A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry

PBS-DLS: A Novel Ultrasensitive Dynamic Light Scattering Immunoassay

Despite significant advances in ultrasensitive detection, current methodologies are often hindered by the need for sophisticated equipment, complex signal amplification processes, and specialized operation. Here, we have developed a novel strategy by universal polyvalent biotin-streptavidin cross-linking aggregation coupled with dynamic light scattering (PBS-DLS) that effectively transduces and amplifies undetected molecular recognition events at low target concentrations, demonstrating its potential application as an ultrasensitive immunoassay. The controllability in the size and quantity of the DLS nanoprobe enables this advanced design to achieve tunable sensitivity down to attomolar levels and a broad detection range spanning six orders of magnitude. By reducing the detection time to approximately 15 min, our PBS-DLS emerges as a promising tool for point-of-care (POC) testing. Moreover, this PBS-DLS immunosensor has been validated through its rapid and ultrasensitive detection of the SARS-CoV-2 nucleocapsid (N) protein (a macromolecular model target) and malachite green (MG, a small molecule model target) in complex sample matrices, outperforming conventional immunoassays and other testing methods. The exceptional sensitivity, simplicity, and speed of this novel approach position it as a highly promising platform for the development of various bioanalytical methods and POC assays.

Comprehensive Transcriptome Analysis Uncovers Hub Long Non-coding RNAs Regulating Potassium Use Efficiency in Nicotiana tabacum

Potassium (K) is the essential element for plant growth. It is one of the critical factors that determine crop yield, quality, and especially leaf development in tobacco. However, the molecular mechanism of potassium use efficiency (KUE), especially non-coding RNA, is still unknown. In this study, tobacco seedlings were employed, and their hydro-cultivation with K treatments of low and sufficient concentrations was engaged. Physiological analysis showed that low potassium treatment could promote malondialdehyde (MDA) accumulation and antioxidant enzyme activities such as peroxidase (POD), ascorbate-peroxidase (APX). After transcriptomic analysis, a total of 10,585 LncRNA transcripts were identified, and 242 of them were significantly differently expressed under potassium starvation. Furthermore, co-expression networks were constructed and generated 78 potential regulation modules in which coding gene and LncRNAs are involved and functional jointly. By further module-trait analysis and module membership (MM) ranking, nine modules, including 616 coding RNAs and 146 LncRNAs, showed a high correlation with K treatments, and 20 hub K-responsive LncRNAs were finally predicted. Following gene ontology (GO) analysis, the results showed potassium starvation inducing the pathway of antioxidative stress which is consistent with the physiology result mentioned above. Simultaneously, a part of detected LncRNAs, such as MSTRG.6626.1, MSTRG.11330.1, and MSTRG.16041.1, were co-relating with a bench of MYB, C3H, and NFYC transcript factors in response to the stress. Overall, this research provided a set of LncRNAs that respond to K concentration from starvation and sufficient supply. Simultaneously, the regulation network and potential co-functioning genes were listed as well. This massive dataset would serve as an outstanding clue for further study in tobacco and other plant species for nutrient physiology and molecular regulation mechanism.

Preparation of fluorescence-encoded microbeads with large encoding capacities and application of suspension array technology

This research study reported a type of reconstructed polystyrene microbeads for fluorescence encoding in suspension array technology (SAT). The present study improved their surface functionalization and compatibility with dyes.

Electrophoretic mobility shift as a molecular beacon-based readout for miRNA detection

MicroRNAs are short, non-coding RNA sequences involved in gene expression regulation. Quantification of miRNAs in biological fluids involves time consuming and laborious methods such as Northern blotting or PCR-based techniques. Molecular beacons (MB) are an attractive means for rapid detection of miRNAs, although the need for sophisticated readout methods limits their use in research and clinical settings. Here, we introduce a novel method based on delayed electrophoretic mobility, as a quantitative means for detection of miRNAs-MB hybridization. Upon hybridization with the target miRNAs, MB form a fluorescent duplex with reduced electrophoretic mobility, thus bypassing the need for additional staining. In addition to emission of light, the location of the fluorescent band on the gel acts as an orthogonal validation of the target identity, further confirming the specificity of binding. The limit of detection of this approach is approximately 100 pM, depending on the MB sequence. The method is sensitive enough to detect specific red blood cell miRNAs molecules in total RNA, with single nucleotide specificity. Altogether, we describe a rapid and affordable method that offers sensitive detection of single-stranded small DNA and RNA sequences.

Optical Biosensor Platforms Display Varying Sensitivity for the Direct Detection of Influenza RNA

Detection methods that do not require nucleic acid amplification are advantageous for viral diagnostics due to their rapid results. These platforms could provide information for both accurate diagnoses and pandemic surveillance. Influenza virus is prone to pandemic-inducing genetic mutations, so there is a need to apply these detection platforms to influenza diagnostics. Here, we analyzed the Fast Evaluation of Viral Emerging Risks (FEVER) pipeline on ultrasensitive detection platforms, including a waveguide-based optical biosensor and a flow cytometry bead-based assay. The pipeline was also evaluated in silico for sequence coverage in comparison to the U.S. Centers for Disease Control and Prevention's (CDC) influenza A and B diagnostic assays. The influenza FEVER probe design had a higher tolerance for mismatched bases than the CDC's probes, and the FEVER probes altogether had a higher detection rate for influenza isolate sequences from GenBank. When formatted for use as molecular beacons, the FEVER probes detected influenza RNA as low as 50 nM on the waveguide-based optical biosensor and 1 nM on the flow cytometer. In addition to molecular beacons, which have an inherently high background signal we also developed an exonuclease selection method that could detect 500 pM of RNA. The combination of high-coverage probes developed using the FEVER pipeline coupled with ultrasensitive optical biosensors is a promising approach for future influenza diagnostic and biosurveillance applications.

Polystyrene Microparticles with Convergently Grown Mesoporous Silica Shells as a Promising Tool for Multiplexed Bioanalytical Assays

Functional core/shell particles are highly sought after in analytical chemistry, especially in methods suitable for single-particle analysis such as flow cytometry because they allow for facile multiplexed detection of several analytes in a single run. Aiming to develop a powerful bead platform of which the core particle can be doped in a straightforward manner while the shell offers the highest possible sensitivity when functionalized with (bio)chemical binders, polystyrene particles were coated with different kinds of mesoporous silica shells in a convergent growth approach. Mesoporous shells allow us to obtain distinctly higher surface areas in comparison with conventional nonporous shells. While assessing the potential of narrow- as well as wide-pore silicas such as Mobil composition of matter no. 41 (MCM-41) and Santa Barbara amorphous material no. 15 (SBA-15), especially the synthesis of the latter shells that are much more suitable for biomolecule anchoring was optimized by altering the pH and both, the amount and type of the mediator salt. Our studies showed that the best performing material resulted from a synthesis using neutral conditions and MgSO₄ as an ionic mediator. The analytical potential of the particles was investigated in flow cytometric DNA assays after their respective functionalization for individual and multiplexed detection of short oligonucleotide strands. These experiments revealed that a two-step modification of the silica surface with amino silane and succinic anhydride prior to coupling of an amino-terminated capture DNA (c-DNA) strand is superior to coupling carboxylic acid-terminated c-DNA to aminated core/shell particles, yielding limits of detection (LOD) down to 5 pM for a hybridization assay, using labeled complementary single-stranded target DNA (t-DNA) 15mers. The potential of the use of the particles in multiplexed analysis was shown with the aid of dye-doped core particles carrying a respective SBA-15 shell. Characteristic genomic sequences of human papillomaviruses (HPV) were chosen as the t-DNA analytes here, since their high relevance as carcinogens and the high number of different pathogens is a relevant model case. The title particles showed a promising performance and allowed us to unequivocally detect the different high- and low-risk HPV types in a single experimental run.

Nanobiosensors for the Detection of Novel Coronavirus 2019-nCoV and Other Pandemic/Epidemic Respiratory Viruses: A Review

The coronavirus disease 2019 (COVID-19) pandemic is considered a public health emergency of international concern. The 2019 novel coronavirus (2019-nCoV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused this pandemic has spread rapidly to over 200 countries, and has drastically affected public health and the economies of states at unprecedented levels. In this context, efforts around the world are focusing on solving this problem in several directions of research, by: (i) exploring the origin and evolution of the phylogeny of the SARS-CoV-2 viral genome; (ii) developing nanobiosensors that could be highly effective in detecting the new coronavirus; (iii) finding effective treatments for COVID-19; and (iv) working on vaccine development. In this paper, an overview of the progress made in the development of nanobiosensors for the detection of human coronaviruses (SARS-CoV, SARS-CoV-2, and Middle East respiratory syndrome coronavirus (MERS-CoV) is presented, along with specific techniques for modifying the surface of nanobiosensors. The newest detection methods of the influenza virus responsible for acute respiratory syndrome were compared with conventional methods, highlighting the newest trends in diagnostics, applications, and challenges of SARS-CoV-2 (COVID-19 causative virus) nanobiosensors.

Supramolecular Microgels with Molecular Beacons at the Interface for Ultrasensitive, Amplification-Free, and SNP-Selective miRNA Fluorescence Detection

In this study, a supramolecular structure with femtomolar biorecognition properties is proposed for use in analytical devices. It is obtained by an innovative interface between synthetic hydrogel polymers and molecular beacon (mb) probes. Supramolecularly structured microgels are synthetized with a core-shell architecture with specific dyes polymerized in a desired compartment. Mb probes are opportunely conjugated at the microgel interface so that their recognition mechanism is preserved and their spatial distribution is optimized to avoid crowding effects. The miR-21, a microRNA involved in various biological processes and usually used as a biomarker in early cancer diagnosis, has been selected as the target. The results demonstrate that by tuning the spatial distribution of molecular probes immobilized on the microgel and/or the amount of microgels, the assay shows scalable sensitivity reaching a limit of detection down to about 10 fM, without amplification steps and with detection time as short as 1 h. The assay results specific toward single mutated targets, and it is stable in the presence of high-interfering oligonucleotides concentrations. The miRNA target is also detected in human serum with performances similar to those observed in PBS buffer because of microgel antifouling properties without the need of any surface treatment. All tests were performed in a low sample volume (20 μL). As a result, mb-microgel represents an innovative biosensor to precisely quantify microRNAs in a direct (mix&read), scalable, and selective way. Such an approach paves the way for creating innovative biosensing interfaces with other probes, such as hairpins, aptamers, and PNA.

A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads

The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters.

Direct Screening for Cytometric Bead Assays for Adenosine Triphosphate

Cytometric bead assays have caught much attention because of their many exceptional advantages. Unfortunately, the immobilization of existing molecular recognition elements including monoclonal antibodies and aptamers onto solid particles may lead to the functional failure of the molecular recognition elements since they are generally obtained in free state. Herein we develop a powerful screening approach for direct and rapid discovery of aptamer based cytometric bead assays (AB-CBAs) by individually measuring the functional activity of every aptamer particles in a library and sorting them at rates of up to 10⁸ particles per hour. The strategy is based on the transformation of molecular libraries into pools of monoclonal aptamer particles so that one individual particle displays ∼10⁵ copies of an identical aptamer sequence. Our library design incorporates a two-color fluorescent reporter system in which changes in aptamer structure generate an optical readout, such that we can use fluorescence-activated cell sorting to rapidly and selectively separate the individual aptamer particles that exhibit large fluorescent signal change upon target binding. For demonstration, we isolated AB-CBA aptamer particles with high signaling performance for ATP after just 3 rounds of screening. We believe that the rapid and direct screening features of this strategy make it an excellent platform for generating AB-CBAs for for a wide range of important analytes.

Biotin-exposure-based immunomagnetic separation coupled with nucleic acid lateral flow biosensor for visibly detecting viable Listeria monocytogenes

Infectious diseases caused by Listeria monocytogenes pose a great threat to public health worldwide. Therefore, a rapid and efficient method for L. monocytogenes detection is needed. In this study, a biotin-exposure-based immunomagnetic separation (IMS) method was developed. That is, biotinylated antibody was first targeted to L. monocytogenes. Then, streptavidin-functionalized magnetic nanoparticles were added and anchored onto L. monocytogenes cells indirectly through the strong noncovalent interaction between streptavidin and biotin. Biotin-exposure-based IMS exhibited an excellent capability to enrich L. monocytogenes. Specifically, more than 90% of L. monocytogenes was captured when the bacterial concentration was lower than 10⁴ colony-forming units (CFU)/mL. Importantly, the antibody dosage was reduced by 10 times of that in our previous study, which used antibody direct-conjugated magnetic nanoparticles. Propidium monoazide (PMA) treatment prior to PCR amplification could eliminate the false-positive results from dead bacteria and detected viable L. monocytogenes sensitively and specifically. For viable L.monocytogenes detection, enriched L. monocytogenes was treated with PMA prior to asymmetric PCR amplification. The detection limits of the combined IMS with nucleic acid lateral flow (NALF) biosensor for viable L. monocytogenes detection were 3.5 × 10³ CFU/mL in phosphate buffer solution and 3.5 × 10⁴ CFU/g in lettuce samples. The whole assay process of recognizing viable L. monocytogenes was completed within 6 h. The proposed biotin-exposure-mediated IMS combined with a disposable NALF biosensor platform posed no health risk to the end user, and possessed potential applications in the rapid screening and identification of foodborne pathogens.

Site-specific one-pot triple click labeling for DNA and RNA

We report site-specific triple click labeling for DNA and RNA in a one-pot setup by performing inverse electron demand Diels–Alder reaction and strain-promoted and copper catalyzed click reactions sequentially.

Biomimetic Molecular Signaling using DNA Walkers on Microparticles

We report the release of catalytic DNA walkers from hydrogel microparticles and the detection of those walkers by substrate-coated microparticles. This might be considered a synthetic biology analog of molecular signal release and reception. One type of particles was coated with components of a DNA one-step strand displacement (OSD) reaction to release the walker. A second type of particle was coated with substrate (or "track") for the molecular walker. We distinguish these particle types using fluorescence barcoding: we synthesized and distinguished multiple particle types with multicolor fluorescence microscopy and automated image analysis software. This represents a step toward amplified, multiplex, and microscopically localized detection based on DNA nanotechnology.

Gene Specific DNA Sensors for Diagnosis of Pathogenic Infections

Gene specific DNA based sensors have potential applications for rapid and real time monitoring of hybridization signal with the target nucleic acid of pathogens. Different types of DNA based sensors and their applications have been studied for rapid and accurate detection of pathogens causing human diseases. These sensors are based on surface plasmon resonance, quantum-dots, molecular beacons, piezoelectric and electrochemical etc. Curbing epidemics at an early stage is one of the massive challenges in healthcare systems. Timely detection of the causative organism may provide a solution to restrain mortality caused by the disease. With the advent of interdisciplinary sciences, bioelectronics has emerged as an effective alternative for disease diagnostics. Gene specific DNA sensors present themselves as cost-effective, sensitive and specific platforms for detection of disease causing pathogens. The mini review explores different transducer based sensors and their potential in diagnosis of acute and chronic diseases.

Computational Biosensors: Molecules, Algorithms, and Detection Platforms

Advanced nucleic acid-based sensor-applications require computationally intelligent biosensors that are able to concurrently perform complex detection and classification of samples within an in vitro platform. Realization of these cutting-edge computational biosensor systems necessitates innovation and integration of three key technologies: molecular probes with computational capabilities, algorithmic methods to enable in vitro computational post processing and classification, and immobilization and detection approaches that enable the realization of deployable computational biosensor platforms. We provide an overview of current technologies, including our contributions towards the development of computational biosensor systems.

On-chip electromagnetic tweezers - 3-dimensional particle actuation using microwire crossbar arrays

Emerging miniaturization technologies for biological and bioengineering applications require precise control over position and actuation of microparticles. While many of these applications call for high-throughput approaches, common tools for particle manipulation, such as magnetic or optical tweezers, suffer from low parallelizability. To address this issue, we introduce a chip-based platform that enables flexible three-dimensional control over individual magnetic microparticles. Our system relies on microwire crossbar arrays for simultaneous generation of magnetic and dielectric forces, which actuate the particles along highly localized traps. We demonstrate the precise spatiotemporal control of individual particles by tracing complex trajectories in three dimensions and investigate the forces that can be generated along different axes. Furthermore, we show that our approach for particle actuation can be parallelized by simultaneously controlling the position and movement of 16 particles in parallel.

Polystyrene Core-Silica Shell Particles with Defined Nanoarchitectures as a Versatile Platform for Suspension Array Technology

The need for rapid and high-throughput screening in analytical laboratories has led to significant growth in interest in suspension array technologies (SATs), especially with regard to cytometric assays targeting a low to medium number of analytes. Such SAT or bead-based assays rely on spherical objects that constitute the analytical platform. Usually, functionalized polymer or silica (SiO2) microbeads are used which each have distinct advantages and drawbacks. In this paper, we present a straightforward synthetic route to highly monodisperse SiO2-coated polystyrene core-shell (CS) beads for SAT with controllable architectures from smooth to raspberry- and multilayer-like shells by varying the molecular weight of poly(vinylpyrrolidone) (PVP), which was used as the stabilizer of the cores. The combination of both organic polymer core and a structurally controlled inorganic SiO2 shell in one hybrid particle holds great promises for flexible next-generation design of the spherical platform. The particles were characterized by electron microscopy (SEM, T-SEM, and TEM), thermogravimetry, flow cytometry, and nitrogen adsorption/desorption, offering comprehensive information on the composition, size, structure, and surface area. All particles show ideal cytometric detection patterns and facile handling due to the hybrid structure. The beads are endowed with straightforward modification possibilities through the defined SiO2 shells. We successfully implemented the particles in fluorometric SAT model assays, illustrating the benefits of tailored surface area which is readily available for small-molecule anchoring. Very promising assay performance was shown for DNA hybridization assays with quantification limits down to 8 fmol.

A bead-based fluorescence immunosensing technique enabled by the integration of Förster resonance energy transfer and optoelectrokinetic concentration

Bead-based immunosensing has been growing as a promising technology in the point-of-care diagnostics due to great flexibility. For dilute samples, functionalized particles can be used to collect dispersed analytes and act as carriers for particle manipulation. To realize rapid and visual immunosensing, Förster resonance energy transfer (FRET) was used herein to ensure only the diabetic biomarker, lipocalin 1, to be detected. The measurement was made in an aqueous droplet sandwiched between two parallel plate electrodes. With an electric field and a focused laser beam applying on the microchip simultaneously, the immunocomplexes in the droplet were further concentrated to enhance the FRET fluorescent signal. The optoelectrokinetic technique, termed rapid electrokinetic patterning (REP), has been proven to be excellent in dynamic and programmable particle manipulation. Therefore, the detection can be complete within several tens of seconds. The lower detection limit of the REP-enabled bead-based diagnosis reached nearly 5 nM. The combinative use of FRET and the optoelectrokinetic technique for the bead-based immunosensing enables a rapid measure to diagnose early stage diseases and dilute analytes.

High sensitive and direct fluorescence detection of single viral DNA sequences by integration of double strand probes onto microgels particles

A novel class of probes for fluorescence detection was developed and combined to microgel particles for a high sensitive fluorescence detection of nucleic acids.

Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection

The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized.

Lab on a single microbead: an ultrasensitive detection strategy enabling microRNA analysis at the single-molecule level

A single microbead-based sensing platform has been developed, which enables the detection of microRNA at the single-molecule level.

Detection of a single nucleic acid molecule is of great significance for both fundamental biochemistry studies and clinical diagnostics. By using microRNA (miRNA) as a model target, herein, we have developed a single-microbead-based sensing (SMBS) platform, which simply enables the detection of miRNA at the single-molecule level. In this strategy, an isothermal exponential amplification reaction (EXPAR) is rationally designed towards specific miRNAs and all products of the EXPAR are integrated onto a single microbead for signal amplification and fluorescence enrichment. This pushes the detection of miRNAs down to 1 aM in a 5 μL sample, corresponding to 3 copies of the miRNA molecule. This new strategy also affords high selectivity and it is capable of distinguishing among homologous miRNA family members even with a single-base difference. Due to its ultrahigh sensitivity and selectivity, the proposed SMBS platform has been successfully applied to the detection of miRNA extracted from a single cell.

An optoelectrokinetic technique for programmable particle manipulation and bead-based biosignal enhancement

Technologies that can enable concentration of low-abundance biomarkers are essential for early diagnosis of diseases. In this study, an optoelectrokinetic technique, termed Rapid Electrokinetic Patterning (REP), was used to enable dynamic particle manipulation in bead-based bioassays. Various manipulation capabilities, such as micro/nanoparticle aggregation, translation, sorting and patterning, were developed. The technique allows for versatile multi-parameter (voltage, light intensity and frequency) based modulation and dynamically addressable manipulation with simple device fabrication. Signal enhancement of a bead-based bioassay was demonstrated using dilute biotin-fluorescein isothiocyanate (FITC) solutions mixed with streptavidin-conjugated particles and rapidly concentrated with the technique. As compared with a conventional ELISA reader, the REP-enabled detection achieved a minimal readout of 3.87 nM, which was a 100-fold improvement in sensitivity. The multi-functional platform provides an effective measure to enhance detection levels in more bead-based bioassays.

Stem-loop DNA-assisted silicon nanowires-based biochemical sensors with ultra-high sensitivity, specificity, and multiplexing capability

A class of stem-loop DNA-assisted silicon nanowires (SiNWs)-based fluorescent biosensor is presented in this report. Significantly, the sensor enables rapid and sensitive detection of DNA targets with a concentration as low as 1 pM. Moreover, the large planar surface of SiNWs facilitates simultaneous assembly with different DNA strands, which is favorable for multiplexed DNA detection. On the other hand, the SiNWs-based sensor is highly efficacious for detecting heavy metal ions. Mercury ions (Hg(2+)) of low concentrations (e.g., 5 pM) are readily identified from its mixture with over 10 kinds of interfering metal ions, even in real water samples. Given that SiNWs can be fabricated in a facile, reproducible and low-cost manner, this kind of SiNWs-based high-performance sensor is expected to be a practical analytical tool for a variety of biological and environment-protection applications.

Detection of single DNA molecule hybridization on a surface by atomic force microscopy

Improving the detection of DNA hybridization is a critical issue for several challenging applications encountered in microarray and biosensor domains. Herein, it is demonstrated that hybridization between complementary single-stranded DNA (ssDNA) molecules loosely adsorbed on a mica surface can be achieved thanks to fine-tuning of the composition of the hybridization buffer. Single-molecule DNA hybridization occurs in only a few minutes upon encounters of freely diffusing complementary strands on the mica surface. Interestingly, the specific hybridization between complementary ssDNA is not altered in the presence of large amounts of nonrelated DNA. The detection of single-molecule DNA hybridization events is performed by measuring the contour length of DNA in atomic force microscopy images. Besides the advantage provided by facilitated diffusion, which promotes hybridization between probes and targets on mica, the present approach also allows the detection of single isolated DNA duplexes and thus requires a very low amount of both probe and target molecules.

A cytometric bead assay for sensitive DNA detection based on enzyme-free signal amplification of hybridization chain reaction

A versatile flow cytometric bead assay (CBA) is developed for sensitive DNA detection by integrating the advantages of hybridization chain reaction (HCR) for enzyme-free signal amplification, flow cytometry for robust and rapid signal readout as well as magnetic beads (MBs) for facile separation. In this HCR-CBA, a biotinylated hairpin DNA (Bio-H1) is firstly immobilized on streptavidin-functionalized MBs. Upon the addition of target DNA, each target would hybridize with one Bio-H1 to open its hairpin structure and subsequently initiate a cascade of hybridization events between two species of fluorescent DNA hairpin probes (H1*/H2*) to form a nicked double helical DNA structure, resulting in amplified accumulation of numerous fluorophores on the MBs. Finally, the fluorescent MBs are directly analyzed by flow cytometry. This technique enables quantitative analysis of the HCR products anchored on the MBs as a function of target DNA concentration, and analysis of each sample can be completed within few minutes. Therefore, the HCR-CBA approach provides a practical DNA assay with greatly improved sensitivity. The detection limit of a model DNA target is 0.5 pM (3σ), which is about 3 orders of magnitude lower compared with traditional hybridization methods without HCR. Furthermore, the signal of complementary target can be clearly distinguished from that of single-base mismatched sequences, indicating the high specificity of the HCR-CBA. Moreover, this strategy is also successfully applied to the DNA analysis in complex biological samples, showing great potential in gene analysis and disease diagnosis in clinical samples.

Highly rapid amplification-free and quantitative DNA imaging assay

There is an urgent need for rapid and highly sensitive detection of pathogen-derived DNA in a point-of-care (POC) device for diagnostics in hospitals and clinics. This device needs to work in a 'sample-in-result-out' mode with minimum number of steps so that it can be completely integrated into a cheap and simple instrument. We have developed a method that directly detects unamplified DNA, and demonstrate its sensitivity on realistically sized 5 kbp target DNA fragments of Micrococcus luteus in small sample volumes of 20 μL. The assay consists of capturing and accumulating of target DNA on magnetic beads with specific capture oligonucleotides, hybridization of complementary fluorescently labeled detection oligonucleotides, and fluorescence imaging on a miniaturized wide-field fluorescence microscope. Our simple method delivers results in less than 20 minutes with a limit of detection (LOD) of ~5 pM and a linear detection range spanning three orders of magnitude.

Fluorescence-based multiplex protein detection using optically encoded microbeads

Potential utilization of proteins for early detection and diagnosis of various diseases has drawn considerable interest in the development of protein-based multiplex detection techniques. Among the various techniques for high-throughput protein screening, optically-encoded beads combined with fluorescence-based target monitoring have great advantages over the planar array-based multiplexing assays. This review discusses recent developments of analytical methods of screening protein molecules on microbead-based platforms. These include various strategies such as barcoded microbeads, molecular beacon-based techniques, and surface-enhanced Raman scattering-based techniques. Their applications for label-free protein detection are also addressed. Especially, the optically-encoded beads such as multilayer fluorescence beads and SERS-encoded beads are successful for generating a large number of coding.

Molecular detection of bacterial pathogens using microparticle enhanced double-stranded DNA probes

Rapid, specific, and sensitive detection of bacterial pathogens is essential toward clinical management of infectious diseases. Traditional approaches for pathogen detection, however, often require time-intensive bacterial culture and amplification procedures. Herein, a microparticle enhanced double-stranded DNA probe is demonstrated for rapid species-specific detection of bacterial 16S rRNA. In this molecular assay, the binding of the target sequence to the fluorophore conjugated probe thermodynamically displaces the quencher probe and allows the fluorophore to fluoresce. By incorporation of streptavidin-coated microparticles to localize the biotinylated probes, the sensitivity of the assay can be improved by 3 orders of magnitude. The limit of detection of the assay is as few as eight bacteria without target amplification and is highly specific against other common pathogens. Its applicability toward clinical diagnostics is demonstrated by directly identifying bacterial pathogens in urine samples from patients with urinary tract infections.

Application of multiple response optimization design to quantum dot-encoded microsphere bioconjugates hybridization assay

The optimization of DNA hybridization for genotyping assays is a complex experimental problem that depends on multiple factors such as assay formats, fluorescent probes, target sequence, experimental conditions, and data analysis. Quantum dot-doped particle bioconjugates have been previously described as fluorescent probes to identify single nucleotide polymorphisms even though this advanced fluorescent material has shown structural instability in aqueous environments. To achieve the optimization of DNA hybridization to quantum dot-doped particle bioconjugates in suspension while maximizing the stability of the probe materials, a nonsequential optimization approach was evaluated. The design of experiment with response surface methodology and multiple optimization response was used to maximize the recovery of fluorescent probe at the end of the assay simultaneously with the optimization of target-probe binding. Hybridization efficiency was evaluated by the attachment of fluorescent oligonucleotides to the fluorescent probe through continuous flow cytometry detection. Optimal conditions were predicted with the model and tested for the identification of single nucleotide polymorphisms. The design of experiment has been shown to significantly improve biochemistry and biotechnology optimization processes. Here we demonstrate the potential of this statistical approach to facilitate the optimization of experimental protocol that involves material science and molecular biology.

Preliminary study of diagnostic utility of molecular beacons in bladder cancer

OBJECTIVES

To investigate the feasibility of molecular beacons (MBs) for screening urine samples from patients with suspected bladder cancer. Our previous study showed that MBs could detect bladder cancer cells and cells shed in the urine from patients with bladder cancer.

METHODS

Samples from 35 patients with bladder cancer and 35 healthy adults were initially evaluated. Cyanine 3-labeled MBs linked to a survivin mRNA probe were used to detect exfoliative cells in urine. Exfoliative cytology, enzyme-linked immunosorbent assay, and Western blotting of the tissues were used to confirm the MB results. We then evaluated the urine samples from 187 patients with suspected bladder cancer. All 187 patients also underwent cystoscopy.

RESULTS

In the initial cohort evaluated, MBs detected cancerous cells in 28 (80%) of the 35 patients with confirmed bladder cancer. Survivin protein was detected by Western blotting in 25 (71.4%) of the 35 patients. The sensitivity and specificity of enzyme-linked immunosorbent assay was 54.3% (20 of 35) and 68.6% (24 of 35), respectively. In a large group of patients with suspected bladder cancer, the sensitivity of MBs was 77.3% (85 of 110) and the specificity was 76.6% (59 of 77) compared with the cystoscopy data. Differences in the protein levels between the tumor grades and stages were not significant.

CONCLUSIONS

Our results have demonstrated that it is feasible to detect survivin mRNA in the exfoliated cells in urine using MBs. With further development, MBs could be used in a noninvasive clinical diagnostic procedure for the early detection of bladder cancer and postoperative follow-up.

Miniaturization of molecular biological techniques for gene assay

The rapid diagnosis of various diseases is a critical advantage of many emerging biomedical tools. Due to advances in preventive medicine, tools for the accurate analysis of genetic mutation and associated hereditary diseases have attracted significant interests in recent years. The entire diagnostic process usually involves two critical steps, namely, sample pre-treatment and genetic analysis. The sample pre-treatment processes such as extraction and purification of the target nucleic acids prior to genetic analysis are essential in molecular diagnostics. The genetic analysis process may require specialized apparatus for nucleic acid amplification, sequencing and detection. Traditionally, pre-treatment of clinical biological samples (e.g. the extraction of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)) and the analysis of genetic polymorphisms associated with genetic diseases are typically a lengthy and costly process. These labor-intensive and time-consuming processes usually result in a high-cost per diagnosis and hinder their practical applications. Besides, the accuracy of the diagnosis may be affected owing to potential contamination from manual processing. Alternatively, due to significant advances in micro-electro-mechanical-systems (MEMS) and microfluidic technology, there are numerous miniature systems employed in biomedical applications, especially for the rapid diagnosis of genetic diseases. A number of advantages including automation, compactness, disposability, portability, lower cost, shorter diagnosis time, lower sample and reagent consumption, and lower power consumption can be realized by using these microfluidic-based platforms. As a result, microfluidic-based systems are becoming promising platforms for genetic analysis, molecular biology and for the rapid detection of genetic diseases. In this review paper, microfluidic-based platforms capable of identifying genetic sequences and diagnosis of genetic mutations are surveyed and reviewed. Some critical issues with the use of microfluidic-based systems for diagnosis of genetic diseases are also highlighted.

Overview of emerging arboviruses

Numerous arboviral outbreaks during the past decade have demonstrated that arthropod-borne pathogens continue to be significant public and animal health threats. These outbreaks have occurred globally and have not been limited to tropical or developing countries, as people and goods can be moved anywhere in the world within days. Several examples of recent outbreaks have been described, including how they were identified, tracked and the resulting outcomes from these events. Fortunately, scientific research, including advances in rapid detection of this diverse group of pathogens, has also been progressing. While arboviruses are likely to continually emerge and re-emerge, improved scientific technologies and approaches will hopefully make each future epidemic less likely to occur.

Kinetic and thermodynamic characterization of single-mismatch discrimination using single-molecule imaging

A single-molecule detection setup based on total internal reflection fluorescence (TIRF) microscopy has been used to investigate association and dissociation kinetics of unlabeled 30mer DNA strands. Single-molecule sensitivity was accomplished by letting unlabeled DNA target strands mediate the binding of DNA-modified and fluorescently labeled liposomes to a DNA-modified surface. The liposomes, acting as signal enhancer elements, enabled the number of binding events as well as the residence time for high affinity binders (K_d < 1 nM, k_off < 0.01 s⁻¹) to be collected under equilibrium conditions at low pM concentrations. The mismatch discrimination obtained from the residence time data was shown to be concentration and temperature independent in intervals of 1–100 pM and 23–46°C, respectively. This suggests the method as a robust means for detection of point mutations at low target concentrations in, for example, single nucleotide polymorphism (SNP) analysis.

Molecular engineering of DNA: molecular beacons

Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem-loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein-DNA interaction studies, and protein recognition.