Multiplexed Discrimination of Single Amino Acid Residues in Polypeptides in a Single SERS Hot Spot

Intra-nanoparticle plasmonic nanogap based spatial-confinement SERS analysis of polypeptides

Sensing and characterizing water-soluble polypeptides are essential in various biological applications. However, detecting polypeptides using Surface-Enhanced Raman Scattering (SERS) remains a challenge due to the dominance of aromatic amino acid residues and backbones in the signal, which hinders the detection of non-aromatic amino acid residues. Herein, intra-nanoparticle plasmonic nanogap were designed by etching the Ag shell in Au@AgNPs (i.e., obtaining AuAg cores) with chlorauric acid under mild conditions, at the same time forming the outermost Au shell and the void between the AuAg cores and the Au shell (AuAg@void@Au). By varying the Ag to added chloroauric acid molar ratios, we pioneered a simple, controllable, and general synthetic strategy to form interlayer-free nanoparticles with tunable Au shell thickness, achieving precise regulation of electric field enhancement within the intra-nanogap. As validation, two polypeptide molecules, bacitracin and insulin B, were successfully synchronously encapsulated and spatial-confined in the intra-nanogap for sensing. Compared with concentrated 50 nm AuNPs and Au@AgNPs as SERS substrates, our simultaneous detection method improved the sensitivity of the assay while benefiting to obtain more comprehensive characteristic peaks of polypeptides. The synthetic strategy of confining analytes while fabricating plasmonic nanostructures enables the diffusion of target molecules into the nanogap in a highly specific and sensitive manner, providing the majority of the functionality required to achieve peptide detection or sequencing without the hassle of labeling.

Surface-Enhanced Raman Spectroscopy: Current Understanding, Challenges, and Opportunities

While surface-enhanced Raman spectroscopy (SERS) has experienced substantial advancements since its discovery in the 1970s, it is an opportunity to celebrate achievements, consider ongoing endeavors, and anticipate the future trajectory of SERS. In this perspective, we encapsulate the latest breakthroughs in comprehending the electromagnetic enhancement mechanisms of SERS, and revisit CT mechanisms of semiconductors. We then summarize the strategies to improve sensitivity, selectivity, and reliability. After addressing experimental advancements, we comprehensively survey the progress on spectrum-structure correlation of SERS showcasing their important role in promoting SERS development. Finally, we anticipate forthcoming directions and opportunities, especially in deepening our insights into chemical or biological processes and establishing a clear spectrum-structure correlation.

Perspective on Tailored Nanostructure-Dominated SPP Effects for SERS

Localized surface plasmon resonance (LSPR) excited by an incident light can normally produce strong surface-enhanced Raman scattering (SERS) at the nanogaps among plasmonic nano-objects (so-called hot spots), which is extensively explored. In contrast, surface plasmon polaritons (SPPs) that can be generated by an incident beam via particular structures with a conservation of wave vectors can excite SERS effects as well. SPPs actually play an indispensable role in high-performance SERS devices but receive much less attention. In this perspective, SPPs and their couplings with LSPR for SERS excitations with differing effectiveness through particular plasmonic/dielectric structures/configurations, along with relevant fabrication approaches, are profoundly reviewed and commented on from a unique perspective from in situ to ex situ excitations of SERS enabled by spatiotemporally separated multiple processes of SPPs. Quantitative design of particular configurations/architectures enabling highly efficient and effective multiple processes of SPPs is particularly emphasized as one giant leap toward ultimate full quantitative design of intrinsically high-performance SERS chips and very critical for their batch manufacturability and applications as well. The viewpoints and prospects about innovative SERS devices based on tailored structure-dominated SPPs effects and their coupling with LSPR are presented and discussed.

Phase-Tunable Molybdenum Boride Ceramics as an Emerging Sensitive and Reliable SERS Platform in Harsh Environments

Traditional surface-enhanced Raman scattering (SERS) sensors rely heavily on the use of plasmonic noble metals, which have limitations due to their high cost and lack of physical and chemical stability. Hence, it is imperative to explore new materials as SERS platforms that can withstand high temperatures and harsh conditions. In this study, the SERS effect of molybdenum boride ceramic powders is presented with an enhancement factor of 5 orders, which is comparable to conventional noble metal substrates. The molybdenum boride powders synthesized through liquid-phase precursor and carbothermal reduction have β-MoB, MoB2 , and Mo2 B5 phases. Among these phases, β-MoB demonstrates the most significant SERS activity, with a detection limit for rhodamine 6G (R6G) molecules of 10-9  m. The impressive SERS enhancement can be attributed to strong molecule interactions and prominent charge interactions between R6G and the various phases of molybdenum boride, as supported by theoretical calculations. Additionally, Raman measurements show that the SERS activity remains intact after exposure to high temperature, strong acids, and alkalis. This research introduces a novel molybdenum boride all-ceramic SERS platform capable of functioning in harsh conditions, thereby showing the promising of boride ultrahigh-temperature ceramics for detection applications in extreme environments.

Self-Assembled Three-Dimensional Polyamide/Silver Nanoparticle Pore Array as a Highly Sensitive and Reproducible SERS Substrate for Pesticide Detection in Water

In this study, silver nanoparticles (AgNPs) are self-assembled onto the polyamide (PA) pore array through hydrogen bonding, resulting in and optimizing the PA/Ag 3D pore array substrates. The best surface-enhanced Raman scattering (SERS) substrate is obtained with a pore depth of 500 nm in the PA array, 30 nm AgNPs, at a pH of 5.0, and a 24 h assembly time. The SERS performance of the substrates is assessed using rhodamine 6G (R6G) as a probe molecule. The detection limit of the R6G molecule reaches 10-13 M, and the relative standard deviation is under 20%, indicating good enhancement ability and reproducibility. Furthermore, label-free detection of pesticide contaminant diquat with a detection limit of 2.69 × 10-9 M is achieved using the optimized 3D substrate, which meets environmental monitoring requirements for drinking water. The findings demonstrate that this 3D SERS substrate has promising potential for use and development in the fields of contaminant detection and chemical sensing.

SERS and machine learning based effective feature extraction for detection and identification of amphetamine analogs

Surface-enhanced Raman spectroscopy (SERS) is extensively researched in diverse disciplines due to its sensitivity and non-destructive nature. It is particularly considered a potential and promising technology for rapid on-site screening in drug detection. In this investigation, a technique was developed for fabricating nanocrystals of Ag@Au SNCs. Ag@Au SNCs, as the basic material of SERS, can detect amphetamine at concentrations as low as 1 μg/mL. The Ag@Au SNCs exhibits a strong surface plasmon resonance effect, which amplifies molecular signals. The SERS spectra of ten substances, including amphetamine and its analogs, showed a strong peak signal. To establish a qualitative distinction, we examined the Raman spectra and conducted density functional theory (DFT) calculations on the ten aforementioned species. The DFT calculation enabled us to determine the vibrational frequency and assign normal modes, thereby facilitating the qualitative differentiation of amphetamines and its analogs. Furthermore, the SERS spectrum of the ten mentioned substances was analysed using the support vector machine learning algorithm, which yielded a discrimination accuracy of 98.0 %.

Recent methodological advances towards single-cell proteomics

Studying the central dogma at the single-cell level has gained increasing attention to reveal hidden cell lineages and functions that cannot be studied using traditional bulk analyses. Nonetheless, most single-cell studies exploiting genomic and transcriptomic levels fail to address information on proteins that are central to many important biological processes. Single-cell proteomics enables understanding of the functional status of individual cells and is particularly crucial when the specimen is composed of heterogeneous entities of cells. With the growing importance of this field, significant methodological advancements have emerged recently. These include miniaturized and automated sample preparation, multi-omics analyses, and combined analyses of multiple techniques such as mass spectrometry and microscopy. Moreover, artificial intelligence and single-molecule detection technologies have advanced throughput and improved sensitivity limitations, respectively, over conventional methods. In this review, we summarize cutting-edge methodologies for single-cell proteomics and relevant emerging technologies that have been reported in the last 5 years, and provide an outlook on this research field.

Plasmonic Nanostructure Biosensors: A Review

Plasmonic nanostructure biosensors based on metal are a powerful tool in the biosensing field. Surface plasmon resonance (SPR) can be classified into localized surface plasmon resonance (LSPR) and propagating surface plasmon polariton (PSPP), based on the transmission mode. Initially, the physical principles of LSPR and PSPP are elaborated. In what follows, the recent development of the biosensors related to SPR principle is summarized. For clarity, they are categorized into three groups according to the sensing principle: (i) inherent resonance-based biosensors, which are sensitive to the refractive index changes of the surroundings; (ii) plasmon nanoruler biosensors in which the distances of the nanostructure can be changed by biomolecules at the nanoscale; and (iii) surface-enhanced Raman scattering biosensors in which the nanostructure serves as an amplifier for Raman scattering signals. Moreover, the advanced application of single-molecule detection is discussed in terms of metal nanoparticle and nanopore structures. The review concludes by providing perspectives on the future development of plasmonic nanostructure biosensors.

Deep Learning Assisted Surface-Enhanced Raman Spectroscopy (SERS) for Rapid and Direct Nucleic Acid Amplification and Detection: Toward Enhanced Molecular Diagnostics

Surface-enhanced Raman scattering (SERS) has evolved into a robust analytical technique capable of detecting a variety of biomolecules despite challenges in securing a reliable Raman signal. Conventional SERS-based nucleic acid detection relies on hybridization assays, but reproducibility and signal strength issues have hindered research on directly amplifying nucleic acids on SERS surfaces. This study introduces a deep learning assisted ZnO-Au-SERS-based direct amplification (ZADA) system for rapid, sensitive molecular diagnostics. The system employs a SERS substrate fabricated by depositing gold on uniformly grown ZnO nanorods. These nanorods create hot spots for the amplification of the target nucleic acids directly on the SERS surface, eliminating the need for postamplification hybridization and Raman reporters. The limit of detection of the ZADA system was superior to those of the conventional amplification methods. Clinical validation of the ZADA system with coronavirus disease 2019 (COVID-19) samples from human patients yielded a sensitivity and specificity of 92.31% and 81.25%, respectively. The integration of a deep learning program further enhanced sensitivity and specificity to 100% and reduced SERS analysis time, showcasing the potential of the ZADA system for rapid, label-free disease diagnosis via direct nucleic acid amplification and detection within 20 min.

Current strategies of plasmonic nanoparticles assisted surface-enhanced Raman scattering toward biosensor studies

With the progressive nanofabrication technology, plasmonic nanoparticles (PNPs) have been increasingly deployed in the field of biosensing. PNPs have favorable biocompatibility, conductivity, and tunable optical properties. In addition, the localized surface plasmon resonance (LSPR) of PNPs plays a vital role in surface-enhanced Raman scattering (SERS). PNPs-based SERS biosensing enables wide-ranging applications for sensitive detection and high spatial and temporal resolution imaging. Numerous reviews of PNPs in the field of SERS biosensing highlight the fabrication or applications in one or more fields. However, the specific strategies for the SERS biosensor construction had not been summarized systematically. Thus, this work offers a comprehensive overview of SERS enhancement strategies based on PNPs, with a focus on SERS label-free detection along with label detection sensing construction, as well as its challenges and future trends.

Single-Molecule Electrical and Spectroscopic Profiling Protein Allostery Using a Gold Plasmonic Nanopore

Direct structural and dynamic characterization of protein conformers in solution is highly desirable but currently impractical. Herein, we developed a single molecule gold plasmonic nanopore system for observation of protein allostery, enabling us to monitor translocation dynamics and conformation transition of proteins by ion current detection and SERS spectrum measurement, respectively. Allosteric transition of calmodulin (CaM) was elaborately probed by the nanopore system. Two conformers of CaM were well-resolved at a single-molecule level using both the ion current blockage signal and the SERS spectra. The collected SERS spectra provided structural evidence to confirm the interaction between CaM and the gold plasmonic nanopore, which was responsible for the different translocation behaviors of the two conformers. SERS spectra revealed the amino acid residues involved in the conformational change of CaM upon calcium binding. The results demonstrated that the excellent spectral characterization furnishes a single-molecule nanopore technique with an advanced capability of direct structure analysis.

Single Molecule Protein Segments Sequencing by a Plasmonic Nanopore

Obtaining sequential and conformational information on proteins is vital to understand their functions. Although the nanopore-based electrical detection can sense single molecule (SM) protein and distinguish among different amino acids, this approach still faces difficulties in slowing down protein translocation and improving ionic current signal-to-noise ratio. Here, we observe the unfolding and multistep sequential translocation of SM cytochrome c (cyt c) through a surface enhanced Raman scattering (SERS) active conical gold nanopore. High bias voltage unfolds SM protein causing more exposure of amino acid residues to the nanopore, which slows down the protein translocation. Specific SERS traces of different SM cyt c segments are then recorded sequentially when they pass through the hotspot inside the gold nanopore. This study shows that the combination of SM SERS with a nanopore can provide a direct insight into protein segments and expedite the development of nanopore toward SM protein sequencing.

Quinine-Fabricated Surface-Enhanced Raman Spectroscopy Chiral Sensing Platform Enables Simultaneous Enantioselective Discrimination and Identification of Aliphatic Amino Acids

Due to low optical activity and structural simplicity, synchronous chiral discrimination and identification of aliphatic amino acids (AAs) are still challenging yet demanding. Herein, we developed a novel surface-enhanced Raman spectroscopy (SERS)-based chiral discrimination-sensing platform for aliphatic AAs, in which l- and d-enantiomers are able to discriminately bind with quinine to generate distinct differences in the SERS vibrational modes. Meanwhile, the plasmonic sub-nanometer gaps supported by the rigid quinine enable the maximization of SERS signal enhancement to reveal feeble signals, allowing for simultaneously acquiring the structural specificity and enantioselectivity of aliphatic amino acid enantiomers in a single SERS spectrum. Different kinds of chiral aliphatic AAs were successfully identified by using this sensing platform, demonstrating its potential and practicality in recognizing chiral aliphatic molecules.

Detection of simple proteins by direct surface-enhanced Raman scattering based on the Hofmeister ion-specific effect

Surface-enhanced Raman scattering (SERS) spectroscopy has unique advantages in detecting biomolecules, but label-free determination of proteins with low scattering cross-sections remains challenging. In this study, such proteins' SERS signals have been optimized using the Hofmeister effect between protein molecules and CsI solution at physiological concentrations (A 100 mmol/L Cesium iodide, CsI). Cs⁺ as chaotro cation ion has a complex interaction mechanism with protein, can not only deprive hydrated water molecules on the surface of protein but also penetrate into the hydrophobic interior of protein. In addition to the above advantages, I^- in excess CsI solution with appropriate concentration can removes the interference of citric acid-based impurities on the surface of silver nanoparticles, and Cs⁺ in excess CsI solution attracts the aggregation of negatively charged silver nanoparticles and cause local electromagnetic field enhancement to achieve high sensitivity in protein detection. This has been combined with principal component analysis to perform a comprehensive analysis of several proteins. Molecular dynamics simulations have been performed to study the mechanism of interaction between CsI and proteins. In addition, the vibrational peak of water has been used as an internal standard to quantify the protein content, and a good linear relationship between peak intensity and concentration was obtained.

Universal Method for Label-Free Detection of Pathogens and Biomolecules by Surface-Enhanced Raman Spectroscopy Based on Gold Nanoparticles

The detection of biomolecules is the key to basic molecular research, diagnostics, drug screening, and other biomedical applications. However, the existing detection techniques can only detect single classes of biomolecules, which warrant the development of a versatile biomolecule detection platform. Here, we developed a universal method for label-free detection of biomolecules via surface-enhanced Raman spectroscopy (SERS) by using sulfhydryl-modified gold nanoparticles as the substrate. The biomolecules can be adsorbed on the surface of gold nanoparticles cleaned by bromide ions to obtain initially enhanced Raman signals, and the aggregator (calcium ion) was further added to form a "hot spot", which enhanced the biomolecular signal again. Through the "two-step enhancement method", we were able to obtain fingerprints of DNA, RNA, amino acids, peptides, proteins, viruses, bacteria, and lipid molecules. This low-toxic, highly sensitive, and widely applicable technique has potential applications in biomedical research, clinical testing, and disease diagnosis and lays the foundation for the development of SERS technology in various fields.

Toward a New Era of SERS and TERS at the Nanometer Scale: From Fundamentals to Innovative Applications

Surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering (TERS) have opened a variety of exciting research fields. However, although a vast number of applications have been proposed since the two techniques were first reported, none has been applied to real practical use. This calls for an update in the recent fundamental and application studies of SERS and TERS. Thus, the goals and scope of this review are to report new directions and perspectives of SERS and TERS, mainly from the viewpoint of combining their mechanism and application studies. Regarding the recent progress in SERS and TERS, this review discusses four main topics: (1) nanometer to subnanometer plasmonic hotspots for SERS; (2) Ångström resolved TERS; (3) chemical mechanisms, i.e., charge-transfer mechanism of SERS and semiconductor-enhanced Raman scattering; and (4) the creation of a strong bridge between the mechanism studies and applications.

A versatile technique for indiscriminate detection of unlabeled biomolecules via double-enhanced Raman scattering

Surface-enhanced Raman scattering is a rapid, highly sensitive and non-destructive technique, whereas, it was still limited to designing different types of enhancing substrates or using probe molecules to only identify single biomolecules. Especially, some special biomolecules have weak Raman signals in solid state, so it is a huge challenge to obtain their enhanced Raman signals in liquid. To solve the problem, a double-enhanced Raman scattering (DERS) detection platform was developed in this study based on silver nanoparticles that were prepared by using an appropriate amount of sodium borohydride and guided by calcium ions to form good "hot spots". This enabled one to successfully obtain fingerprints of various types of biomolecules under the identical experimental conditions. The addition of sodium borohydride as reducing agent could protect silver nanoparticles from oxidation, and biomolecules were adsorbed on the exposed silver surface and demonstrated their initially enhanced Raman signals. Furthermore, the "hot spots" formed by silver nanoparticles without silver oxide coating could further enhance the Raman signal of biomolecules, making the enhancement factor up to 10 [8]. To sum up, the possibility of fast identification of different species of biomolecules via DERS has wide application prospects in the fields of biomarker detection and medical diagnosis.

Nanoparticle-based surface enhanced Raman spectroscopic imaging of biological arrays

Surfaces serve as the communication link between the adsorbate and the substrate. Hence, a thorough understanding of the surface chemistries directly interfacing with biological molecules and other adsorbates would provide insight into the fabrication approach as well as the adsorption characteristics of biomolecules adsorbed on the surface. This paper presents a surface-enhanced Raman spectroscopy (SERS) method for high-sensitivity detection and reading of protein microarrays based on gold nanoparticle labels. The reagent employed was 30 nm gold nanoparticles modified with a bifunctional Raman reporter molecule, 5,5'-dithiobis(succinimidyl-2-nitrobenzoate) (DSNB), to integrate anti-bovine IgG for an antigen response in the immunoassay and generate an intense SERS signal. The signal from the DSNB reporter molecule, particularly the strong symmetric nitro stretch was used for the detection of antigen-antibody interactions. Issues related to the sensitivity and selectivity of the assay were also addressed. This work provides useful insights into SERS-based immunoassays and serves as the basis for an eventful adventure into interfacial biomolecular interactions.

Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering

The study of biologically relevant molecules and their interaction with external stimuli on a single molecular scale is of high importance due to the availability of distributed rather than averaged information. Surface enhanced Raman scattering (SERS) provides direct chemical information, but is rather challenging on the single molecule (SM) level, where it is often assumed to require a direct contact of analyte molecules with the metal surface. Here, we detect and investigate the molecular states of single hemin by SM-SERS. A DNA aptamer based G-quadruplex mediated recognition of hemin directs its placement in the SERS hot-spot of a DNA Origami Nanofork Antenna (DONA). The configuration of the DONA structure allows the molecule to be trapped at the plasmonic hot-spot preferentially in no-contact configuration with the metal surface. Owing to high field enhancement at the plasmonic hot spot, the detection of a single folded G-quadruplex becomes possible. For the first time, we present a systematic study by SM-SERS where most hemin molecule adopt a high spin and oxidation state (III) that showed state crossover to low spin upon strong-field-ligand binding. The present study therefore, provides a platform for studying biologically relevant molecules and their properties at SM sensitivity along with demonstrating a conceptual advancement towards successful monitoring of single molecular chemical interaction using DNA aptamers.

Recent Progress on Solid Substrates for Surface-Enhanced Raman Spectroscopy Analysis

Surface-enhanced Raman spectroscopy (SERS) is a powerful vibrational spectroscopy technique with distinguished features of non-destructivity, ultra-sensitivity, rapidity, and fingerprint characteristics for analysis and sensors. The SERS signals are mainly dependent on the engineering of high-quality substrates. Recently, solid SERS substrates with diverse forms have been attracting increasing attention due to their promising features, including dense hot spot, high stability, controllable morphology, and convenient portability. Here, we comprehensively review the recent advances made in the field of solid SERS substrates, including their common fabrication methods, basic categories, main features, and representative applications, respectively. Firstly, the main categories of solid SERS substrates, mainly including membrane substrate, self-assembled substrate, chip substrate, magnetic solid substrate, and other solid substrate, are introduced in detail, as well as corresponding construction strategies and main features. Secondly, the typical applications of solid SERS substrates in bio-analysis, food safety analysis, environment analysis, and other analyses are briefly reviewed. Finally, the challenges and perspectives of solid SERS substrates, including analytical performance improvement and largescale production level enhancement, are proposed.

Label-Free SERS Detection of Protein Damage in Organelles under Electrostimulation with 2D AuNPs-based Nanomembranes as Substrates

Proteins as the material basis of life are the main undertakers of life activities. However, it is difficult to identify the related proteins in organelles during stimuli-induced stress responses in cells and remains a great challenge in early diagnosis and treatment of disease. Here, proteins in the cell nucleus and mitochondria of cells under the electrical stimulation (ES) process were collected and sensitively detected based on label-free surface-enhanced Raman spectroscopy (SERS) by using AuNP-based nanomembranes as high-performance SERS substrates. Due to the existence of rich "hot spots" on the 2D plasmonic sensing platform, high-quality SERS spectra of proteins were obtained with superior sensitivity and repeatability. From the SERS analyses in vitro, it was found that the conformation of some proteins in the two kinds of organelles from cancerous HCT-116 cells (compared with normal NCM-460 cells) changed significantly and the expression levels of tyrosine, phenylalanine, and tryptophan were significantly promoted during the stimulation process. Although currently the exact proteins are still unknown, the damage of proteins in the organelles of cells at the amino acid level under ES can be revealed by the method. The developed plasmonic SERS sensing platform would be promising for bioassay and cell studies.

Applications of Single-Molecule Vibrational Spectroscopic Techniques for the Structural Investigation of Amyloid Oligomers

Amyloid oligomeric species, formed during misfolding processes, are believed to play a major role in neurodegenerative and metabolic diseases. Deepening the knowledge about the structure of amyloid intermediates and their aggregation pathways is essential in understanding the underlying mechanisms of misfolding and cytotoxicity. However, structural investigations are challenging due to the low abundance and heterogeneity of those metastable intermediate species. Single-molecule techniques have the potential to overcome these difficulties. This review aims to report some of the recent advances and applications of vibrational spectroscopic techniques for the structural analysis of amyloid oligomers, with special focus on single-molecule studies.

Phosphonium-Based Ionic Liquid Significantly Enhances SERS of Cytochrome c on TiO2 Nanotube Arrays

Surface-enhanced Raman scattering (SERS) is an attractive technique for studying trace detection. It is of utmost importance to further improve the performance and understand the underlying mechanisms. An ionic liquid (IL), the anion of which is derived from biomass, [P6,6,6,14][FuA] was synthesized and used as a trace additive to improve the SERS performance of cytochrome c (Cyt c) on TiO2 nanotube arrays (TNAs). An increased and better enhancement factor (EF) by four to five times as compared to the system without an IL was obtained, which is better than that from using the choline-based amino acid IL previously reported by us. Dissociation of the ILs improved the ionic conductivity of the system, and the long hydrophobic tails of the [P6,6,6,14]+ cation contributed to a strong electrostatic interaction between Cyt c and the TNA surface, thereby enhancing the SERS performance. Atomic force microscopy did verify strong electrostatic interactions between the Cyt c molecules and TNAs after the addition of the IL. This work demonstrates the importance of introducing the phosphonium-based IL to enhance the SERS performance, which will stimulate further development of more effective ILs on SERS detection and other relevant applications in biology.

Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing

Sequence identification of peptides and proteins is central to proteomics. Protein sequencing is mainly conducted by insensitive mass spectroscopy because proteins cannot be amplified, which hampers applications such as single-cell proteomics and precision medicine. The commercial success of portable nanopore sequencers for single DNA molecules has inspired extensive research and development of single-molecule techniques for protein sequencing. Among them, three challenges remain: (1) discrimination of the 20 amino acids as building blocks of proteins; (2) unfolding proteins; and (3) controlling the motion of proteins with nonuniformly charged sequences. In this context, the emergence of label-free optical analysis techniques for single amino acids and peptides by solid-state nanopores shows promise for addressing the first challenge. In this Perspective, we first discuss the current challenges of single-molecule fluorescence detection and nanopore resistive pulse sensing in a protein sequencing. Then, label-free optical methods are described to show how they address the single-amino-acid identification within single peptides. They include localized surface plasmon resonance detection and surface-enhanced Raman spectroscopy on plasmonic nanopores. Notably, we report new data to show the ability of plasmon-enhanced Raman scattering to record and discriminate the 20 amino acids at a single-molecule level. In addition, we discuss briefly the manipulation of molecule translocation and liquid flow in plasmonic nanopores for controlling molecule movement to allow high-resolution reading of protein sequences. We envision that a combination of Raman spectroscopy with plasmonic nanopores can succeed in single-molecule protein sequencing in a label-free way.

Controlling the Shrinkage of 3D Hot Spot Droplets as a Microreactor for Quantitative SERS Detection of Anticancer Drugs in Serum Using a Handheld Raman Spectrometer

Quantitative measurement is one of the ultimate targets for surface-enhanced Raman spectroscopy (SERS), but it suffers from difficulties in controlling the uniformity of hot spots and placing the target molecules in the hot spot space. Here, a convenient approach of three-phase equilibrium controlling the shrinkage of three-dimensional (3D) hot spot droplets has been demonstrated for the quantitative detection of the anticancer drug 5-fluorouracil (5-FU) in serum using a handheld Raman spectrometer. Droplet shrinkage, triggered by the shaking of aqueous nanoparticle (NP) colloids with immiscible oil chloroform (CHCl₃) after the addition of negative ions and acetone, not only brings the nanoparticles in close proximity but can also act as a microreactor to enhance the spatial enrichment capability of the analyte in plasmonic sites and thereby realize simultaneously controlling 3D hot spots and placing target molecules in hot spots. Moreover, the shrinking process of Ag colloid droplets has been investigated using a high-speed camera, an in situ transmission electron microscope (in situ TEM), and a dark-field microscope (DFM), demonstrating the high stability and uniformity of nanoparticles in droplets. The shrunk Ag NP droplets exhibit excellent SERS sensitivity and reproducibility for the quantitative analysis of 5-FU over a large range of 50-1000 ppb. Hence, it is promising for quantitative analysis of complex systems and long-term monitoring of bioreactions.

Single-atom sites on perovskite chips for record-high sensitivity and quantification in SERS

Surface enhanced Raman scattering (SERS) is a rapid and nondestructive technique that is capable of detecting and identifying chemical or biological compounds. Sensitive SERS quantification is vital for practical applications, particularly for portable detection of biomolecules such as amino acids and nucleotides. However, few approaches can achieve sensitive and quantitative Raman detection of these most fundamental components in biology. Herein, a noble-metal-free single-atom site on a chip strategy was applied to modify single tungsten atom oxide on a lead halide perovskite, which provides sensitive SERS quantification for various analytes, including rhodamine, tyrosine and cytosine. The single-atom site on a chip can enable quantitative linear SERS responses of rhodamine (10^-6-1 mmol L^-1), tyrosine (0.06-1 mmol L^-1) and cytosine (0.2-45 mmol L^-1), respectively, which all achieve record-high enhancement factors among plasmonic-free semiconductors. The experimental test and theoretical simulation both reveal that the enhanced mechanism can be ascribed to the controllable single-atom site, which can not only trap photoinduced electrons from the perovskite substrate but also enhance the highly efficient and quantitative charge transfer to analytes. Furthermore, the label-free strategy of single-atom sites on a chip can be applied in a portable Raman platform to obtain a sensitivity similar to that on a benchtop instrument, which can be readily extended to various biomolecules for low-cost, widely demanded and more precise point-of-care testing or in-vitro detection.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material is available for this article at 10.1007/s40843-022-1968-5 and is accessible for authorized users.

A versatile technique based on surface-enhanced Raman spectroscopy for label-free detection of amino acids and peptide formation in body fluids

As an effective analytical method, surface-enhanced Raman spectroscopy (SERS) is widely used in the detection of nucleic acids, amino acids, and other biomolecules. However, obtaining the SERS signal of nonaromatic amino acids is still a challenge. In this work, excess sodium borohydride was used as a reducing agent to prevent the surface of silver nanoparticles from being coated with AgO to enable amino acid molecules to reach the surface of silver nano-substrates. Calcium ions were used as aggregators for silver nano-substrates to successfully achieve the label-free and accurate fingerprint determination of various nonaromatic amino acids. Different types of amino acids were distinguished based on the changes in their peak intensity that were obtained using colorless and transparent organic dichloromethane (DCM) as the internal standard. A Raman signal for low-concentration amino acids in body fluids was detected, and the detection limit for tyrosine was 5 ng/mL. Moreover, the physical and chemical properties of peptides and the formation of peptide chains were further analyzed. The proposed method can potentially be applied to protein sequencing.

Surface-enhanced Raman spectroscopy detection of organic molecules and in situ monitoring of organic reactions by ion-induced silver nanoparticle clusters

Surface-enhanced Raman spectroscopy (SERS) finds wide applications in the field of organic molecule detection. However, reliable SERS detection of organic molecules and in situ monitoring of organic reactions under natural conditions by metal colloids are still challenging due to the formation of unstable nanoparticle clusters in solution and the low solubility of the organic molecules. Here, we approach the problems by introducing calcium ions to aggregate silver nanoparticles to form stable hot spots and acetone to promote uniform distribution of organic molecules on the nanoparticle surface. Significantly, our method exhibits stable SERS detection of up to 6 types of organic molecules in liquid. With acetone signals as an internal standard, we are able to determine molecule concentrations as well as monitor 3 kinds of organic reactions in situ. Our method shows potential for biomedical analysis, environmental analysis, and organic catalysis research.

Simultaneous and ultra-sensitive SERS detection of SLPI and IL-18 for the assessment of donor kidney quality using black phosphorus/gold nanohybrids

Due to the global challenge of donor kidney shortage, expanding the pool of deceased donors has been proposed to include expanded criteria donors. However, the lack of methods to precisely measure donor kidney injury and predict the outcome still leads to high discard rates and recipient complications. As such, evaluation of deceased donor kidney quality is critical prior to transplantation. Biomarkers from donor urine or serum provide potential advantages for the precise measure of kidney quality. Herein, simultaneous detection of secretory leukocyte peptidase inhibitor (SLPI) and interleukin 18 (IL-18), two important kidney injury biomarkers, has been achieved, for the first time, with an ultra-high sensitivity using surface enhanced Raman scattering (SERS). Specifically, black phosphorus/gold (BP/Au) nanohybrids synthesized by depositing Au nanoparticles (NPs) onto the BP nanosheets serve as SERS-active substrates, which offer a high-density of inherent and accessible hot-spots. Meanwhile, the nanohybrids possess biocompatible surfaces for the enrichment of target biomarkers through the affinity with BP nanosheets. Quantitative detection of SLPI and IL-18 were then achieved by characterizing SERS signals of these two biomarkers. The results indicate high sensitivity and excellent reproducibility of this method. The limits of detection reach down to 1.53×10^-8 mg/mL for SLPI and 0.23×10^-8 mg/mL for IL-18. The limits of quantification are 5.10×10^-8 mg/mL and 7.67×10^-9 mg/mL for SLPI and IL-18. In addition, simultaneous detection of these biomarkers in serum was investigated, which proves the feasibility in biologic environment. More importantly, this method is powerful for detecting multiple analytes inheriting from excellent multiplexing ability of SERS. Giving that the combined assessment of SLPI and IL-18 expression level serves as an indicator of donor kidney quality and can be rapidly and reproducibly conducted, this SERS-based method holds great prospective in clinical practice.

Nanoparticle Fragmentation Below the Melting Point Under Single Picosecond Laser Pulse Stimulation

Understanding the laser-nanomaterials interaction including nanomaterial fragmentation has important implications in nanoparticle manufacturing, energy, and biomedical sciences. So far, three mechanisms of laser-induced fragmentation have been recognized including non-thermal processes and thermomechanical force under femtosecond pulses, and the phase transitions under nanosecond pulses. Here we show that single picosecond (ps) laser pulse stimulation leads to anomalous fragmentation of gold nanoparticles that deviates from these three mechanisms. The ps laser fragmentation was weakly dependent on particle size, and it resulted in a bimodal size distribution. Importantly, ps laser stimulation fragmented particles below the whole particle melting point and below the threshold for non-thermal mechanism. We propose a framework based on near-field enhancement and nanoparticle surface melting to account for the ps laser-induced fragmentation observed here. This study reveals a new form of surface ablation that occurs under picosecond laser stimulation at low fluence.

Multiplexed Profiling of Extracellular Vesicles for Biomarker Development

Extracellular vesicles (EVs) are cell-derived membranous particles that play a crucial role in molecular trafficking, intercellular transport and the egress of unwanted proteins. They have been implicated in many diseases including cancer and neurodegeneration. EVs are detected in all bodily fluids, and their protein and nucleic acid content offers a means of assessing the status of the cells from which they originated. As such, they provide opportunities in biomarker discovery for diagnosis, prognosis or the stratification of diseases as well as an objective monitoring of therapies. The simultaneous assaying of multiple EV-derived markers will be required for an impactful practical application, and multiplexing platforms have evolved with the potential to achieve this. Herein, we provide a comprehensive overview of the currently available multiplexing platforms for EV analysis, with a primary focus on miniaturized and integrated devices that offer potential step changes in analytical power, throughput and consistency.

Probing Multidimensional Structural Information of Single Molecules Transporting through a Sub-10 nm Conical Plasmonic Nanopore by SERS

Probing the orientation and oxygenation state of single molecules (SMs) is of great importance for understanding the advanced structure of individual molecules. Here, we manipulate molecules transporting through the hot spot of a sub-10 nm conical gold nanopore and acquire the multidimensional structural information of the SMs by surface enhanced Raman scattering (SERS) detection. The sub-10 nm size and conical shape of the plasmonic nanopore guarantee its high detection sensitivity. SERS spectra show a high correlation with the orientations of small-sized single rhodamine 6G (R6G) during transport. Meanwhile, SERS spectra of a single hemoglobin (Hb) reveal both the vertical/parallel orientations of the porphyrin ring and oxygenated/deoxygenated states of Hb. The present study provides a new strategy for bridging the primary sequence and the advanced structure of SMs.

Broadband SERS Enhancement by DNA Origami Assembled Bimetallic Nanoantennas with Label-Free Single Protein Sensing

Engineering hotspots in surface-enhanced Raman spectroscopy (SERS) through precisely controlled assembly of plasmonic nanostructures capable of expanding intense field enhancement are highly desirable to enhance the potentiality of SERS as a label-free optical tool for single molecule detection. Inspired by DNA origami technique, we constructed plasmonic dimer nanoantennas with a tunable gap decorated with Ag-coated Au nanostars on origami. Herein, we demonstrate the single-molecule SERS enhancements of three dyes with emission in different spectral regions after incorporation of single dye molecules in between two nanostars. The enhancement factors (EFs) achieved in the range of 10⁹-10¹⁰ for all the single dye molecules, under both resonant and nonresonant excitation conditions, would enable enhanced photostability during time-series measurement. We further successfully explored the potential of our designed nanoantennas to accommodate and detect a single thrombin protein molecule after selective placement in the wide nanogap of 10 nm. Our results suggest that such nanoantennas can serve as a broadband SERS enhancer and enable specific detection of target biological molecules with single-molecule sensitivity.

General Surface-Enhanced Raman Spectroscopy Method for Actively Capturing Target Molecules in Small Gaps

Over the past decade, many efforts have been devoted to designing and fabricating substrates for surface-enhanced Raman spectroscopy (SERS) with abundant hot spots to improve the sensitivity of detection. However, there have been many difficulties involved in causing molecules to enter hot spots actively or effectively. Here, we report a general SERS method for actively capturing target molecules in small gaps (hot spots) by constructing a nanocapillary pumping model. The ubiquity of hot spots and the inevitability of molecules entering them lights up all the hot spots and makes them effective. This general method can realize the highly sensitive detection of different types of molecules, including organic pollutants, drugs, poisons, toxins, pesticide residues, dyes, antibiotics, amino acids, antitumor drugs, explosives, and plasticizers. Additionally, in the dynamic detection process, an efficient and stable signal can be maintained for 1-2 min, which increases the practicality and operability of this method. Moreover, a dynamic detection process like this corresponds to the processes of material transformation in some organisms, so the method can be used to monitor transformation processes such as the death of a single cell caused by photothermal stimulation. Our method provides a novel pathway for generating hot spots that actively attract target molecules, and it can achieve general ultratrace detection of diverse substances and be applied to the study of cell behaviors in biological systems.

Hydrated Ionic Liquids Boost the Trace Detection Capacity of Proteins on TiO2 Support

Trace detection based on surface-enhanced Raman scattering (SERS) has attracted considerable attention, and exploiting efficient strategies to stretch the limit of detection and understanding the mechanisms on molecular level are of utmost importance. In this work, we use ionic liquids (ILs) as trace additives in a protein-TiO2 system, allowing us to obtain an exceptionally low limit of detection down to 10-9 M. The enhancement factors (EFs) were determined to 2.30 × 104, 6.17 × 104, and 1.19 × 105, for the three systems: one without ILs, one with ILs in solutions, and one with ILs immobilized on the TiO2 substrate, respectively, corresponding to the molecular forces of 1.65, 1.32, and 1.16 nN quantified by the atomic force microscopy. The dissociation and following hydration of ILs, occurring in the SERS system, weakened the molecular forces but instead improved the electron transfer ability of ILs, which is the major contribution for the observed excellent detection. The weaker diffusion of the hydrated IL ions immobilized on the TiO2 substrate did provide a considerably greater EF value, compared to the ILs in the solution. This work clearly demonstrates the importance of the hydration of ions, causing an improved electron transfer ability of ILs and leading to an exceptional SERS performance in the field of trace detection. Our results should stimulate further development to use ILs in SERS and related applications in bioanalysis, medical diagnosis, and environmental science.

Metal-Modified Montmorillonite as Plasmonic Microstructure for Direct Protein Detection

Thanks to its negative surface charge and high swelling behavior, montmorillonite (MMT) has been widely used to design hybrid materials for applications in metal ion adsorption, drug delivery, or antibacterial substrates. The changes in photophysical and photochemical properties observed when fluorophores interact with MMT make these hybrid materials attractive for designing novel optical sensors. Sensor technology is making huge strides forward, achieving high sensitivity and selectivity, but the fabrication of the sensing platform is often time-consuming and requires expensive chemicals and facilities. Here, we synthesized metal-modified MMT particles suitable for the bio-sensing of self-fluorescent biomolecules. The fluorescent enhancement achieved by combining clay minerals and plasmonic effect was exploited to improve the sensitivity of the fluorescence-based detection mechanism. As proof of concept, we showed that the signal of fluorescein isothiocyanate can be harvested by a factor of 60 using silver-modified MMT, while bovine serum albumin was successfully detected at 1.9 µg/mL. Furthermore, we demonstrated the versatility of the proposed hybrid materials by exploiting their plasmonic properties to develop liquid label-free detection systems. Our results on the signal enhancement achieved using metal-modified MMT will allow the development of highly sensitive, easily fabricated, and cost-efficient fluorescent- and plasmonic-based detection methods for biomolecules.

Plasmonic structure with nanocavity cavities for SERS detection of pesticide thiram

Excessive thiram residues in food have the potential to negatively impact human health. Hence, the development of a convenient and fast detection method is highly desirable. In this study, an efficient, repeatable, and sensitive surface-enhanced Raman scattering (SERS) active chip was manufactured via a low-cost colloidal lithography technique. The plasmonic structure was composed of a series of silver nanospheres and nanowires. Interestingly, this type structure creates a nanocavity space with a characteristic geometry generating a strong electromagnetic field coupling. The finite-different time-domain software was employed to simulate the electromagnetic field distribute on the nanocavity. Accordingly, SERS active chip that displays ultra-low concentration detection of thiram (10^-11 M) was realized. Moreover, the excellent reproducibility of thiram (10^-6 M) practical detection on an apple pericarp has great potential for application in food safety.

Raman Enhancement of Nanoparticle Dimers Self-Assembled Using DNA Origami Nanotriangles

Surface-enhanced Raman scattering is a powerful approach to detect molecules at very low concentrations, even up to the single-molecule level. One important aspect of the materials used in such a technique is how much the signal is intensified, quantified by the enhancement factor (EF). Herein we obtained the EFs for gold nanoparticle dimers of 60 and 80 nm diameter, respectively, self-assembled using DNA origami nanotriangles. Cy5 and TAMRA were used as surface-enhanced Raman scattering (SERS) probes, which enable the observation of individual nanoparticles and dimers. EF distributions are determined at four distinct wavelengths based on the measurements of around 1000 individual dimer structures. The obtained results show that the EFs for the dimeric assemblies follow a log-normal distribution and are in the range of 106 at 633 nm and that the contribution of the molecular resonance effect to the EF is around 2, also showing that the plasmonic resonance is the main source of the observed signal. To support our studies, FDTD simulations of the nanoparticle's electromagnetic field enhancement has been carried out, as well as calculations of the resonance Raman spectra of the dyes using DFT. We observe a very close agreement between the experimental EF distribution and the simulated values.

Optical tweezers-controlled hotspot for sensitive and reproducible surface-enhanced Raman spectroscopy characterization of native protein structures

Surface-enhanced Raman spectroscopy (SERS) has emerged as a powerful tool to detect biomolecules in aqueous environments. However, it is challenging to identify protein structures at low concentrations, especially for the proteins existing in an equilibrium mixture of various conformations. Here, we develop an in situ optical tweezers-coupled Raman spectroscopy to visualize and control the hotspot between two Ag nanoparticle-coated silica beads, generating tunable and reproducible SERS enhancements with single-molecule level sensitivity. This dynamic SERS detection window is placed in a microfluidic flow chamber to detect the passing-by proteins, which precisely characterizes the structures of three globular proteins without perturbation to their native states. Moreover, it directly identifies the structural features of the transient species of alpha-synuclein among its predominant monomers at physiological concentration of 1 μM by reducing the ensemble averaging. Hence, this SERS platform holds the promise to resolve the structural details of dynamic, heterogeneous, and complex biological systems.

Recent advances in plasmonic nanocavities for single-molecule spectroscopy

Plasmonic nanocavities are able to engineer and confine electromagnetic fields to subwavelength volumes. In the past decade, they have enabled a large set of applications, in particular for sensing, optical trapping, and the investigation of physical and chemical phenomena at a few or single-molecule levels. This extreme sensitivity is possible thanks to the highly confined local field intensity enhancement, which depends on the geometry of plasmonic nanocavities. Indeed, suitably designed structures providing engineered local optical fields lead to enhanced optical sensing based on different phenomena such as surface enhanced Raman scattering, fluorescence, and Förster resonance energy transfer. In this mini-review, we illustrate the most recent results on plasmonic nanocavities, with specific emphasis on the detection of single molecules.

Breaking the symmetry of nanosphere lithography with anisotropic plasma etching induced by temperature gradients

We report a novel anisotropic process, termed plasma etching induced by temperature gradients (PE-TG), which we use to modify the 3D morphology of a hexagonally close-packed polystyrene sphere array. Specifically, we combined an isotropic oxygen plasma (generated by a plasma cleaner) and a vertical temperature gradient applied from the bottom to the top of a colloidal mask to create an anisotropic etching process. As a result, an ordered array of well-defined and separated nano mushrooms is obtained. We demonstrate that the features of the mushrooms, namely the hat size and their intrinsic undercut, as well as the pillar diameter and height, can be easily tuned by adjusting the main parameters of the process i.e. the temperature gradient and etching time, or the spheres' size. We show that PS mushroom arrays can be used as nanostructured templates to fabricate plasmonic arrays, such as gold-capped nano mushrooms and ultra-small nanoapertures, by using vertical and oblique gold sputtering deposition respectively. PE-TG reveals a new, cheap and facile approach to produce plasmonic nanostructures of great interest in the fields of molecular sensing, surface-enhanced Raman scattering (SERS), energy harvesting and optoelectronics. We study the optical properties of the Au-capped nano mushroom arrays and their performance as biosensing platforms by performing SERS measurements.

An overview of surface-enhanced Raman scattering substrates by pulsed laser deposition technique: fundamentals and applications

Metallic nanoparticles (NPs), as an efficient substrate for surface-enhanced Raman scattering (SERS), attract much interests because of their various shapes and sizes. The appropriate size and morphology of metallic NPs are critical to serve as the substrate for achieving an efficient SERS. Pulsed laser deposition (PLD) is one of the feasible physical methods employed to synthesize metallic NPs with controllable sizes and surface characteristics. It has been recognized to be a successful tool for the deposition of SERS substrates due to its good controllability and high reproducibility in the manufacture of metallic NPs. This review provides an overview about the recent advances for the preparation of SERS substrates by PLD technique. The influences of parameters on the sizes and morphologies of metallic NPs during the deposition processes in PLD technique including laser output parameters, gas medium, liquid medium, substrate temperature, and properties of 3D substrate are presented. The applications of SERS substrates produced by PLD in the environmental monitoring and biomedical analysis are summarized. This knowledge could serve as a guideline for the researchers in exploring further applications of PLD technique in the production of SERS substrate.