) recovered from respiratory tract specimens in which 31 of them were from cystic fibrosis (CF) patients were analysed. Biofilm production was detected in 96.8% of CF isolates in which 32.3% exhibited strong positive phenotype and in 47.4% of non-CF isolates in which strong positive phenotype was not observed (p <0.05). All CF isolates were methicillin susceptible, whereas 53.4% of non-CF isolates (n = 31) were methicillin resistant. No resistance was observed for vancomycin, chloramphenicol and trimethoprim/sulfamethoxazole in any of the isolates. PVL genes were detected only in two isolates (2.3%), one from each group, CF and non-CF, which both were methicillin susceptible. Biofilm rather than PVL production appears to be an important virulence factor in CF patients.

Gold-nanoparticle based electrochemical DNA sensor for the detection of fish pathogen Aphanomyces invadans

Epizootic ulcerative syndrome (EUS) is a devastating fish disease caused by the fungus, Aphanomyces invadans. Rapid diagnosis of EUS is needed to control and treat this highly invasive disease. The current diagnostic methods for EUS are labor intensive. We have developed a highly sensitive and specific electrochemical genosensor towards the 18S rRNA and internal transcribed spacer regions of A. invadans. Multiple layers of latex were synthesized with the help of polyelectrolytes, and labeled with gold nanoparticles to enhance sensitivity. The gold-latex spheres were functionalized with specific DNA probes. We describe here the novel application of this improved platform for detection of PCR product from real sample of A. invadans using a premix sandwich hybridization assay. The premix assay was easier, more specific and gave higher sensitivity of one log unit when compared to the conventional method of step-by-step hybridization. The limit of detection was 0.5 fM (4.99 zmol) of linear target DNA and 1 fM (10 amol) of PCR product. The binding positions of the probes to the PCR amplicons were optimized for efficient hybridization. Probes that hybridized close to the 5' or 3' terminus of the PCR amplicons gave the highest signal due to minimal steric hindrance for hybridization. The genosensor is highly suitable as a surveillance and diagnostic tool for EUS in the aquaculture industry.

Validation of a sandwich hybridization assay for marine copepod detection

The sandwich hybridization assay (SHA) is a rapid and robust RNA detection method for identifying and quantifying planktonic organisms in marine samples. Although tests for taxonomic specificity with pure cultures of target organisms yield encouraging results, the inevitable presence of non-target organisms in environmental samples might confound qualitative and quantitative aspects of the assay. This study examined the sensitivity of SHA to detect known quantities of cultured Tigriopus californicus (Copepoda: Podoplea) in environmental samples that contained naturally occurring copepods, other organisms, and unknown chemical backgrounds. SHA reliably detected culture-raised T. californicus in addition to naturally occurring podoplean copepods. Additionally, cultured Pseudo-nitzschia australis (Bacillariophyceae: Bacillariales), a harmful bloom-forming algal species typically found in water samples from the Monterey Bay, California, slightly enhanced SHA detection of T. californicus. Because SHA detects total RNA, factors that regulate RNA content within individuals may confound inferences about the number of copepods in a sample. Body size, physiological state, life-history stage, and gravidity of females all affected detectable levels of RNA in T. californicus individuals. For zooplankton taxa with complex life histories, the translation of molecular counts to quantities of individuals remains challenging.

High Affinity γPNA Sandwich Hybridization Assay for Rapid Detection of Short Nucleic Acid Targets with Single Mismatch Discrimination

Hybridization analysis of short DNA and RNA targets presents many challenges for detection. The commonly employed sandwich hybridization approach cannot be implemented for these short targets due to insufficient probe-target binding strengths for unmodified DNA probes. Here, we present a method capable of rapid and stable sandwich hybridization detection for 22 nucleotide DNA and RNA targets. Stable hybridization is achieved using an n-alkylated, polyethylene glycol γ-carbon modified peptide nucleic acid (γPNA) amphiphile. The γPNA's exceptionally high affinity enables stable hybridization of a second DNA-based probe to the remaining bases of the short target. Upon hybridization of both probes, an electrophoretic mobility shift is measured via interaction of the n-alkane modification on the γPNA with capillary electrophoresis running buffer containing nonionic surfactant micelles. We find that sandwich hybridization of both probes is stable under multiple binding configurations and demonstrate single base mismatch discrimination. The binding strength of both probes is also stabilized via coaxial stacking on adjacent hybridization to targets. We conclude with a discussion on the implementation of the proposed sandwich hybridization assay as a high-throughput microRNA detection method.

Meditating Metal Coenhanced Fluorescence and SERS Around Gold Nanoaggregates in Nanosphere as Bifunctional Biosensor for Multiple DNA Targets

Gold nanoparticles (Au NPs) are very attractive candidate nanoparticles in biological assay because of their high chemical stabilities, high homogeneities, good biocompatibilities, and low toxicities. However, molecular beacon assays via encapsulating the combined fluorescence or surface-enhanced Raman scattering (SERS) signals of reporters and Au NPs in nanobarcodes particles usually suffer from fluorescence quenching or weak Raman enhancement when Au NPs are employed (especially with size smaller than 15 nm). Herein, we present a new design of simultaneously realizing metal-enhanced fluorescence and coenhanced surface-enhanced Raman scattering by facilely embedding Ag nanoparticle into the shell of two kinds of Au nanoaggregate (5 and 10 nm), meanwhile, fluorophore is located between the silver core and gold nanoparticle layers and the distance among them is adjusted by SiO2 spacer (Ag@first SiO2 spacer@FiTC+SiO2@second SiO2 spacer@Au nanoaggregate). In this architecture, Ag nanoparticle not only is utilized as an efficient fluorescence enhancer to overcome the common fluorescence quenching around Au nanoaggregates but also behaves like a mirror. Thus, incident light that passes through the SERS-active Au nanoaggregate and the intervening dielectric layer of SiO2 could be reflected multiply from the surface of Ag nanoparticle and coupled with the light at the nanogap between the Au nanoaggregates to further amplify Raman intensity. This results in enhancement factors for fluorescence and SERS ~1.6-fold and more than 300-fold higher than the control samples without silver core under identical experimental conditions, respectively. Moreover, fluorophore and SERS reporters are assembled onto different layers of the concentric hybrid microsphere, resulting in a feasible fabrication protocol when a large number of agents need to be involved into the dual-mode nanobarcodes. A proof-of-concept chip-based DNA sandwich hybridization assay using genetically modified organisms as a model system has been investigated based on the concentric hybrid microsphere. The high specificity and sensitivity of the assays suggest that the new architecture has a potential for various bioanalytical applications and provides opportunities for other similar metal nanoparticles to realize coenhancement effect.

Development of taxonomic rRNA-targeted probes of two harmful algae: Prorocentrum minimum and Kareniamikimotoi by fluorescence in situ hybridization

Harmful algal blooms recently have been under the spotlight throughout the world, because of their negative impact on the marine environment, aquaculture, fisheries as well as public health. The development of methods for rapid and precise identification and quantification of causative species is essential for the warning andmonitoring of blooms, among which the techniques based on taxonomic probes are themost favored. In this study, two harmful algae, i.e., Prorocentrum minimum and Karenia mikimotoi were taken into consideration. The partial large subunit rDNA (D1-D2) of both species were firstly PCR-amplified, cloned and sequenced. The obtained sequences were then introduced to carry out alignment analysis for gene specific regions. Three respective candidate probes for each species were designed and used to screen the optimal probe by performing fluorescence in situ hybridization (FISH) tests. The results showed that the probes Pmin0443 and Kmik0602 displayed the best hybridization for P. minimum and K. mikimotoi, respectively. Both the specific (taxonomic) (Pmin0443 and Kmik0602) and the control probes (UniC0512 and UniR0499) were used for cross-reactivity tests with other microalgae in our laboratory. The probes Pmin0443 and Kmik0602 are specific and could be served as taxonomic probes introduced into the techniques targeting rRNA, such as FISH, sandwich hybridization, and DNA-microarray assay of P. minimum and K. mikimotoi in the future. Finally, FISH analyses with both probes were performed on the simulated field samples. The probes could hybridize exclusively with the target cells well, and no significant difference (p > 0.05) was observed in the cell densities of the samples determined by FISH and light microscopy (LM). All suggest that the probes are specific and could be introduced into FISH for the monitoring of both harmful algae.

A novel high throughput nucleic acid sandwich hybridization assay on a gold substrate

Biosensors will become increasingly important for medical diagnostics. An essential part of biosensor development is assay optimization; to find the optimal conditions a large number of variables need to be tested and high throughput online measurements are time-consuming or sometimes impossible. In this study, an offline high throughput nucleic acid sandwich hybridization assay is developed for pre-screening assay conditions on a gold substrate. The assay is performed in a 48-well plate using alkanethiolated ssDNA molecules, which bind to the substrate surface through a specific thiol–gold interaction and function as the recognition site for target DNA. The hybridization reaction was analyzed using an enzymatic read-out system measuring DNA–DNA interactions in a highly specific and sensitive manner, since only fully complementary nucleotide sequences were detected with a lower limit of detection of 10 pmol l−1. This high throughput low cost offline method has been demonstrated to be flexible and is expected to improve and accelerate biosensor development.

The quantitative real-time PCR applications in the monitoring of marine harmful algal bloom (HAB) species

In the last decade, various molecular methods (e.g., fluorescent hybridization assay, sandwich hybridization assay, automatized biosensor detection, real-time PCR assay) have been developed and implemented for accurate and specific identification and estimation of marine toxic microalgal species. This review focuses on the recent quantitative real-time PCR (qrt-PCR) technology developed for the control and monitoring of the most important taxonomic phytoplankton groups producing biotoxins with relevant negative impact on human health, the marine environment, and related economic activities. The high specificity and sensitivity of the qrt-PCR methods determined by the adequate choice of the genomic target gene, nucleic acid purification protocol, quantification through the standard curve, and type of chemical detection method make them highly efficient and therefore applicable to harmful algal bloom phenomena. Recent development of qrt-PCR-based assays using the target gene of toxins, such as saxitoxin compounds, has allowed more precise quantification of toxigenic species (i.e., Alexandrium catenella) abundance. These studies focus only on toxin-producing species in the marine environment. Therefore, qrt-PCR technology seems to offer the advantages of understanding the ecology of harmful algal bloom species and facilitating the management of their outbreaks.

Effect of Tags and Labels on the Performance of Enzyme‐Amplified Electrochemical Genomagnetic Assays

AbstractA magnetic microsphere‐based hybridization assay for the electrochemical detection of pathogen‐specific DNA sequences is reported. Enzyme‐linked sandwich hybridization assays with different tags (biotin, fluorescein or digoxigenin) and enzyme conjugates (streptavidin‐alkaline phosphatase, streptavidin‐peroxidase, antifluorescein‐peroxidase or antidigoxigenin‐peroxidase) are comparatively evaluated. Sensitivity and limit of detection depend on both the choice of the enzyme and the tag. The highest sensitivity and lowest limit of detection were obtained when antibody Fab fragments conjugated to peroxidase were used as reporter molecule. The digoxigenin system yields the lowest detection limit, mainly due to producing much lower background signals.

Nucleic Acid Sandwich Hybridization Assay with Quantum Dot-Induced Fluorescence Resonance Energy Transfer for Pathogen Detection

This paper reports a nucleic acid sandwich hybridization assay with a quantum dot (QD)-induced fluorescence resonance energy transfer (FRET) reporter system. Two label-free hemagglutinin H5 sequences (60-mer DNA and 630-nt cDNA fragment) of avian influenza viruses were used as the targets in this work. Two oligonucleotides (16 mers and 18 mers) that specifically recognize two separate but neighboring regions of the H5 sequences were served as the capturing and reporter probes, respectively. The capturing probe was conjugated to QD655 (donor) in a molar ratio of 10:1 (probe-to-QD), and the reporter probe was labeled with Alexa Fluor 660 dye (acceptor) during synthesis. The sandwich hybridization assay was done in a 20 μL transparent, adhesive frame-confined microchamber on a disposable, temperature-adjustable indium tin oxide (ITO) glass slide. The FRET signal in response to the sandwich hybridization was monitored by a homemade optical sensor comprising a single 400 nm UV light-emitting diode (LED), optical fibers, and a miniature 16-bit spectrophotometer. The target with a concentration ranging from 0.5 nM to 1 μM was successfully correlated with both QD emission decrease at 653 nm and dye emission increase at 690 nm. To sum up, this work is beneficial for developing a portable QD-based nucleic acid sensor for on-site pathogen detection.

Review: advances in electrochemical genosensors-based methods for monitoring blooms of toxic algae

Harmful algal blooms (HABs), which have expanded worldwide in their occurrence and frequency, are a serious menace to aquatic ecosystems and humans. The development of rapid, accurate and cost-effective detection systems for toxic algal monitoring in aquatic environments is urgently required. Although many efforts have been devoted to develop reliable tools to monitor the entire spectrum of existing toxic algae, a portable semi-automated system that enables HAB monitoring at a low cost is still not available for general purchase. This work reviews the challenges and opportunities in translating the remarkable progress of electrochemical genosensors-based methods towards practical in situ HAB monitoring applications. It is specifically focused on reviewing the optimised methods for a detection system based on a sandwich hybridisation assay (SHA) performed over transducer platforms of different materials, geometries and dimensions and presenting the diverse advantages and disadvantages among them. Probe design and specificity and optimisation of the genosensor in terms of hybridisation conditions and electrochemical signal are discussed as well as their long-term stability and storage and semi-automation attempts. With continuous innovation and attention to key challenges, we expect semi-automatic devices containing DNA-based electrochemical biosensors to have an important impact upon monitoring of serious HAB events.

A novel and efficient assay for identification and quantification of Acidithiobacillus ferrooxidans in bioleaching samples

Acidithiobacillus ferrooxidans is a Gram-negative, acidophilic, and chemolithotrophic bacterium that is active in bioleaching. The leaching efficacy is directly influenced by the biomass changes of this specie in bioleaching microbial community. In order to perform a simple and sensitive assay on A. ferrooxidans from mixed strains in this process, a novel assay was developed based on sandwich hybridization assay with the aid of S1 nuclease treatment and fluorescent labeling. In the work, a designed DNA probe complementary to the conservative region of its 16S rRNA was synthesized, which showed high accuracy for distinguishing homologous species with the exclusion of even-only two base pairs difference. The specificity of this assay was verified in different systems with mixed strains, and the quantitative result was proved by comparison of microscopic cell counting. The detection sensitivity was about 8 × 10(2) cells/ml and the inter-assay coefficient of variation of three independent assays was from 3.8 to 7.7 %, respectively. In addition, the cycle of assay was about 3-4 h when the cost estimated was less than $0.5 per sample. This assay method might be applied for identifying and monitoring any kind of bacterial strain from a mixed microbial flora in bioleaching or other areas.

Identification and enumeration of Microcystis using a sandwich hybridization assay

Based on sequence analyses of phycocyanin intergenic spacers (PC-IGS) from Microcystis, Anabaena, Aphanizomenon, and Planktothrix (Oscillatoria) strains, a genus-specific probe pair TF/TR was designed, and a sandwich hybridization assay was established to quantitatively detect Microcystis. Through BLAST and cyanobacterial culture tests, TF/TR was demonstrated to be specific for Microcystis. A calibration curve for the sandwich hybridization assay was established, and the lowest detected concentration was 100 cell/ml. Laboratory and field samples were analyzed with both sandwich hybridization assay and microscopy. The biotic and abiotic components of the samples were of little disturbance to the sandwich hybridization assay. The results showed no distinct difference between the two methods. In this study, a sandwich hybridization assay was established to detect Microcystis, providing an alternative to traditional microscopic, morphology-based methods.

Detection of microcystin-producingMicrocystisin Guanqiao Lake using a sandwich hybridization assay

Based on sequence analyses of the mcyJ gene from Microcystis strains, a probe pair TJF and TJR was designed and a sandwich hybridization assay (SHA) was established to quantitatively detect microcystin-producing Microcystis. Through BLAST and cyanobacterial culture tests, TJF and TJR were demonstrated to be specific for microcystin-producing Microcystis. A calibration curve for the SHA was established, and the lowest detected concentration was 100 cells·mL(-1). Laboratory cultures and field samples from Guanqiao Lake were analyzed with both the SHA and microscopy. The cell number of microcystin-producing Microcystis and that of total Microcystis were compared. The biotic and abiotic components of the samples were of little disturbance to the SHA. In this study, a SHA was established to detect Microcystis, providing an alternative to PCR-ELISA and real-time PCR technology.

Multiplexed SERS detection of DNA targets in a sandwich-hybridization assay using SERS-encoded core–shell nanospheres

In this study, a class of surface enhanced Raman spectroscopy (SERS) encoded core–shell nanospheres was synthesized as nano-SERS-tags for detecting specific DNA targets based on the sandwich hybridization assays. These core–shell nanospheres were synthesized by first depositing a layer of Ag-NPs (nanoparticles) onto the poly(styrene-co-acrylic acid) core and then the formation of a layer of uniform silica as the outer shell. The Ag-NPs served as SERS substrates with Raman active molecular probes adsorbed onto the Ag-NPs as indicative SERS molecular barcodes, and the silica coating shell was used for protecting the Ag-NPs and the Raman molecules from the exterior chemical and biological interference. The silica surfaces of nano-SERS-tags were further conjugated with probe DNA (pDNA) (nano-SERS-probes). The detection of single-stranded oligonucleotide (ssDNA) targets was successfully accomplished using the nano-SERS-probes in a chip-based sandwich hybridization assay in a mixed ssDNA target solution. The as-prepared nano-SERS-probes exhibited high chemical stability during the laser SERS experiments and the results were reproducible after a long-term storage. At least four different tags (a four “color” system) were quantitatively differentiated when simultaneously applied in the assays, indicating an excellent multiplexing potential of the method. Therefore, the as-prepared nano-SERS-probes are suitable for high specific detection of biomolecules with high sensitivity and remarkable multiplexing capability associated with the SERS method.

Robotic sampling, in situ monitoring and molecular detection of marine zooplankton

Recent advances in robotic technologies provide new opportunities to conduct high-resolution sampling of patchily distributed zooplankton and associated environmental variables. We used two robots and molecular probes to assess the temporal and spatial variability of zooplankton in water samples obtained from Monterey Bay, California. The Autonomous Underwater Vehicle (AUV) Dorado is a mobile platform that carries ten, 1.8-L bottles ("Gulpers") capable of rapidly acquiring discrete seawater samples, and an extensive sensor suite for gathering contextual environmental data during day-long expeditions. Molecular assays were conducted ex situ at a shore-based laboratory. In contrast, the Environmental Sample Processor (ESP) was deployed as a stationary (moored) device capable of repeatedly “sipping” water to conduct in situ molecular assays and record environmental data during month-long deployments. Molecular analyses were conducted with the sandwich hybridization assay (SHA), which employed 18S ribosomal RNA oligonucleotide probes designed to detect calanoid and podoplean copepods, and the larvae of barnacles, mussels, polychaete worms, brachyuran crabs, and invasive green crabs (Carcinus maenas). Both the stationary and mobile sampling protocols revealed the greatest zooplankton diversity and abundance in relatively warm waters, higher in chlorophyll and lower in salinity and nitrate. Diversity and abundance were least in recently upwelled waters with the inverse conditions. High-resolution sampling revealed that while calanoid copepods were generally associated with elevated chlorophyll, they were most abundant in upwelling fronts, in some cases. These narrow features appear to provide favorable conditions for the growth and aggregation of certain zooplankton.

Characterization of a Dipartite Iron Uptake System from Uropathogenic Escherichia coli Strain F11

In the uropathogenic Escherichia coli strain F11, in silico genome analysis revealed the dicistronic iron uptake operon fetMP, which is under iron-regulated control mediated by the Fur regulator. The expression of fetMP in a mutant strain lacking known iron uptake systems improved growth under iron depletion and increased cellular iron accumulation. FetM is a member of the iron/lead transporter superfamily and is essential for iron uptake by the Fet system. FetP is a periplasmic protein that enhanced iron uptake by FetM. Recombinant FetP bound Cu(II) and the iron analog Mn(II) at distinct sites. The crystal structure of the FetP dimer reveals a copper site in each FetP subunit that adopts two conformations: CuA with a tetrahedral geometry composed of His(44), Met(90), His(97), and His(127), and CuB, a second degenerate octahedral geometry with the addition of Glu(46). The copper ions of each site occupy distinct positions and are separated by ∼1.3 Å. Nearby, a putative additional Cu(I) binding site is proposed as an electron source that may function with CuA/CuB displacement to reduce Fe(III) for transport by FetM. Together, these data indicate that FetMP is an additional iron uptake system composed of a putative iron permease and an iron-scavenging and potentially iron-reducing periplasmic protein.

A Novel SERRS Sandwich-Hybridization Assay to Detect Specific DNA Target

In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR). In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method) with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.

Evaluation of probe orientation and effect of the digoxigenin-enzymatic label in a sandwich hybridization format to develop toxic algae biosensors

Biosensors, which use an electrochemical detection of a species by means of a sandwich hybridization assay (SHA) of the target sequence between a capture probe with an attachment label and a signal probe with a detection label, typically array the probes over an electrode surface. This arrangement is such that the modification of the capture probe is distal to the signal probe detection label in the 5′–3′ orientation of the RNA of the target species. This work reports on the proof of concept of a DNA-based device that uses SHA to anchor a target sequence on the surface of a transducer platform for sensing three different toxic algae. The probe orientation, the effect of a double DIG label and the use of a directly HRP-labelled signal probe on the electrochemical sensor performance are evaluated here. Results show that the electrochemical responses obtained for Prymnesium parvum and Gymnodinium catenatum with the thiol (biotin)-modified capture probe distal to the signal probe with a DIG label are comparable to those from Prymnesium parvum and Pseudo-nitzschia australis with the probes in a proximal orientation. Different probe orientations did not lead to significant improvement in signal intensity. A double DIG-enzymatic label and the use of a directly HRP-labelled signal probe did not led to further improvements in biosensor performance.

Application of a sandwich hybridisation assay for rapid detection of the Northern Pacific seastar, Asterias amurensis

A sandwich hybridisation assay (SHA) has been developed to detect Asterias amurensis (Lütken 1871), commonly known as the northern Pacific seastar, which is an unwanted, and as yet undetected, pest in New Zealand waters. Probes in SHA format have been developed that target the ribosomal RNA internal transcribed spacer region of A. amurensis. The successful assay utilises the capture probe ITS-C2-110 and the combined signal probes ITS-S1-93 and ITS-S3-240. It has been successfully tested for specificity, including cross-reactivity testing against the common and related seastars, Patiriella regularis (Verrill 1867), P. mortenseni (O'Loughlin et al. 2002), Coscinasterias muricata (Verrill 1867) and Stichaster australis (Verrill 1871). The SHA is a rapid and potentially portable RNA-based test, and opens up the opportunity for direct analysis of water samples, for example, portside during surveillance of marine pests.