Encoding peptide sequences with surface-enhanced Raman spectroscopic nanoparticles

Ultrasensitive amplification-free detection of circulating miRNA via droplet-based processing of SERS tag-miRNA-magnetic nanoparticle sandwich nanocomplexes on a paper-based electrowetting-on-dielectric platform

MicroRNAs (miRNAs) have emerged as a promising class of biomarkers for early detection of various cancers, including ovarian cancer. However, quantifying miRNAs in human blood samples is challenging owing to the issues of sensitivity and specificity. In this study, hsa-miR-200a-3p of the miR-200a sub-family, which is a biomarker of ovarian cancer, was used as the analyte to demonstrate the analytical capability of an integrated biosensing platform using an extremely sensitive surface-enhanced Raman scattering (SERS) nanotag-nanoaggregate-embedded beads (NAEBs), magnetic nanoparticles (MNPs), a pair of highly specific locked nucleic acid (LNA) probes, and a semi-automated paper-based electrowetting-on-dielectric (pEWOD) device to provide labor-less and thorough sample cleanup and recovery. A sandwich approach where NAEBs are modified by one LNA-1 probe and MNPs are modified by another LNA-2 probe was applied. Then, the target analyte miRNA-200a-3p was introduced to form a sandwich nanocomplex through hybridization with the pair of LNA probes. The pEWOD device was used to achieve short cleanup time and good recovery of the nanocomplex, bringing the total analysis time to less than 30 min. The detection limit of this approach can reach 0.26 fM through SERS detection. The versatility of this method without the need for RNA extraction from clinical samples is expected to have good potential in detecting other miRNAs.

Applications of Gold Nanoparticles in Plasmonic and Nanophotonic Biosensing

The unique properties of plasmonic nanoparticles and nanostructures have enabled a broad range of applications in a diverse set of fields, ranging from biological sensing, cancer therapy, to catalysis. They have been some of the most studied nanomaterials due in part to their chemical stability and biocompatibility as well as supporting theoretical efforts. The synthesis and fabrication of plasmonic nanoparticles and nanostructures have now reached high precision and sophistication. We review here their fundamental optical properties, discuss their tailoring for biological environments, and then detail examples on how they have been used to innovate in the biological and biomedical fields.

Orthogonal Combinatorial Raman Codes Enable Rapid High-Throughput-Out Library Screening of Cell-Targeting Ligands

High-throughput assays play an important role in the fields of drug discovery, genetic analysis, and clinical diagnostics. Although super-capacity coding strategies may facilitate labeling and detecting large numbers of targets in a single assay, practically, the constructed large-capacity codes have to be decoded with complicated procedures or are lack of survivability under the required reaction conditions. This challenge results in either inaccurate or insufficient decoding outputs. Here, we identified chemical-resistant Raman compounds to build a combinatorial coding system for the high-throughput screening of cell-targeting ligands from a focused 8-mer cyclic peptide library. The accurate in situ decoding results proved the signal, synthetic, and functional orthogonality for this Raman coding strategy. The orthogonal Raman codes allowed for a rapid identification of 63 positive hits at one time, evidencing a high-throughput-out capability in the screening process. We anticipate this orthogonal Raman coding strategy being generalized to enable efficient high-throughput-out screening of more useful ligands for cell targeting and drug discovery.

Periodic Surface-Enhanced Raman Scattering-Encoded Magnetic Beads for Reliable Quantitative Surface-Enhanced Raman Scattering-Based Multiplex Bioassay

Surface-enhanced Raman scattering (SERS)-based immunoassay on encoded beads is highly attractive with the advantages of ultrasensitivity, multiplex and high throughput. However, it was a great challenge to screen out in-focus signals of the immunoconjugated SERS nanoprobes on spherical bead conveniently. Here, periodic SERS-encoded magnetic beads (PSE-MBs) were developed through droplet optofluidic technique by using monodisperse SERS-encoded magnetic nanospheres as building blocks. The designed PSE-MBs not only exhibit huge coding capacity, but also provide the strongest and reproducible SERS coding signals as "in-focus beacons". When PSE-MBs are used as capture carriers in SERS-based immunoassay, both multiple target analytes and in-focus signals of SERS nanoprobes could be easily identified according to the collected SERS coding signals. Thus, reliable quantitative analysis of multiple target analytes could be conveniently achieved by such detection protocol. Additionally, the magnetic ingredient in PSE-MBs made the operation easily during the bioassay. The multiple advantages of PSE-MBs including large coding capacity, in-focus beacons and magnetic operation endorse them to be robust capture carriers in reliable quantitative SERS-based multiplex immunoassay.

Functional Micro-/Nanomaterials for Multiplexed Biodetection

When analyzing biological phenomena and processes, multiplexed biodetection has many advantages over single-factor biodetection and is highly relevant to both human health issues and advancements in the life sciences. However, many key problems with current multiplexed biodetection strategies remain unresolved. Herein, the main issues are analyzed and summarized: 1) generating sufficient signal to label targets, 2) improving the signal-to-noise ratio to ensure total detection sensitivity, and 3) simplifying the detection process to reduce the time and labor costs of multiple target detection. Then, available solutions made possible by designing and controlling the properties of micro- and nanomaterials are introduced. The aim is to emphasize the role that micro-/nanomaterials can play in the improvement of multiplexed biodetection strategies. Through analyzing existing problems, introducing state-of-the-art developments regarding relevant materials, and discussing future directions of the field, it is hopeful to help promote necessary developments in multiplexed biodetection and associated scientific research.

Sensitive and Multiplexed SERS Nanotags for the Detection of Cytokines Secreted by Lymphoma

The sensitive and simultaneous detection of cytokines will provide new insights into the physiological process and disease pathways due to the complex nature of cytokine networks. However, the key challenge is the lack of probes that can simultaneously detect multiple cytokines in a single sample. In this contribution, we proposed an alternative approach for sensitive cytokine detection in a multiplex manner by the use of a new set of surface-enhanced Raman spectroscopy (SERS) nanotags. Typically, the newly designed SERS nanotags are composed of gold nanoparticles as the core, tuneable Raman molecules as the reporters, and a thin silver layer as the shell. As demonstrated through rigorous numerical simulations, enhanced Raman signal is achieved due to a strong localization of light in the 0.2 nm thin, optically deep-subwavelength region between the Au core and the Ag shell. Sensitive detection of cytokines is realized by forming a sandwich immunoassay. The detection limit is down to 4.5 pg mL^-1 (S/N = 3). The specificity of the assay is proved as negligible signals were detected for the false targets. Furthermore, multiple cytokines are simultaneously detected in a single assay from the secretion of B-lymphocyte cell line (Raji) after concanavalin A (Con A) stimulation. The results indicate that our method holds a significant potential for sensitive and multiplexed detection of cytokines and offers the opportunity for future applications in clinical settings.

Two-dimensional SERS encoding method for on-bead peptide sequencing in high-throughput bioanalysis

We developed a ready-to-read on-bead peptide encoding method for high-throughput screening bioassays. With two-dimensional surface-enhanced Raman scattering nano-identifiers (2D-SERS IDs) which are concurrently labelled with two SERS codes (coupling steps and kinds of amino acid), we could possibly generate more than 10 trillion codes with only 30 Raman label compounds.

Dual-wavelength digital holographic phase and fluorescence microscopy combining with Raman spectroscopy for micro-quartz pieces-based dual-channel encoded suspension array

Dual-wavelength digital holographic phase and fluorescence microscopy (DW-DHPFM), combining with Raman spectroscopy, is designed to achieve the detection and analysis of biomolecules with a new dual-channel encoding method. This employs the Raman reporter molecules assembled micro-quartz pieces (MQPs) as microcarriers of suspension array (SA). The dual-wavelength digital holographic phase microscopy (DW-DHPM) and Raman spectroscopy are served as the decoding platforms, and the fluorescence microscopy is used to quantify target analytes. Considering the independence between encoding and label signal, the above two encoding channels could effectively avoid the crosstalk in immunoassay process, and the combination of two encoding methods expand the encoding capacity with a considerable magnitude. Accurate and stable decoding abilities are verified by multiplexed immunoassay experiment and the quantitative analysis of targets with high-sensitivity is confirmed by concentration gradient experiments.

Fast and accurate decoding of Raman spectra-encoded suspension arrays using deep learning

A deep learning network called “residual neural network” (ResNet) was used to decode Raman spectra-encoded suspension arrays (SAs).

Multilayer Ag-Embedded Silica Nanostructure as a Surface-Enhanced Raman Scattering-Based Chemical Sensor with Dual-Function Internal Standards

Surface-enhanced Raman scattering (SERS) spectroscopy is attractive in various detection analysis fields. However, the quantitative method using SERS spectroscopy remains as an area to be developed. The key issues in developing quantitative analysis methods by using SERS spectroscopy are the fabrication of reliable SERS-active materials such as nanoparticle-based structures and the acquisition of the SERS signal without any disturbance that may change the SERS signal intensity and frequency. Here, the fabrication of seamless multilayered core-shell nanoparticles with an embedded Raman label compound as an internal standard (ML_RLC dots) for quantitative SERS analysis is reported. The embedded Raman label compound in the nanostructure provides a reference value for calibrating the SERS signals. By using the ML_RLC dots, it is possible to gain target analyte signals of different concentrations while retaining the Raman signal of the internal standard. The ML_4-BBT dots, containing 4-bromobenzenethiol (4-BBT) as an internal standard, are successfully applied in the quantitative analysis of 4-fluorobenzenethiol and thiram, a model pesticide. Additionally, ratiometric analysis was proved practical through normalization of the relative SERS intensity. The ratiometric strategy could be applied to various SERS substrates for quantitative detection of a wide variety of targets.

Multiplexed microarrays based on optically encoded microbeads

In recent years, there has been growing interest in optically-encoded or tagged functionalized microbeads as a solid support platform to capture proteins or nucleotides which may serve as biomarkers of various diseases. Multiplexing technologies (suspension array or planar array) based on optically encoded microspheres have made possible the observation of relatively minor changes in biomarkers related to specific diseases. The ability to identify these changes at an early stage may allow the diagnosis of serious diseases (e.g. cancer) at a time-point when curative treatment may still be possible. As the overall accuracy of current diagnostic methods for some diseases is often disappointing, multiplexed assays based on optically encoded microbeads could play an important role to detect biomarkers of diseases in a non-invasive and accurate manner. However, detection systems based on functionalized encoded microbeads are still an emerging technology, and more research needs to be done in the future. This review paper is a preliminary attempt to summarize the state-of-the-art concerning diagnostic microbeads; including microsphere composition, synthesis, encoding technology, detection systems, and applications.

Endoscopic imaging using surface-enhanced Raman scattering

In this review, we assessed endoscopic imaging using surface-enhanced Raman scattering (SERS). As white-light endoscopy, the current standard for gastrointestinal endoscopy, is limited to morphology, Raman endoscopy using surface-enhanced Raman scattering nanoparticles (SERS endoscopy) was introduced as one of the novel functional modalities. SERS endoscopy has multiplex capability and high sensitivity with low autofluorescence and photobleaching. As a result, multiple molecular characteristics of the lesion can be accurately evaluated in real time while performing endoscopy using SERS probes and appropriate instrumentation. Especially, recently developed dual modality of fluorescence and SERS endoscopy offers easy localization with identification of multiple target molecules. For clinical use of SERS endoscopy in the future, problems of limited field of view and cytotoxicity should be addressed by fusion imaging, topical administration, and non-toxic coating of nanoparticles. We expect SERS endoscopic imaging would be an essential endoscopic technique for diagnosis of cancerous lesions, assessment of resection margins and evaluation of therapeutic responses.

High-Throughput Peptide Screening on a Bimodal Imprinting Chip Through MS-SPRi Integration

Screening of high affinity and high specificity peptide probes towards various targets is important in the biomedical field while traditional peptide screening procedure is manual and tedious. Herein, a bimodal imprinting microarray system to embrace the whole peptide screening process is presented. Surface Plasmon Resonance imaging (SPRi) and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) are combined for both quantitative and qualitative identification of the peptide. The method provides a solution for high efficiency peptide screening.

Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection

Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and "point of care" platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields.

Direct identification of on-bead peptides using surface-enhanced Raman spectroscopic barcoding system for high-throughput bioanalysis

Recently, preparation and screening of compound libraries remain one of the most challenging tasks in drug discovery, biomarker detection, and biomolecular profiling processes. So far, several distinct encoding/decoding methods such as chemical encoding, graphical encoding, and optical encoding have been reported to identify those libraries. In this paper, a simple and efficient surface-enhanced Raman spectroscopic (SERS) barcoding method using highly sensitive SERS nanoparticles (SERS ID) is presented. The 44 kinds of SERS IDs were able to generate simple codes and could possibly generate more than one million kinds of codes by incorporating combinations of different SERS IDs. The barcoding method exhibited high stability and reliability under bioassay conditions. The SERS ID encoding based screening platform can identify the peptide ligand on the bead and also quantify its binding affinity for specific protein. We believe that our SERS barcoding technology is a promising method in the screening of one-bead-one-compound (OBOC) libraries for drug discovery.

A fast and reliable readout method for quantitative analysis of surface-enhanced Raman scattering nanoprobes on chip surface

Surface-enhanced Raman scattering techniques have been widely used for bioanalysis due to its high sensitivity and multiplex capacity. However, the point-scanning method using a micro-Raman system, which is the most common method in the literature, has a disadvantage of extremely long measurement time for on-chip immunoassay adopting a large chip area of approximately 1-mm scale and confocal beam point of ca. 1-μm size. Alternative methods such as sampled spot scan with high confocality and large-area scan method with enlarged field of view and low confocality have been utilized in order to minimize the measurement time practically. In this study, we analyzed the two methods in respect of signal-to-noise ratio and sampling-led signal fluctuations to obtain insights into a fast and reliable readout strategy. On this basis, we proposed a methodology for fast and reliable quantitative measurement of the whole chip area. The proposed method adopted a raster scan covering a full area of 100 μm × 100 μm region as a proof-of-concept experiment while accumulating signals in the CCD detector for single spectrum per frame. One single scan with 10 s over 100 μm × 100 μm area yielded much higher sensitivity compared to sampled spot scanning measurements and no signal fluctuations attributed to sampled spot scan. This readout method is able to serve as one of key technologies that will bring quantitative multiplexed detection and analysis into practice.

Graphene oxide-encoded Ag nanoshells with single-particle detection sensitivity towards cancer cell imaging based on SERRS

Developing ultrasensitive Raman nanoprobes is one of the emerging interests in the field of biosensing and bioimaging. Herein, we constructed a new type of surface-enhanced resonance Raman scattering nanoprobe composed of an Ag nanoshell as a surface-enhanced Raman scattering-active nanostructure, which was encapsulated with 4,7,10-trioxa-1,13-tridecanediamine-functionalized graphene oxide as an ultrasensitive Raman reporter exhibiting strong resonance Raman scattering including distinct D and G modes. The designed nanoprobe was able to produce much more intense and simpler Raman signals even at a single particle level than the Ag nanoshell bearing a well-known Raman reporter, which is beneficial for the sensitive detection of a target in a complex biological system. Finally, this ultrasensitive nanoprobe successfully demonstrated its potential for bioimaging of cancer cells using Raman spectroscopy.

One-step synthesis of silver nanoshells with bumps for highly sensitive near-IR SERS nanoprobes

A seedless, one-step synthetic route to uniform bumpy silver nanoshells (AgNSs) as highly NIR sensitive SERS substrates is reported. These substrates can incorporate Raman label compounds and biocompatible polymers on their surface. AgNS based NIR-SERS probes are successfully applied to cell tracking in a live animal using a portable Raman system.

A continuous flow microfluidic-MS system for efficient OBOC screening

A microfluidic chip based method utilized for effective screening of high-throughput peptide libraries was achieved. 10⁵beads was processed within 4 hours and peptide ligands towardtarget protein AHA and APN were successfully discovered.

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.

Surface-enhanced Raman scattering-active nanostructures and strategies for bioassays

Surface-enhanced Raman scattering (SERS) techniques offer a number of advantages in molecular detection and analysis, particularly in terms of the multiplex detection of biomolecules. So far, many new SERS-based substrates and analytical techniques have been reported. For easy understanding, various SERS techniques are classified into the following four categories: adsorption-mediated direct detection; antibody- or ligand-mediated direct detection; binding catalyzed indirect detection; and tag-based indirect detection. Among these, recent successes of SERS tagging/encoding (nano/micro) materials and detection methods are highlighted, including our recent works. Some novel SERS-based strategies for the detection of several biological molecules are also introduced.