Digital Concentration Readout of DNA by Absolute Quantification of Optically Countable Gold Nanorods

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.

Gold Nanorods: The Most Versatile Plasmonic Nanoparticles

Gold nanorods (NRs), pseudo-one-dimensional rod-shaped nanoparticles (NPs), have become one of the burgeoning materials in the recent years due to their anisotropic shape and adjustable plasmonic properties. With the continuous improvement in synthetic methods, a variety of materials have been attached around Au NRs to achieve unexpected or improved plasmonic properties and explore state-of-the-art technologies. In this review, we comprehensively summarize the latest progress on Au NRs, the most versatile anisotropic plasmonic NPs. We present a representative overview of the advances in the synthetic strategies and outline an extensive catalogue of Au-NR-based heterostructures with tailored architectures and special functionalities. The bottom-up assembly of Au NRs into preprogrammed metastructures is then discussed, as well as the design principles. We also provide a systematic elucidation of the different plasmonic properties associated with the Au-NR-based structures, followed by a discussion of the promising applications of Au NRs in various fields. We finally discuss the future research directions and challenges of Au NRs.

Nucleic acid amplification-free detection of DNA and RNA at ultralow concentration

The broad spectrum of approaches for nucleic acid amplification-free detection of DNA and RNA at single-digit attomolar (10^-18 M) concentration and lower is reviewed. These low concentrations correspond roughly to the most clinically desirable detection range for pathogen-specific nucleic acid as well as the detection limits of commercially available, nucleic acid amplification tests based primarily on polymerase chain reaction (PCR). The need for more rapid and inexpensive, yet still highly accurate tests, has become evident during the pandemic. It is expected that publication of reports describing improved tests will accelerate soon, and this review covers the wide variety of detection methods based on both optical and electrical measurements that have been conceived over recent years, enabled generally by the advent of nanotechnology.

Individual Plasmonic Nanoprobes for Biosensing and Bioimaging: Recent Advances and Perspectives

With the advent of nanofabrication techniques, plasmonic nanoparticles (PNPs) have been widely applied in various research fields ranging from photocatalysis to chemical and bio-sensing. PNPs efficiently convert chemical or physical stimuli in their local environment into optical signals. PNPs also have excellent properties, including good biocompatibility, large surfaces for the attachment of biomolecules, tunable optical properties, strong and stable scattering light, and good conductivity. Thus, single optical biosensors with plasmonic properties enable a broad range of uses of optical imaging techniques in biological sensing and imaging with high spatial and temporal resolution. This work provides a comprehensive overview on the optical properties of single PNPs, the description of five types of commonly used optical imaging techniques, including surface plasmon resonance (SPR) microscopy, surface-enhanced Raman scattering (SERS) technique, differential interference contrast (DIC) microscopy, total internal reflection scattering (TIRS) microscopy, and dark-field microscopy (DFM) technique, with an emphasis on their single plasmonic nanoprobes and mechanisms for applications in biological imaging and sensing, as well as the challenges and future trends of these fields.

Plasmonic Photothermal Nanoparticles for Biomedical Applications

Recent advances of plasmonic nanoparticles include fascinating developments in the fields of energy, catalyst chemistry, optics, biotechnology, and medicine. The plasmonic photothermal properties of metallic nanoparticles are of enormous interest in biomedical fields because of their strong and tunable optical response and the capability to manipulate the photothermal effect by an external light source. To date, most biomedical applications using photothermal nanoparticles have focused on photothermal therapy; however, to fully realize the potential of these particles for clinical and other applications, the fundamental properties of photothermal nanoparticles need to be better understood and controlled, and the photothermal effect-based diagnosis, treatment, and theranostics should be thoroughly explored. This Progress Report summarizes recent advances in the understanding and applications of plasmonic photothermal nanoparticles, particularly for sensing, imaging, therapy, and drug delivery, and discusses the future directions of these fields.

Intracellular Trafficking Network and Autophagy of PHBHHx Nanoparticles and their Implications for Drug Delivery

3-hydroxybutyrate-co-3-hydroxyhexanoate (PHBHHx), which is naturally generated by biodegradable polyhydroxyalkanoates synthesized by bacteria, is an attractive material for drug delivery due to its controllable physical properties, non-toxicity, environmental friendliness, degradable properties and good biocompatibility. However, the intracellular trafficking network pathways, especially the autophagy mechanism of PHBHHx nanoparticles (NPs), have rarely been investigated. In this paper, we successfully prepared the NPs used solvent displacement method and investigated the autophagy pathways and other intracellular trafficking mechanisms based on NPs with the assistance of Rab proteins. We found that NPs were internalized in cells mainly via clathrin endocytosis and caveolin endocytosis. Beside the classical pathways, we discovered two new pathways: the micropinocytosis early endosome (EEs)-micropinocytosis-lysosome pathway and the EEs-liposome-lysosome pathway. NPs were delivered to cells through endocytosis recycling vesicles and GLUT4 exocytosis vesicles. Similar to other nanoparticles, NPs also induced intracellular autophagy and were then degraded via endolysosomal pathways. 3-MA and CQ were used as autophagy inhibitors to avoid the degradation of NPs through lysosomes by blocking endolysosomal pathways. Tumor volumes and weights were significantly decreased when autophagy inhibitors and chemical drugs packaged in NPs were cooperatively used.

Ultrasensitive amplification-free detection of protein kinase based on catalyzed assembly and enumeration of gold nanoparticles

A single-particle enumeration method based on phosphorylation-directed in situ assembly of gold nanoparticles is developed for the ultrasensitive sensing of cellular protein kinase A activity. In comparison to existing strategies, the proposed new method demonstrates five orders of linear range and improves the detection limit up to 10-to-1000 fold without the involvement of target amplification.

An aptasensor based on the microscopic enumeration of encoding gold nanoparticles for the detection of C-reactive protein

C-reactive protein (CRP) is a crucial clinical biomarker for inflammatory and cardiovascular diseases. Therefore, the sensitive, selective and convenient detection of CRP is of great significance. Using gold nanoparticles (AuNPs) and combining the specific interaction between an aptamer and CRP, we developed a simple and convenient assay for CRP detection. The aptamer-based probe was fabricated through the hybridization of CRP-aptamer immobilized on magnetic beads (MBs) to a short complementary DNA (cDNA) chain attached to AuNPs to form a MB–Aptamer–AuNP sandwich structure. Upon the addition of CRP, aptamer–cDNA dehybridization occurred due to the strong interaction between CRP and the aptamer, resulting in the release of AuNPs, which were subjected to DFM imaging and subsequently counted using the MATLAB program. The number of AuNPs was therefore positively correlated to the concentration of CRP and a detection limit as low as 2.71 nM was achieved. The current approach could also exclude the disturbance of other proteins, including thrombin, IgG, Lys and BSA. In addition, the concentration of CRP detected was in good agreement with the amount cast in bovine and mouse serum, indicating that the proposed probe is robust and accurate, and it is very promising for practical applications where CRP detection is necessary. The current strategy is also promising for the detection of other proteins where a suitable aptamer is selected.

An aptasensor based on the displacement of encoding AuNPs by analyte molecules was presented. Combined with magnetic separation and DFM imaging, the number of displaced AuNPs was counted, which was correlated to the concentration of the CRP.

Amplification-free, sequence-specific 16S rRNA detection at 1 aM

A nucleic acid amplification-free, optics-free platform has been demonstrated for sequence-specific detection of Escherichia coli (E. coli) 16S rRNA at 1 aM (10-18 M) against a 106-fold (1 pM) background of Pseudomonas putida (P. putida) RNA. This work was driven by the need for simple, rapid, and low cost means for species-specific bacterial detection at low concentration. Our simple, conductometric sensing device functioned by detecting blockage of a nanopore fabricated in a sub-micron-thick glass membrane. Upon sequence-specific binding of target 16S rRNA, otherwise charge-neutral, PNA oligonucleotide probe-polystyrene bead conjugates become electrophoretically mobile and are driven to the glass nanopore of lesser diameter, which is blocked, thereby generating a large, sustained and readily observable step decrease in ionic current. No false positive signals were observed with P. putida RNA when this device was configured to detect E. coli 16S rRNA. Also, when a universal PNA probe complementary to the 16S rRNA of both E. coli and P. putida was conjugated to beads, a positive response to rRNA of both bacterial species was observed. Finally, the device readily detected E. coli at 10 CFU mL-1 in a 1 mL sample, also against a million-fold background of viable P. putida. These results suggest that this new device may serve as the basis for small, portable, low power, and low-cost systems for rapid detection of specific bacterial species in clinical samples, food, and water.

Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels

DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology's Achilles' heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule ("digital") regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform's primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique's simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.

Core-shell assay based aptasensor for sensitive and selective thrombin detection using dark-field microscopy

In this work, we developed a robust and ultrasensitive bio-sensor based on the target-aptamer recognition strategy and microscopic enumeration of gold nanoparticles (AuNPs) using dark field microscopy (DFM). The aptasensor with a core-shell structure consisting of a magnetic bead (MB), aptamer and AuNPs was fabricated by complementary hybridization of the DNA probe on the AuNPs surface to the aptamer coupled to the MB. Upon addition of the target molecule, the strong interaction between the aptamer and the target molecule, thrombin, results in the release of the AuNPs from the MB. The quantities of thrombin is therefore linearly correlated to the number of the released AuNPs, which can be digitally counted using DFM. To demonstrate the feasible use of the aptasensor for target detection, thrombin was evaluated as the model target. The limit of detection was determined to be 2.54 fM with dynamic range of 6 fM-100 fM. When the concentration of thrombin exceeded 100 fM, the counted number of AuNPs didn't correlate linearly to molecules of thrombin anymore, as the nanoparticles aggregated partly due to high concentration. However, the color of the solution changes to purple and the concentration of free AuNPs can be conveniently quantified by UV-Vis spectroscopy for up to 100 nM. It is noteworthy that our aptasensor is very easy to operate and requires neither complex isolation and amplification processes nor expensive instruments and consumables. Furthermore, this strategy can be easily generalized to other targets by replacing the corresponding aptamers and show great potential for the detection of biomarkers in clinical samples.

Digital quantification of DNA by mapping polarization degree related with coding gold nanorods

The development of highly sensitive and low-cost methods for detecting DNA is of critical importance. Here, we describe a strategy for the highly sensitive and low-cost digital detection of target DNA. Individual DNA molecules were encoded with a single gold nanorod (Au NR), which was then separated and enriched using the magnetic immune-separation process, followed by dehybridization and dispersion into a buffer solution and immobilization on glass slides for polarized dark-field microscopic imaging. With the imaging we can get the first three data sets of the Stokes vector, and the experimental degree of the linear polarization of the light scattered by the Au NR was obtained. Using the Monte Carlo simulation program, the Muller matrix of the Au NRs was simulated and the simulated degree of the linear polarization was calculated to be 0.58. Based on the experimental and simulated degree of the linear polarization, the Au NRs were identified and quantified with an in-house Matlab program, and the concentration of the target DNA at the femtomolar level was therefore achieved.

Microscopic Differentiation of Plasmonic Nanoparticles for the Ratiometric Read-out of Target DNA

The development of highly sensitive and rapid methods for detecting DNA is of critical importance. Here, we describe a strategy for the digital detection of target DNA at the femto-molar level. Individual DNA molecules were encoded with a single gold nanorod (AuNR), separated and enriched by magnetic immune-separation. The coding gold nanorods were then de-hybridized and dispersed into a gold nanosphere (AuNS) solution at a certain concentration, and both gold nanoparticles were immobilized on glass slides for dark-field microscopic imaging. Using an in-house Matlab program, the concentration of the target DNA was calculated based on the ratio of the coding gold nanorods to gold nanospheres. By combining the coding of individual biomolecules with a single gold nanorod and the use of gold nanospheres as an internal standard, a method for the rapid and accurate digital detection of target DNA to the femto-molar level was developed.

Digital immunoassay of a prostate-specific antigen using gold nanorods and magnetic nanoparticles

We have demonstrated a highly sensitive digital immunoassay for PSA detection.