Advances in Optical Single-Molecule Detection: En Route to Supersensitive Bioaffinity Assays

Machine-Learning-Assisted Microfluidic Nanoplasmonic Digital Immunoassay for Cytokine Storm Profiling in COVID-19 Patients

Cytokine storm, known as an exaggerated hyperactive immune response characterized by elevated release of cytokines, has been described as a feature associated with life-threatening complications in COVID-19 patients. A critical evaluation of a cytokine storm and its mechanistic linkage to COVID-19 requires innovative immunoassay technology capable of rapid, sensitive, selective detection of multiple cytokines across a wide dynamic range at high-throughput. In this study, we report a machine-learning-assisted microfluidic nanoplasmonic digital immunoassay to meet the rising demand for cytokine storm monitoring in COVID-19 patients. Specifically, the assay was carried out using a facile one-step sandwich immunoassay format with three notable features: (i) a microfluidic microarray patterning technique for high-throughput, multiantibody-arrayed biosensing chip fabrication; (ii) an ultrasensitive nanoplasmonic digital imaging technology utilizing 100 nm silver nanocubes (AgNCs) for signal transduction; (iii) a rapid and accurate machine-learning-based image processing method for digital signal analysis. The developed immunoassay allows simultaneous detection of six cytokines in a single run with wide working ranges of 1-10,000 pg mL-1 and ultralow detection limits down to 0.46-1.36 pg mL-1 using a minimum of 3 μL serum samples. The whole chip can afford a 6-plex assay of 8 different samples with 6 repeats in each sample for a total of 288 sensing spots in less than 100 min. The image processing method enhanced by convolutional neural network (CNN) dramatically shortens the processing time ∼6,000 fold with a much simpler procedure while maintaining high statistical accuracy compared to the conventional manual counting approach. The immunoassay was validated by the gold-standard enzyme-linked immunosorbent assay (ELISA) and utilized for serum cytokine profiling of COVID-19 positive patients. Our results demonstrate the nanoplasmonic digital immunoassay as a promising practical tool for comprehensive characterization of cytokine storm in patients that holds great promise as an intelligent immunoassay for next generation immune monitoring.

Microchamber-Free Digital Flow Cytometric Analysis of T4 Polynucleotide Kinase Phosphatase Based on Single-Enzyme-to-Single-Bead Space-Confined Reaction

Digital bioassays have attracted extensive attention in biomedical applications due to their ultrahigh sensitivity. However, traditional digital bioassays require numerous microchambers such as droplets or microwells, which restricts their application scope. Herein, we propose a microchamber-free flow cytometric method for the digital quantification of T4 polynucleotide kinase phosphatase (T4 PNKP) based on an unprecedented phenomenon that each T4 PNKP molecule-catalyzed reaction can be spatially self-confined on a single microbead, which ultimately enables the one-target-to-one-fluorescence-positive microbead digital signal transduction. The digital signal-readout mode can clearly detect T4 PNKP concentrations as low as 1.28 × 10^-10 U/μL, making it most sensitive method to date. Significantly, T4 PNKP can be specifically distinguished from other phosphatases and nucleases in complex samples by digitally counting the fluorescence-positive microbeads, which cannot be realized by traditional bulk measurement-based methods. Taking advantage of the novel space-confined enzymatic feature of T4 PNKP, this digital mechanism can use T4 PNKP as the enzyme label to fabricate digital sensing systems toward various biomolecules such as digital enzyme-linked immunosorbent assay (ELISA). Therefore, this work not only enlarges the toolbox for high-sensitivity biomolecule detection but also opens new gates to fabricate next-generation digital assays.

Entrapment of horseradish peroxidase into nanometer-scale metal-organic frameworks: a new nanocarrier for signal amplification in enzyme-linked immunosorbent assay

Horseradish peroxidase (HRP) was highly loaded into large holes of nanometer-scale metal-organic frameworks (i.e., PCN-333(Al)) for signal amplification in enzyme-linked immunosorbent assay (ELISA). The enzyme-labeled antibody complex prepared using nanometer-scale PCN-333(Al) maintained a high catalytic efficiency. Its V_m and K_cat values with 3,3',5,5'-Tetramethylbenzidine (TMB)-H₂O₂ as substrates were 4.84 × 10^-5 mM/s and 4.84 × 10⁴ min^-1, respectively. We demonstrated an HRP@PCN-333 signal amplification strategy for colorimetric assay of human prostate-specific antigen (PSA). The linear range of PSA detection by using this method was 15-165 pg/mL, and the limit of detection was 6 pg/mL (S/N = 3), indicating the potential application of this method in detecting disease markers under clinical conditions. The presented strategy exhibited the characteristics of significantly increased amount of labeled enzymes, improved stability and utilization of enzymes, simple preparation process of enzyme-labeled antibodies, and low cost.

Effect of Particle Size and Surface Chemistry of Photon-Upconversion Nanoparticles on Analog and Digital Immunoassays for Cardiac Troponin

Sensitive immunoassays are required for troponin, a low-abundance cardiac biomarker in blood. In contrast to conventional (analog) assays that measure the integrated signal of thousands of molecules, digital assays are based on counting individual biomarker molecules. Photon-upconversion nanoparticles (UCNP) are an excellent nanomaterial for labeling and detecting single biomarker molecules because their unique anti-Stokes emission avoids optical interference, and single nanoparticles can be reliably distinguished from the background signal. Here, the effect of the surface architecture and size of UCNP labels on the performance of upconversion-linked immunosorbent assays (ULISA) is critically assessed. The size, brightness, and surface architecture of UCNP labels are more important for measuring low troponin concentrations in human plasma than changing from an analog to a digital detection mode. Both detection modes result approximately in the same assay sensitivity, reaching a limit of detection (LOD) of 10 pg mL^-1 in plasma, which is in the range of troponin concentrations found in the blood of healthy individuals.

A Flexible Synthetic Approach to Fluorescent Chromeno[4,3-b]pyridines and Pyrano[3,2-c]chromenes from Electron-Deficient 3-Vinylchromones

We report a flexible approach to the synthesis of phenanthrene-like heterocycles through organocatalytic ANRORC (Addition of the Nucleophile, Ring Opening, and Ring Closure) reaction of electron-deficient 3-vinylchromones with cyanoacetamide. Addition of highly basic DBU (1,8-diazabicyclo[5.4.0]undec-7-ene) or tetramethylguanidine (TMG) at 80 °C leads to chromeno[4,3-b]pyridines in good yields, whereas Et3 N at 20 °C made it possible to obtain the less accessible pyrano[3,2-c]chromenes and their 2-imines. The synthesis proceeds in mild conditions (EtOH, 20-80 °C), is versatile and applicable for a wide scope of reactants. The obtained compounds show bright fluorescence in the range 460-595 nm with high quantum yields (up to 0.84) in various solvents (MeCN, DMSO, EtOH, H2 O).

Surface functionalization of nanomaterials by aryl diazonium salts for biomedical sciences

Nanoparticles (NPs) can be prepared by simple reactions and methods from a number of materials. Their small size opens up a number of applications in different fields, among which biomedicine, including: i) drug delivery, ii) biosensors, iii) bioimaging, iv) antibacterial activity. To be able to perform such tasks, NPs must be modified with a variety of functional molecules, such as drugs, targeting groups, chemical tags or antibacterial agents, and must also be prevented from aggregation. The attachment must be stable to resist during the transportation to the targeted location. Diazonium salts, which have been widely used for coupling applications and surface modification, fulfil such criteria. Moreover, they are simple to prepare and can be easily substituted with a large number of organic groups. This review describes the use of these compounds in nanomedicine with a focus on the construction of nanohybrids derived from metal, oxide and carbon-based NPs as well as viruses.

Biochemical Sensing with Nanoplasmonic Architectures: We Know How but Do We Know Why?

Here, the research field of nanoplasmonic sensors is placed under scrutiny, with focus on affinity-based detection using refractive index changes. This review describes how nanostructured plasmonic sensors can deliver unique advantages compared to the established surface plasmon resonance technique, where a planar metal surface is used. At the same time, it shows that these features are actually only useful in quite specific situations. Recent trends in the field are also discussed and some devices that claim extraordinary performance are questioned. It is argued that the most important challenges are related to limited receptor affinity and nonspecific binding rather than instrumental performance. Although some nanoplasmonic sensors may be useful in certain situations, it seems likely that conventional surface plasmon resonance will continue to dominate biomolecular interaction analysis. For detection of analytes in complex samples, plasmonics may be an important tool, but probably not in the form of direct refractometric detection.

Quantification of Tumor Protein Biomarkers from Lung Patient Serum Using Nanoimpact Electrochemistry

Protein quantification with high throughput and high sensitivity is essential in the early diagnosis and elucidation of molecular mechanisms for many diseases. Conventional approaches for protein assay often suffer from high costs, long analysis time, and insufficient sensitivity. The recently emerged nanoimpact electrochemistry (NIE), as a contrast, allows in situ detection of analytes one at a time with simplicity, fast response, high throughput, and the potential of reducing the detection limits down to the single entity level. Herein, we propose a NIE-enabled electrochemical immunoassay using silver nanoparticles (AgNPs) as labels for the detection of CYFRA21-1, a typical protein marker for lung carcinoma. This strategy is based on the measurement of the impact frequency and the charge intensity of the electrochemical oxidation of individual AgNPs before and after they are modified with anti-CYFRA21-1 and in turn immunocomplexed with CYFRA21-1. Both the frequency and intensity modes of single-nanoparticle electrochemistry correlate well with each other, resulting in a self-validated immunoassay that provides linear ranges of two orders of magnitude and a limit of detection of 0.1 ng/mL for CYFRA21-1 analysis. The proposed immunoassay also exhibits excellent specificity when challenged with other possible interfering proteins. In addition, the CYFRA21-1 content is validated by a conventional, well-known enzyme-linked immunosorbent assay and successfully quantified in a diluted healthy serum with a satisfactory recovery. Moreover, CYFRA21-1 detection in serum samples of lung cancer patients is successfully demonstrated, suggesting the feasibility of the NIE-based immunoassay in clinically relevant diagnosis. To the best of our knowledge, this is the first report to construct NIE-based electrochemical immunoassays for the specific detection of tumor protein biomarkers.

When Fluorescent Sensing Meets Electrochemical Amplifying: A Powerful Platform for Gene Detection with High Sensitivity and Specificity

Ultrasensitive and ultraselective detection of the gene requires emergency development to meet the medical demands and infectious disease control. Herein we report a versatile and scalable method based on electrochemical-chemical-cyclic amplification (EC-CA) and fluorescence detection for ultrasensitive gene sensing. The EC-CA is achieved by an electro-Fenton reaction (EFR). The hydroxyl radicals generated at EFR are trapped by terephthalic acid to form highly fluorescent 2-hydroxyterephthalic acid, which can be sensitively detected by a fluorescence spectrophotometer. The method is the first to be able to amplify the signal and reduce the noise simultaneously by using the conventional analytical methods directly. This described method can be used for reliable Fe³⁺ quantification in the range from 0.1 nM to 0.08 mM. The calculated limit of detection (LOD) is 0.02 nM. Then, hepatitis B virus (HBV) and p53 gene were detected by this proposed method through introducing the Fe₃O₄ nanoparticles into the gene hybridization system. The LODs for HBV and p53 gene even topped out at 2.6 pM and 1.7 fM, respectively. We demonstrated that the finally recorded signal was triply amplified through the EC cycle, Fe₃O₄ nanoparticles, and sensitive fluorescence detection. At the same time, the background signal arisen from matrix effects and readout noise was effectively suppressed. This method shows it is simple, convenient, and operational through the detection of Fe³⁺, HBV, and the p53 gene in blood samples, respectively. We believe our method will make a significant, near-term impact on the development of high-sensitivity methods that are versatile and scalable.

PEG-Neridronate-Modified NaYF4:Gd3+,Yb3+,Tm3+/NaGdF4 Core-Shell Upconverting Nanoparticles for Bimodal Magnetic Resonance/Optical Luminescence Imaging

Upconverting nanoparticles are attracting extensive interest as a multimodal imaging tool. In this work, we report on the synthesis and characterization of gadolinium-enriched upconverting nanoparticles for bimodal magnetic resonance and optical luminescence imaging. NaYF4:Gd3+,Yb3+,Tm3+ core upconverting nanoparticles were obtained by a thermal coprecipitation of lanthanide oleate precursors in the presence of oleic acid as a stabilizer. With the aim of improving the upconversion emission and increasing the amount of Gd3+ ions on the nanoparticle surface, a 2.5 nm NaGdF4 shell was grown by the epitaxial layer-by-layer strategy, resulting in the 26 nm core-shell nanoparticles. Both core and core-shell nanoparticles were coated with poly(ethylene glycol) (PEG)-neridronate (PEG-Ner) to have stable and well-dispersed upconverting nanoparticles in a biological medium. FTIR spectroscopy and thermogravimetric analysis indicated the presence of ∼20 wt % of PEG-Ner on the nanoparticle surface. The addition of inert NaGdF4 shell resulted in a total 26-fold enhancement of the emission under 980 nm excitation and also affected the T 1 and T 2 relaxation times. Both r 1 and r 2 relaxivities of PEG-Ner-modified nanoparticles were much higher compared to those of non-PEGylated particles, thus manifesting their potential as a diagnostic tool for magnetic resonance imaging. Together with the enhanced luminescence efficiency, upconverting nanoparticles might represent an efficient probe for bimodal in vitro and in vivo imaging of cells in regenerative medicine, drug delivery, and/or photodynamic therapy.

Click-Coupling to Electrostatically Grafted Polymers Greatly Improves the Stability of a Continuous Monitoring Sensor with Single-Molecule Resolution

Sensing technologies for the real-time monitoring of biomolecules will allow studies of dynamic changes in biological systems and the development of control strategies based on measured responses. Here, we describe a molecular architecture and coupling process that allow continuous measurements of low-concentration biomolecules over long durations in a sensing technology with single-molecule resolution. The sensor is based on measuring temporal changes of the motion of particles upon binding and unbinding of analyte molecules. The biofunctionalization involves covalent coupling by click chemistry to PLL-g-PEG bottlebrush polymers. The polymer is grafted to a surface by multivalent electrostatic interactions, while the poly(ethylene glycol) suppresses nonspecific binding of biomolecules. With this biofunctionalization strategy, we demonstrate the continuous monitoring of single-stranded DNA and a medically relevant small-molecule analyte (creatinine), in sandwich and competitive assays, in buffer and in filtered blood plasma, with picomolar, nanomolar, and micromolar analyte concentrations, and with continuous sensor operation over 10 h.

Biosensing based on upconversion nanoparticles for food quality and safety applications

Food safety and quality regulations inevitably call for sensitive and accurate analytical methods to detect harmful contaminants in food and to ensure safe food for the consumer. Both novel and well-established biorecognition elements, together with different transduction schemes, enable the simple and rapid analysis of various food contaminants. Upconversion nanoparticles (UCNPs) are inorganic nanocrystals that convert near-infrared light into shorter wavelength emission. This unique photophysical feature, along with narrow emission bandwidths and large anti-Stokes shift, render UCNPs excellent optical labels for biosensing because they can be detected without optical background interferences from the sample matrix. In this review, we show how this exciting technique has evolved into biosensing platforms for food quality and safety monitoring and highlight recent applications in the field.

Laser-induced breakdown spectroscopy as a readout method for immunocytochemistry with upconversion nanoparticles

Immunohistochemistry (IHC) and immunocytochemistry (ICC) are widely used to identify cancerous cells within tissues and cell cultures. Even though the optical microscopy evaluation is considered the gold standard, the limited range of useful labels and narrow multiplexing capabilities create an imminent need for alternative readout techniques. Laser-induced breakdown spectroscopy (LIBS) enables large-scale multi-elemental analysis of the surface of biological samples, e.g., thin section or cell pellet. It is, therefore, a potential alternative for IHC and ICC readout of various labels or tags (Tag-LIBS approach). Here, we introduce Tag-LIBS as a method for the specific determination of HER2 biomarker. The cell pellets were labeled with streptavidin-conjugated upconversion nanoparticles (UCNP) through a primary anti-HER2 antibody and a biotinylated secondary antibody. The LIBS scanning enabled detecting the characteristic elemental signature of yttrium as a principal constituent of UCNP, thus indirectly providing a reliable way to differentiate between HER2-positive BT-474 cells and HER2-negative MDA-MB-231 cells. The comparison of results with upconversion optical microscopy and luminescence intensity scanning confirmed that LIBS is a promising alternative for the IHC and ICC readout.

Single-Particle Counting Based on Digital Plasmonic Nanobubble Detection for Rapid and Ultrasensitive Diagnostics

Rapid and sensitive diagnostics of infectious diseases is an urgent and unmet need as evidenced by the COVID-19 pandemic. Here we report a novel strategy, based on DIgitAl plasMONic nanobubble Detection (DIAMOND), to address these gaps. Plasmonic nanobubbles are transient vapor bubbles generated by laser heating of plasmonic nanoparticles and allow single-particle detection. Using gold nanoparticles labels and an optofluidic setup, we demonstrate that DIAMOND achieves a compartment-free digital counting and works on homogeneous assays without separation and amplification steps. When applied to the respiratory syncytial virus diagnostics, DIAMOND is 150 times more sensitive than commercial lateral flow assays and completes measurements within 2 minutes. Our method opens new possibilities to develop single-particle digital detection methods and facilitate rapid and ultrasensitive diagnostics.

One Sentence Summary

Single-particle digital plasmonic nanobubble detection allows rapid and ultrasensitive detection of viruses in a one-step homogeneous assay.

Single-cell omics analyses with single molecular detection: challenges and perspectives

The ultimate goal of single-cell analyses is to obtain the biomolecular content for each cell in unicellular and multicellular organisms at different points of their life cycle under variable environmental conditions. These require an assessment of: a) the total number of cells, b) the total number of cell types, and c) the complete and quantitative single molecular detection and identification for all classes of biopolymers, and organic and inorganic compounds, in each individual cell. For proteins, glycans, lipids, and metabolites, whose sequences cannot be amplified by copying as in the case of nucleic acids, the detection limit by mass spectrometry is about 10⁵ molecules. Therefore, proteomic, glycomic, lipidomic, and metabolomic analyses do not yet permit the assembly of the complete single-cell omes. The construction of novel nanoelectrophoretic arrays and nano in microarrays on a single 1-cm-diameter chip has shown proof of concept for a high throughput platform for parallel processing of thousands of individual cells. Combined with dynamic secondary ion mass spectrometry, with 3D scanning capability and lateral resolution of 50 nm, the sensitivity of single molecular quantification and identification for all classes of biomolecules could be reached. Further development and routine application of such technological and instrumentation solution would allow assembly of complete omes with a quantitative assessment of structural and functional cellular diversity at the molecular level.

Multiparameter single-particle motion analysis for homogeneous digital immunoassay

Digital homogeneous non-enzymatic immunosorbent assay (digital Ho-Non ELISA) is a new class of digital immunoassay. In this paper, we developed a multiparameter single-particle motion analysis method for a highly sensitive digital Ho-Non ELISA.

Microfluidic compartmentalization to identify gene biomarkers of infection

Infectious diseases caused by pathogens, such as SARS-COV, H7N9, severe fever with thrombocytopenia syndrome virus, and human immunodeficiency virus, have fatal outcomes with common features of severe fever and subsequent bacterial invasion progressing to multiorgan failure. Gene biomarkers are promising to distinguish specific infections from others with similar presenting symptoms for the prescription of correct therapeutics, preventing pandemics. While routine laboratory methods based on polymerase chain reaction (PCR) to measure gene biomarkers have provided highly sensitive and specific viral detection techniques over the years, they are still hampered by their precision and resource intensity precluding their point-of-care use. Recently, there has been growing interest in employing microfluidic technologies to advance current methods for infectious disease determination via gene biomarker measurements. Here, based on the requirement of infection detection, we will review three microfluidic approaches to compartmentalize gene biomarkers: (1) microwell-based PCR platforms; (2) droplet-based PCR; and (3) point-of-care devices including centrifugal chip, SlipChip, and self-powered integrated microfluidic point-of-care low-cost enabling chip. By capturing target genes in microwells with a small sample volume (∼μl), sensitivity can be enhanced. Additionally, with the advance of significant sample volume minimization (∼pl) using droplet technology, gene quantification is possible. These improvements in cost, automation, usability, and portability have thereby allowed point-of-care applications to decentralize testing platforms from laboratory-based settings to field use against infections.

Advances in Optical Single-Molecule Detection: En Route to Supersensitive Bioaffinity Assays

The ability to detect low concentrations of analytes and in particular low-abundance biomarkers is of fundamental importance, e.g., for early-stage disease diagnosis. The prospect of reaching the ultimate limit of detection has driven the development of single-molecule bioaffinity assays. While many review articles have highlighted the potentials of single-molecule technologies for analytical and diagnostic applications, these technologies are not as widespread in real-world applications as one should expect. This Review provides a theoretical background on single-molecule-or better digital-assays to critically assess their potential compared to traditional analog assays. Selected examples from the literature include bioaffinity assays for the detection of biomolecules such as proteins, nucleic acids, and viruses. The structure of the Review highlights the versatility of optical single-molecule labeling techniques, including enzymatic amplification, molecular labels, and innovative nanomaterials.

Versatile Bioconjugation Strategies of PEG-Modified Upconversion Nanoparticles for Bioanalytical Applications

Lanthanide-doped upconversion nanoparticles (UCNPs) display highly beneficial photophysical features for background-free bioimaging and bioanalysis; however, they are instable in high ionic strength buffers, have no functional groups, and are nonspecifically interacting. Here, we have prepared NIR-excitable UCNPs that are long-term colloidally stable in buffered media and possess functional groups. Heterobifunctional poly(ethylene glycol) (PEG) linkers bearing neridronate and alkyne or maleimide were attached to UCNPs via a ligand exchange. Streptavidin (SA)-conjugates were prepared by click reaction of UCNP@PEG-alkyne and SA-azide. Antihuman serum albumin pAbF antibody was modified with azide groups and conjugated to UCNP@PEG-alkyne via click reaction; alternatively, the antibody, after mild reduction of its disulfide bonds, was conjugated to UCNP@PEG-maleimide. We employed these nanoconjugates as labels for an upconversion-linked immunosorbent assay. SA-based labels achieved the lowest LOD of 0.17 ng/mL for the target albumin, which was superior compared to a fluorescence immunoassay (LOD 0.59 ng/mL) or an enzyme-linked immunoassay (LOD 0.56 ng/mL).