Plasmonic Imaging of Multivalent NTD-Nucleic Acid Interactions for Broad-Spectrum Antiviral Drug Analysis

The discovery and identification of broad-spectrum antiviral drugs are of great significance for blocking the spread of pathogenic viruses and corresponding variants of concern. Herein, we proposed a plasmonic imaging-based strategy for assessing the efficacy of potential broad-spectrum antiviral drugs targeting the N-terminal domain of a nucleocapsid protein (NTD) and nucleic acid (NA) interactions. With NTD and NA conjugated gold nanoparticles as core and satellite nanoprobes, respectively, we found that the multivalent binding interactions could drive the formation of core-satellite nanostructures with enhanced scattering brightness due to the plasmonic coupling effect. The core-satellite assembly can be suppressed in the presence of antiviral drugs targeting the NTD-NA interactions, allowing the drug efficacy analysis by detecting the dose-dependent changes in the scattering brightness by plasmonic imaging. By quantifying the changes in the scattering brightness of plasmonic nanoprobes, we uncovered that the constructed multivalent weak interactions displayed a 500-fold enhancement in affinity as compared with the monovalent NTD-NA interactions. We demonstrated the plasmonic imaging-based strategy for evaluating the efficacy of a potential broad-spectrum drug, PJ34, that can target the NTD-NA interactions, with the IC50 as 24.35 and 14.64 μM for SARS-CoV-2 and SARS-CoV, respectively. Moreover, we discovered that ceftazidime holds the potential as a candidate drug to inhibit the NTD-NA interactions with an IC50 of 22.08 μM from molecular docking and plasmonic imaging-based drug analysis. Finally, we validated that the potential antiviral drug, 5-benzyloxygramine, which can induce the abnormal dimerization of nucleocapsid proteins, is effective for SARS-CoV-2, but not effective against SARS-CoV. All these demonstrations indicated that the plasmonic imaging-based strategy is robust and can be used as a powerful strategy for the discovery and identification of broad-spectrum drugs targeting the evolutionarily conserved viral proteins.

Nonamplification Multiplexed Assay of Endonucleases and DNA Methyltransferases by Colocalized Particle Counting

Restriction endonucleases (ENases) and DNA methyltransferases (MTases) are important enzymes in biological processes, and detection of ENases/MTases activity is significant for biological and pharmaceutical studies. However, available nonamplification methods with a versatile design, desirable sensitivity, and signal production mode of unbiased quantification toward multiple nucleases are rare. By combining deliberately designed hairpin DNA probes with the colocalized particle counting technique, we present a nonamplification, separation-free method for multiplexed detection of ENases and MTases. In the presence of target ENases, the hairpin DNA is cleaved and the resulting DNA sequence forms a sandwich structure to tie two different-colored fluorescent microbeads together to generate a colocalization signal that can be easily detected using a standard fluorescence microscope. The multiplexed assay is realized via different color combinations. For the assay of methyltransferase, methylation by MTases prevents cleavage of the hairpin by the corresponding ENase, leading to decreased colocalization events. Three ENases can be simultaneously detected with high selectivity, minimal cross-talk, and detection limits of (4.1-6.4) × 10^-4 U/mL, and the corresponding MTase activity can be measured without a change of the probe design. The potential for practical application is evaluated with human serum samples and different ENase and MTase inhibitors with satisfactory results. The proposed method is separation-free, unbiased toward multiple targets, and easy to implement, and the strategy has the potential to be extended to other targets.

Plasmonic Nanoparticles: Basics to Applications (I)

This review presents the main characteristics of metal nanoparticles (NPs), especially consisting of noble metal such as Au and Ag, and brief information on their synthesis methods. The physical and chemical properties of the metal NPs are described, with a particular focus on the optically variable properties (surface plasmon resonance based properties) and surface-enhanced Raman scattering of plasmonic materials. In addition, this chapter covers ways to achieve advances by utilizing their properties in the biological studies and medical fields (such as imaging, diagnostics, and therapeutics). These descriptions will help researchers new to nanomaterials for biomedical diagnosis to understand easily the related knowledge and also will help researchers involved in the biomedical field to learn about the latest research trends.

Single-Particle Mobility Analysis Enables Ratiometric Detection of Cancer Markers under Darkfield Tracking Microscopy

Here, we introduced a single-particle mobility analysis-based ratiometric strategy for quantitative detection of disease-related biomarkers using antibody-conjugated gold nanoparticles (AuNPs) as probes under darkfield tracking microscopy (DFTM). On the basis of the capability of discriminating nanoparticles with different hydrodynamic sizes and detecting the changes in hydrodynamic effect, single-particle mobility analysis enables us to determine the amount of aggregated and monodispersed nanoprobes for the sandwich-like immunoassay strategy, making it possible to quantify the biotargets by analyzing the relative changes in the aggregate-to-monomer ratio of nanoprobes. By using capture antibody and detection antibody conjugated AuNPs as nanoprobes, we demonstrated ratiometric detection of carcinoembryonic antigen (CEA) over a linear dynamic range from 50 to 750 pM, which is acceptable for clinical diagnostic analysis of CEA in tumor patients. This ratiometric detection technique exhibited excellent anti-interference ability in the presence of nonspecific proteins or complicated protein mixtures. It can be anticipated that this robust technique is promising for the accurate detection of disease biomarkers and other biomolecules for biochemical and diagnostic applications.

Recent advances of plasmonic nanoparticle-based optical analysis in homogeneous solution and at the single-nanoparticle level

Plasmonic nanoparticles with special localized surface plasmon resonance (LSPR) characters have been widely applied for optical sensing of various targets. With the combination of single nanoparticle imaging techniques, dynamic information of reactions and biological processes is obtained, facilitating the deep understanding of their principle and design of outstanding nanomaterials. In this review, we summarize the recently adopted optical analysis of diverse analytes based on plasmonic nanoparticles both in homogeneous solution and at the single-nanoparticle level. A brief introduction of LSPR is first discussed. Colorimetric and fluorimetric homogeneous detection examples by using different sensing mechanisms and strategies are provided. Single plasmonic nanoparticle-based analysis is concluded in two aspects: visualization of chemical reactions and understanding of biological processes. The basic sensing mechanisms and performances of these systems are introduced. Finally, this review highlights the challenges and future trend of plasmonic nanoparticle-based optical analysis systems.

Colocalized Particle Counting Platform for Zeptomole Level Multiplexed Quantification

For multiplexed detection, it is important yet challenging to simultaneously meet the requirement of sensitivity, throughput, and implementation convenience for practical applications. Using the detection of DNAs and miRNAs for illustration, we present a colocalized particle counting platform that can realize the separation-free multiplexed detection of 6 nucleic acid targets with a zeptomole sensitivity and a dynamic range of up to 5 orders of magnitude. The presence of target induces the formation of a sandwich nanostructure via hybridization; thus, there is an occurrence of colocalization of two microbeads with two different colors. The sequence specific coding is realized by an arbitrary combination of two fluorescence channels with different emitting colors. The platform presents robustness in detecting multiple nucleic acid targets with a minimal cross talk and matrix effect as well as the ability to distinguish the specific miRNA from members of the same family. The results of simultaneous detection of 3 miRNAs in 3 different cell lines present straight consistency with that of the standard qRT-PCR. This platform can be adapted to other multiplexing designs such as the "turn-off" mode, in which the proportion of colocalized microbeads is decreased due to the strand-displacement reaction initiated by the specific target. This separation-free platform offers the possibility to achieve the on-site multiplexed detection with compatibility to different experimental designs and extensibility to other signal sources for enumeration.

Plasmon Resonance Energy Transfer: Coupling between Chromophore Molecules and Metallic Nanoparticles

Plasmon resonance energy transfer (PRET) from a single metallic nanoparticle to the molecules adsorbed on its surface has attracted more and more attentions in recent years. Here, a molecular beacon (MB)-regulated PRET coupling system composed of gold nanoparticles (GNPs) and chromophore molecules has been designed to study the influence of PRET effect on the scattering spectra of GNPs. In this system, the chromophore molecules are tagged to the 5'-end of MB, which can form a hairpin structure and modified on the surface of GNPs by its thiol-labeled 3'-end. Therefore, the distance between GNPs and chromophore molecules can be adjusted through the open and close of the MB loop. From the peak shift, the PRET interactions of different GNPs-chromophore molecules coupling pairs have been calculated by discrete dipole approximation and the fitting results match well with the experimental data. Therefore, the proposed system has been successfully applied for the analysis of PRET situation between various metallic nanoparticles and chromophore molecules, and provides a useful tool for the potential application in screening the PRET-based nanoplasmonic sensors.

Analytical methods based on the light-scattering of plasmonic nanoparticles at the single particle level with dark-field microscopy imaging

This minireview summarizes analytical methods based on the light-scattering of gold nanoparticles with the dark-field microscopy imaging technique at the single particle level.

A universal and enzyme-free immunoassay platform for biomarker detection based on gold nanoparticle enumeration with a dark-field microscope

We develop a universal and enzyme-free magnetic bead-based sandwich-format immunoassay platform for biomarker detection by combining secondary antibody functionalized AuNPs and automatic AuNP counting.

A novel scattering switch-on detection technique for target-induced plasmon-coupling based sensing by single-particle optical anisotropy imaging

A novel scattering switch-on detection technique by using flash-lamp polarization darkfield microscopy (FLPDM) has been proposed for target-induced plasmon-coupling based sensing in homogeneous solution.

Gold nanoparticles as sensitive optical probes

Recent advances in Au NP based optical sensing systems for various analytes based on absorption, fluorescence and SERS are summarized.

Enzyme-Free Amplification by Nano Sticky Balls for Visual Detection of ssDNA/RNA Oligonucleotides

Visual detection of nucleic acids provides simple and rapid screening for infectious diseases or environmental pathogens. However, sensitivity is the current bottleneck, which may require enzymatic amplification for targets in low abundance and make them incompatible with detection at resource-limited sites. Here we report an enzyme-free amplification that provides a sensitive visual detection of ssDNA/RNA oligonucleotides on the basis of nano "sticky balls". When target oligonucleotides are present, magnetic microparticles (MMPs) and gold nanoparticles (AuNPs) were linked together, allowing the collection of AuNPs after magnetic attraction. Subsequently, the collected AuNPs, which carry many oligonucleotides, were used as the sticky balls to link a second pair of MMPs and polymer microparticles (PMPs). Thus, because the magnetic field can attract the MMPs as well as the linked PMPs to the sidewall, the reduction of suspended PMPs yields a change of light transmission visible by the naked eye. Our results demonstrate that the limit of detection is 10 amol for ssDNAs (228 fM in 45 μL) and 75 amol for ssRNAs (1.67 pM in 45 μL). This method is also compatible with the serum environment and detection of a microRNA, miR-155, derived from human breast cancer cells. With significantly improved sensitivity for visual detection, it provides great potential for point-of-care applications at resource-limited sites.

Femtomolar oligonucleotide detection by a one-step gold nanoparticle-based assay

A sequence-specific oligonucleotide detection method based on the tail-to-tail aggregation of functionalized gold nanoparticles in the presence of target analytes is presented together with its optimization and capabilities for detection of single nucleotide polymorphisms (SNPs). In this single-step method, capture probes are freely accessible for hybridization, resulting in an improved assay performance compared to substrate-based assays. The analytes bring the nanoparticles close to each other via hybridization, causing a red shift of the nanoparticle plasmon peak detected by a spectrophotometer or CCD camera coupled to a darkfield imaging system. Optimal conditions for the assay were found to be (i) use of capture probes complementary to the target without any gap, (ii) maximum possible probe density on the gold nanoparticles, and (iii) 1M ionic strength buffer. The optimized assay has a 1 fM limit of detection and fM to 10 pM dynamic range, with detection of perfect match sequences being three orders of magnitude more sensitive than targets with single nucleotide mismatches.

A single gold nanorod as a plasmon resonance energy transfer based nanosensor for high-sensitivity Cu(II) detection

Plasmon resonance energy transfer (PRET) has been widely applied in the detection of bio-recognition, heavy metal ions and cellular reactions with high sensitivity, based on the overlap between the plasmon resonance scattering band of nanoparticles and the absorption band of the surface-modified chromophore molecules. Previous sensors based on PRET were all implemented on gold nanospheres with scattering light in the range of 530 to 600 nm. In this work, a PRET-based nanosensor was developed on a thiol-di(2-picolyl)amine-modified single gold nanorod for the detection of Cu(2+) ions in aqueous solution with high sensitivity and selectivity. Compared to nanospheres, gold nanorods with tunable and wide plasmon resonance bands from the near-infrared to the infrared region exhibit promising potential for development as sensing probes.

Visual detection of nucleic acids based on Mie scattering and the magnetophoretic effect

Visual detection of nucleic acid biomarkers by magnetically attracted microparticles that change solution turbidity via Mia scattering.