Precisely Encoded Barcodes through the Structure-Fluorescence Combinational Strategy: A Flexible, Robust, and Versatile Multiplexed Biodetection Platform with Ultrahigh Encoding Capacities.

With the rapid development of suspension array technology, microbeads-based barcodes as the core element with sufficient encoding capacity are urgently required for high-throughput multiplexed detection. Here, a novel structure-fluorescence combinational encoding strategy is proposed for the first time to establish a barcode library with ultrahigh encoding capacities. Based on the never revealed transformability of the structural parameters (e.g., porosity and matrix component) of mesoporous microbeads into scattering signals in flow cytometry, the enlargement of codes number has been successfully realized in combination with two other fluorescent elements of fluorescein isothiocyanate isomer I (FITC) and quantum dots (QDs). The barcodes are constructed with precise architectures including FITC encapsulated within mesopores and magnetic nanoparticles as well as QDs immobilized on the outer surface to achieve the ultrahigh encoding level of 300 accompanied with superparamagnetism. To the best of knowledge, it is the highest record of single excitation laser-based encoding capacity up to now. Moreover, a ten-plexed tumor markers bioassay based on the tailored-designed barcodes has been evaluated to confirm their feasibility and effectiveness, and the results indicate that the barcodes platform is a promising and robust tool for practical multiplexed biodetection.

Circular RNA circPIP5K1A contributes to cancer stemness of osteosarcoma by miR-515-5p/YAP axis.

BACKGROUND: Osteosarcoma is a common type of bone tumors and frequently occurs in children and adolescents. Cancer stem cells (CSCs) are a unique sub-type of self-renewal cancer cells and the stemness of cancer cells are involved in the spread, recurrence, metastasis, and even therapeutic resistance. However, the regulation mechanisms of CSCs in osteosarcoma are poorly understood. Circular RNA (circRNA) is a unique sort of non-coding RNAs and widely participate in the modulation of cancer progression. METHODS: In this study, we identified the critical function of circular RNA circPIP5K1A in stemness of osteosarcoma cells. RESULTS: CircPIP5K1A expression was significantly enhanced in clinical osteosarcoma tissues compared with the adjacent normal tissues. The depletion of circPIP5K1A by siRNA repressed osteosarcoma cell viabilities and induced osteosarcoma cell apoptosis. The suppression of circPIP5K1A attenuated the capabilities of invasion and migration of osteosarcoma cells. The circPIP5K1A knockdown increased E-Cadherin expression and decreased Vimentin expression in osteosarcoma cells. The sphere formation abilities of osteosarcoma cells were repressed by the depletion of circPIP5K1A. The CD133+CD44+ cell population of osteosarcoma cells was reduced by circPIP5K1A knockdown. The expression of ALDH1 and Nanog was decreased by the inhibition of circPIP5K1A in osteosarcoma cells. Mechanically, circPIP5K1A enhanced YAP expression by targeting miR-515-5p. MiR-515-5p inhibited stemness of osteosarcoma cells. The CSCs properties of osteosarcoma cells were repressed by circPIP5K1A knockdown or miR-515-5p mimic, while miR-515-5p inhibitor or YAP overexpression reversed circPIP5K1A knockdown-induced repression. Tumor xenograft analysis in nude mice demonstrated that the depletion of circPIP5K1A represses osteosarcoma cell growth in vivo. CONCLUSION: In conclusion, we identified that circular RNA circPIP5K1A contributed to cancer stemness of osteosarcoma by miR-515-5p/YAP axis. Targeting circPIP5K1A may be considered as a potential therapeutic strategy for osteosarcoma treatment.

Multiplexed Luminescence Oxygen Channeling Immunoassay Based on Dual-Functional Barcodes with a Host-Guest Structure: A Facile and Robust Suspension Array Platform.

The development of a powerful immunoassay platform with capacities of both simplicity and high multiplexing is promising for disease diagnosis. To meet this urgent need, for the first time, a multiplexed luminescent oxygen channeling immunoassay (multi-LOCI) platform by implementation of LOCI with suspension array technology is reported. As the microcarrier of the platform, a unique dual-functional barcode with a host-guest structure composed of a quantum dot host bead (QDH) and LOCI acceptor beads (ABs) is designed, in which QDH provides function of high coding capacity while ABs facilitate the LOCI function. The analytes bridge QDH@ABs and LOCI donor beads (DBs) into a close proximity, forming a QDH@ABs-DBs "host-guest-satellite" superstructure that generates both barcode signal from QDH and LOCI signal induced by singlet oxygen channeling between ABs and DBs. Through imaging-based decoding, different barcodes are automatically distinguished and colocalized with LOCI signals. Importantly, the assay achieves simultaneous detection of multiple analytes within one reaction, simply by following a "mix-and-measure" protocol without the need for tedious washing steps. Furthermore, the multi-LOCI platform is validated for real sample measurements. With the advantages of robustness, simplicity, and high multiplexing, the platform holds great potential for the development of point-of-care diagnostics.

Ligation-Rolling Circle Amplification on Quantum Dot-Encoded Microbeads for Detection of Multiplex G-Quadruplex-Forming Sequences.

The combination of microbead array with assay chemistry of isothermal amplification enables the continuous development of nucleic acid detection techniques. Herein we report the implementation of ligation-rolling circle amplification (RCA) reaction on quantum dots-encoded microbead (Qbead) for the detection of multiplex G-quadruplex (G4) forming sequences. The reaction time of RCA on the Qbead was optimized to be 60 min. Zinc phthalocyanine (ZnPc), a molecular "light switch", was selected as the G4-specific label. In the presence of target, the target-triggered ligation-RCA produced long DNA concatemer consisting of tandem repeats of G4-forming sequence, and the labeling helped generate G4/ZnPc nanowires on the Qbead. With the G4/ZnPc nanowires as fluorescent labels, the array of three encoded Qbeads was capable of detecting three G4-forming sequences by flow cytometry in a high-throughput and specific manner. Alternatively, with the G4/ZnPc nanowires as catalytic labels, chemiluminescence of H2O2-mediated oxidation of luminol could be used for detecting the target G4-forming sequences with high sensitivity. The catalytic chemiluminescence achieved a limit of detection of 0.5 ng of genomic DNA with 5 logs of linear dynamic range for the detection of the blood sample of a myeloproliferative neoplasms patient. Together the proposed isothermal amplification-on-Qbead assay featured robust detection platform, significant signal amplification, and flexible detection strategy, holding high potential in application in large-scale or "focused" nucleic acid testing.

Ratiometric Quantum Dot-Ligand System Made by Phase Transfer for Visual Detection of Double-Stranded DNA and Single-Nucleotide Polymorphism.

We have developed a proof-of-concept quantum dot-ligand (QD-L) system for visual selective detection of nucleic acids, in combination with a ratiometric fluorescence technique. This system comprises a dual-emission QDs nanohybrid formed by embedding a red-emission QD (rQD) in a silica nanoparticle and electrostatically assembling green-emission QDs (gQDs) onto the silica surface, as the signal displaying unit, and a hydrophobic compound, dipyrido[3,2-a:2',3'-c]phenazine (dppz), attached onto the gQDs surface via phase transfer, as the ligand as well as fluorescence quencher of gQDs. This system is successfully used for quantification of double-stranded DNA (dsDNA). Because of its avid binding with dppz, dsDNA can break up the QD-L system, displacing the dppz ligand from the gQDs surface and restoring the gQDs emission. Since the red emission of embedded rQDs stays constant, variations of the dual-emission intensity ratios display continuous color changes from orange to bright green, which can be clearly observed by the naked eye. More importantly, this system is advantageous in terms of specificity over a QD ionic conjugate, because the electrical neutrality of dppz excludes its nonspecific electrostatic association with dsDNA. The QD-L system also is capable of detecting single-nucleotide polymorphism, exhibiting sequence-specific ratiometric fluorescence as a QD-bioconjugate does, but possessing the obvious advantage in terms of low cost, with the avoidance of modification, labeling, and purification processes. Therefore, the QD-L system provides an extremely simple but general strategy for detecting nucleic acids in a facile, sensitive, and specific manner.

Fluorescence resonance energy transfer-based ratiometric fluorescent probe for detection of Zn(2+) using a dual-emission silica-coated quantum dots mixture.

In this work, we report the design and application of a new ratiometric fluorescent probe, which contains different-colored quantum dots (QDs) as dual fluorophores, ultrathin silica shell as spacer, and meso-tetra(4-sulfonatophenyl)porphine dihydrochloride (TSPP) as receptor, for Zn(2+) detection in aqueous solution and living cells. In the architecture of our designed probe, the silica shell plays the key roles in controlling the locations of QDs, TSPP, and Zn(2+), preventing the direct contact between QDs and Zn(2+) but affording fluorescence resonance energy transfer (FRET) from dual-color QDs to TSPP. In the presence of Zn(2+), the analyte-receptor reaction changes the absorption in the range of the Q-band of TSPP and accordingly the efficiencies of two independent FRET processes from the dual-colored QDs to the acceptor, respectively, leading to fluorescence enhancement of green-emission QDs whereas fluorescence quenching of yellow-emission QDs. Benefiting from the well-resolved dual emissions from different-colored QDs and the large range of emission ratios, the probe solution displays continuous color changes from yellow to green, which can be clearly observed by the naked eye. Under physiological conditions, the probe exhibits a stable response for Zn(2+) from 0.3 to 6 µM, with a detection limit of 60 nM in aqueous solutions. With respect to single-emission probes, this ratiometric probe has demonstrated to feature excellent selectivity for Zn(2+) over other physiologically important cations such as Fe(3+) and Cu(2+). It has been preliminarily used for ratiometric imaging of Zn(2+) in living cells with satisfying resolution.

Revolutionizing the capture efficiency of ultrasensitive digital ELISA via an antibody oriented-immobilization strategy.

Bead-based digital ELISA, the most sensitive protein quantification method, has drawn much attention to exploring ultra-low abundance biomarkers in the life sciences and clinical applications. However, its major challenge refers to the low antigen capture efficiency in the immunoreaction process due to the low probability of collision between the deficient concentration of the analytes and the captured antibody-immobilized on the beads. Here, we achieved significantly improved reaction efficiency in the digital signal formation by fixing the orientation of antibodies and revealed the kinetic mechanism for the first time. A facile and fast antibody conjugation strategy that formed boronate ester complexes was designed to retain the uniform orientation of antibodies with controllable antibody density. Remarkably, the oriented immobilized antibody exhibited stronger antigen-binding capacity and faster antigen-binding speed compared to randomly immobilized antibodies, with capture efficiency increasing approximately 14-fold at 15 µg of antibody per 1 mg microbeads (0.035 antibody nm-2) under 0.5 h incubation. Combined with theoretical analysis, we verified that the improved capture efficiency of the oriented antibodies mainly originated from the considerable rise in the binding rate constant (kon) rather than the increase in antigen-binding sites, which further prominently decreased the limit of detection (LoD) in a shorter incubation time compared with the randomly immobilized antibody. In conclusion, the antibody oriented conjugation method effectively overcomes the low capture efficiency challenge of bead-based digital ELISA. It paves a promising way for further improving the digital immunoassay performance and promotes the early diagnosis of diseases by recognizing more ultra-low abundance significant biomarkers.

Multiplex Digital Immunoassays with Reduced Pre-partition Reaction via Massively Parallel Reagent Delivery on a Bead-Based SlipChip.

The emergence of digital immunoassays has advanced the sensitivity of protein analysis to ultrahigh sensitivity at the attomolar level. However, the background signal generated by the premixing of immunocomplexes and fluorogenic substrates can limit the precise quantification, especially in multiplexed assays. Herein, a bead-based SlipChip (bb-SlipChip) microfluidic device capable of massively parallel two-step sample loading is presented. The background signal can be suppressed through a two-step loading mechanism. Specifically, encapsulate the beads into the microwells first and then, through a slipping process, deliver the fluorogenic substrate in parallel into 281,200 microwells of 68 fL to perform the digital immunoassay. The quantification capability is demonstrated with a duplex assay of IL-6 and IL-10, achieving a limit of detection of 5.2 and 15.3 fg/mL, which is approximately 2-3 times improved compared to a commercial Simoa system. The bb-SlipChip provides a robust and universal method for digital immunoassay and can be extended to higher multiplexed detection as well as other biomedical applications involving microbeads.

Bead-Based Multiplexed Droplet Digital Polymerase Chain Reaction in a Single Tube Using Universal Sequences: An Ultrasensitive, Cross-Reaction-Free, and High-Throughput Strategy.

The multiplexed digital polymerase chain reaction (PCR) is widely used in molecular diagnosis owing to its high sensitivity and throughput for multiple target detection compared with the single-plexed digital PCR; however, current multiplexed digital PCR technologies lack efficient coding strategies that do not compromise the sensitivity and signal-to-noise (S/N) ratio. Hence, we propose a fluorescent-encoded bead-based multiplexed droplet digital PCR method for ultra-high coding capacity, along with the creative design of universal sequences (primer and fluorescent TaqMan probe) for ultra-sensitivity and high S/N ratios. First, pre-amplification is used to introduce universal primers and universal fluorescent TaqMan probes to reduce primer interference and background noise, as well as to enrich regions of interest in targeted analytes. Second, fluorescent-encoded beads (FEBs), coupled with the corresponding target sequence-specific capture probes through streptavidin-biotin conjugation, are used to partition amplicons via hybridization according to the Poisson distribution. Finally, FEBs mixed with digital PCR mixes are isolated into droplets generated via Sapphire chips (Naica Crystal Digital PCR system) to complete the digital PCR and result analysis. For proof of concept, we demonstrate that this method achieves high S/N ratios in a 5-plexed assay for influenza viruses and SARS-CoV-2 at concentrations below 10 copies and even close to a single molecule per reaction without cross-reaction, further verifying the possibility of clinical actual sample detection with 100% accuracy, which paves the way for the realization of digital PCR with ultrahigh coding capacity and ultra-sensitivity.

Evolution of "On-Barcode" Luminescence Oxygen Channeling Immunoassay by Exploring the Barcode Structure and the Assay System.

The multiplexed luminescence oxygen channeling immunoassay (multi-LOCI) platform we developed recently that combines conventional LOCI and suspension array technology is capable of realizing facile "mix-and-measure" multiplexed assays without tedious washing steps. However, previous work lacks comprehensive studies of the structure-performance relationship of the host-guest-structured barcode, which may obstruct the evolution and further translation of this exciting new technology to practical applications. Accordingly, this work revealed that polyelectrolyte interlayers played a crucial role in tuning the packing density of guest acceptor beads (ABs). More interestingly, we noticed that "sparse" barcodes (barcodes with low ABs packing density) exhibited comparable assay performance with "compact" ones (barcodes with high ABs packing density). The high robustness of barcodes allows for multi-LOCI to be a more universal and flexible assay platform. Furthermore, through optimization of the assay system including the laser power, as well as the concentrations of donor beads and biotinylated detection antibodies, the multi-LOCI platform showed a significant improvement in sensitivity compared with our previous work, with the limit of detection decreasing to as low as ca. 1 pg/mL. Impressively, multi-LOCI that enabled simultaneous detection of multiple analytes exhibited comparable sensitivity with the classical single-plexed LOCI, due to the ingenious structural design of the multi-LOCI barcode and the unique "on-barcode" assay format.

Breaking through the Poisson Distribution: A compact high-efficiency droplet microfluidic system for single-bead encapsulation and digital immunoassay detection.

Droplet encapsulation of a single cell or bead is widely used in digital detection, single-cell sequencing, and drug screening. However, the encapsulation of particles is totally random restricted by the Poisson distribution. The theoretical possibility of single-particle encapsulation is usually only approximately 10%. In ultra-high multiplexed digital detection or other applications that needing to measure large numbers of particles, the number of the partitions required to be counted is extremely high, further result in great increase of statistical number of invalid droplets and the redundancy of detection data. Here, a bead ordered arrangement droplet (BOAD) system is proposed to break through the Poisson distribution. BOAD system tactfully combines sheath flow, Dean vortex, and compression flow channel to achieve orderly arrangement of particles for the first time, and could achieve the fastest orderly arrangement of particles in the shortest structure. The efficiency of single-bead encapsulation is improved to as high as 86%. Further application to encapsulate encoding beads and IL-10-targeted magnetic beads demonstrates the potential for bead-based ultra-high multiplexed digital detection. Thus, use of the BOAD system is very promising for many applications needing high single-particle encapsulation ratio in limited partitions, such as multiplexed digital bio-detection, single-cell analysis, drug screening, and single exosome detection.

A facile polymer mediated dye incorporation method for fluorescence encoded microbeads with large encoding capacities.

Here we report a facile dye incorporation method for fluorescence encoded microbeads, which is achieved by tuning the mixed polymer type (blank and dye-labeled polymers) and their doping ratio through electrostatic loading into mesoporous beads. This method is universal to various carriers and could render large encoding capacities.

Supramolecularly Assembled Ratiometric Fluorescent Sensory Nanosystem for "Traffic Light"-Type Lead Ion or pH Sensing.

The combination of functional nucleic acids and nanomaterials enables the continuous development of hybrid nanosystems that have found wide applications including chemo/biosensing. Herein, we report the supramolecular assembly of a "sesame biscuit"-like superstructural nanosystem based on aptamer, quantum dot (QD), and graphene oxide (GO), and its diverse applications in Pb2+ and pH sensing. The nanosystem was assembled via adsorbing silica-encapsulated green-emitting QD onto the edge of GO by ionic interaction, followed by absorbing aptamer-modified red-emitting QD onto the GO surface via the π-stacking interaction. The nanosystem showed the characteristic of the nonquenched green fluorescence due to silica encapsulation and quenched red fluorescence owing to nanomaterial surface energy transfer. The nanosystem responded to Pb2+/pH in ratiometric fluorescence: the red fluorescence varied upon analyte-driven conformational changes of the aptamer, whereas the green one remained constant. Under optimized conditions, the nanosystem was demonstrated to be capable of quantifying Pb2+ with a detection limit of 11.7 pM, as well as pH with a sensing resolution of 0.1 pH unit. More importantly, the ratiometric nanosystem facilitated visualization of analytes in a distinct "traffic light" manner, which was exemplified by semiquantification of exogenous Pb2+ in living cells. To demonstrate practicality, fluorescent test strips were fabricated by immobilizing the nanosystem on paper. The fluorescent test strips displayed traffic light-type fluorescence color changes, with the capacity for on-site, naked-eye detection of Pb2+ in real samples, as well as point-of-care pH testing in routine urinalysis.

Hybridization chain reactions on silica coated Qbeads for the colorimetric detection of multiplex microRNAs.

A robust Qbead platform that integrated with target-binding, hybridization chain reaction and staining was developed for the direct multiplexed detection of endogenous miRNAs by amplified Qbead-colour change.

QD-Biopolymer-TSPP Assembly as Efficient BiFRET Sensor for Ratiometric and Visual Detection of Zinc Ion.

In this work, we report a new type of quantum dot (QD)-based fluorescence resonance energy transfer (FRET) assembly and its utility for sensing Zn2+ in different media. The assembly on the QD scaffold is via first coating of poly(dA) homopolymer/double-stranded DNA, followed by loading of meso-tetra(4-sulfonatophenyl)porphine dihydrochloride (TSPP), both of which are electrostatic, offering the advantages of cost-efficiency and simplicity. More importantly, the biopolymer coating minimizes the interfacial thickness to be ≤2 nm for QD-TSPP FRET, which results in improvements of up to 60-fold for single FRET efficiency and nearly 4-fold for total FRET efficiency of the QD-biopolymer-TSPP assemblies in comparison with silica-coating-based QD-TSPP assemblies. On the basis of Zn2+-chelation-induced spectral modulation, dual-emission QD-poly(dA)-TSPP assemblies are developed as a ratiometric Zn2+ sensor with increased sensitivity and specificity. The sensor either in solution or on a paper substrate displays continuous color changes from yellow to bright green toward Zn2+, exhibiting excellent visualization capability. By utilizing the competitive displacement of Zn2+, the sensor is also demonstrated to have good reversibility. Furthermore, the sensor is successfully used to visualize exogenous Zn2+ in living cells. Together the QD-biopolymer-TSPP assembly provides an inexpensive, sensitive, and reliable sensing platform not only for on-site analytical applications but also for high-resolution cellular imaging.

A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.

In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs.

A combined approach to cartographic displacement for buildings based on skeleton and improved elastic beam algorithm.

Scale reduction from source to target maps inevitably leads to conflicts of map symbols in cartography and geographic information systems (GIS). Displacement is one of the most important map generalization operators and it can be used to resolve the problems that arise from conflict among two or more map objects. In this paper, we propose a combined approach based on constraint Delaunay triangulation (CDT) skeleton and improved elastic beam algorithm for automated building displacement. In this approach, map data sets are first partitioned. Then the displacement operation is conducted in each partition as a cyclic and iterative process of conflict detection and resolution. In the iteration, the skeleton of the gap spaces is extracted using CDT. It then serves as an enhanced data model to detect conflicts and construct the proximity graph. Then, the proximity graph is adjusted using local grouping information. Under the action of forces derived from the detected conflicts, the proximity graph is deformed using the improved elastic beam algorithm. In this way, buildings are displaced to find an optimal compromise between related cartographic constraints. To validate this approach, two topographic map data sets (i.e., urban and suburban areas) were tested. The results were reasonable with respect to each constraint when the density of the map was not extremely high. In summary, the improvements include (1) an automated parameter-setting method for elastic beams, (2) explicit enforcement regarding the positional accuracy constraint, added by introducing drag forces, (3) preservation of local building groups through displacement over an adjusted proximity graph, and (4) an iterative strategy that is more likely to resolve the proximity conflicts than the one used in the existing elastic beam algorithm.

Ligand displacement-induced fluorescence switch of quantum dots for ultrasensitive detection of cadmium ions.

This paper reports the construction of a simple CdTe quantum dots (QDs)-based sensor with 1,10-phenanthroline (Phen) as ligand, and the demonstration of a novel ligand displacement-induced fluorescence switch strategy for sensitive and selective detection of Cd(2+) in aqueous phase. The complexation of Phen at the surface quenches the green photoluminescence (PL) of QDs dominated by a photoinduced hole transfer (PHT) mechanism. In the presence of Cd(2+), the Phen ligands are readily detached from the surface of CdTe QDs, forming [Cd(Phen)2(H2O)2](2+) in solution, and as a consequence the PL of CdTe QDs switches on. The detection limit for Cd(2+) is defined as ∼0.01 nM, which is far below the maximum Cd(2+) residue limit of drinking water allowed by the U.S. Environmental Protection Agency (EPA). Two consecutive linear ranges allow a wide determination of Cd(2+) from 0.02 nM to 0.6 µM. Importantly, this CdTe QDs-based sensor features to distinctly discriminate between Cd(2+) and Zn(2+), and succeeds in real water samples. This extremely simple strategy reported here represents an attempt for the development of fluorescent sensors for ultrasensitive chemo/biodetection.