Tip-Enhanced Raman Imaging of Single-Stranded DNA with Single Base Resolution

Emerging SERS and TERS MoS2 platforms for the characterization of plasma-derived extracellular vesicles

Extracellular vesicles (EVs) play a crucial role in intercellular communication processes. In addition, their biomolecular cargoes such as lipids, proteins, and nucleic acids are useful for identifying potential biomarkers related to different stages of cancer disease. However, the small size and heterogenicity of tumor-related EVs represent a major challenge in properly identifying the content of EVs' cargoes with common characterization protocols. To address these issues, surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) are powerful alternatives to assign the vibrational fingerprints to the biomolecules contained in cancer EVs, providing high specificity and spatial resolution. Transition metal dichalcogenides are particularly interesting as SERS and TERS substrates due to the high sensitivity of their 2D surface through coulombic and van der Waals interactions when in contact with an analyte or small object such as the charged membranes of EVs. These interactions induce subtle changes in the work function of the flakes which can be measured through drastic changes of optical processes. We investigate the use of MoS2 flakes synthesized by atmospheric pressure chemical vapor deposition as a potential label-free SERS and TERS platform for the identification of plasma EVs. To exemplify this technology, we isolated plasma EV samples from donors with early-stage [FIGO (I/II)] with high-grade serous carcinoma (HGSC) by size exclusion chromatography (SEC). Both surface- and tip-enhanced measurements were conducted individually, enabling the identification of a series of markers from ovarian cancer donors, highlighting the complementarity of SERS and TERS measurements.

Modulated-Illumination Intermittent-Contact Tip-Enhanced Raman Spectroscopy

This article presents a proof-of-concept for a new imaging method that combines tip-enhanced Raman spectroscopy with intermittent-contact atomic force microscopy to provide simultaneous nanometer-scale mechanical imaging with chemical contrast. The foremost difference from a standard tip-enhanced Raman microscope is the Raman illumination, which is modulated by the cantilever drive signal so that illumination is only active when the tip is close to the surface. This approach significantly reduces contact forces and thermal damage due to constant illumination while simultaneously reducing background Raman signals. Near-field optical and dynamic cantilever simulations highlight the effect of the imaging parameters on the tip-sample force and the evanescent field enhancement. The experimental images obtained with this new imaging method demonstrate a lateral resolution sufficient to identify single-walled carbon nanotube bundles with a full width at half-maximum of 20 nm.

Spatial Resolution in Nanoscale TERS Imaging: Current Status, Challenges, and Guidelines

Tip-enhanced Raman spectroscopy (TERS) was invented almost 25 years ago and was quickly recognized as one of the few nano-optical techniques that confine light at the nanoscale to explore light-matter interactions at the nanoscale. Even several years after its invention, the spatial resolution in TERS studies is not only somewhat controversial, especially for AFM-based TERS measurements of samples at room temperature, but also not reported in the literature in a consistent, generally accepted fashion. This Mini-Review discusses the current situation and how spatial resolution in TERS is reported in different ways that yield different values because no standard method is defined. More importantly, the spatial resolution in TERS is influenced by various experimental conditions and other factors in a comprehensive fashion, which have often been ignored. We consider all possible factors that affect spatial resolution in TERS and provide guidelines on how to determine and report spatial resolution.

Real-Space Spectral Determination of Short Single-Stranded DNA Sequence Structures

Resolving the sequence and structure of flexible biomolecules such as DNA is crucial to understanding their biological mechanisms and functions. Traditional structural biology methods remain challenging for the analysis of small and disordered biomolecules, especially those that are difficult to label or crystallize. Recent development of single-molecule tip-enhanced Raman spectroscopy (TERS) offers a label-free approach to identifying nucleobases in a single DNA chain. However, a clear demonstration of sequencing both spatially and spectrally at single-base resolution is still elusive due to the challenges caused by weak Raman signals and the flexibility of DNA molecules. Here, we report a proof-of-principle demonstration to this end, spectrally resolving in real space individual nucleobases and their sequence structures within a short, single-stranded DNA molecule artificially designed. This breakthrough is achieved through the development of subnanometer-resolved low-temperature TERS methodology for such thermally unstable flexible biomolecules. Further TERS mapping over individual nucleobases provides additional structural information about the molecular configurations and even the locations of functional groups, offering a way to track modification types and binding sites in biomolecules.

Integrating, Validating, and Expanding Information Space in Single-Molecule Surface-Enhanced Raman Spectroscopy for Biomolecules

Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) is an ultrahigh-resolution spectroscopic method for directly obtaining the complex vibrational mode information on individual molecules. SM-SERS offers a wide range of submolecular information on the hidden heterogeneity in its functional groups and varying structures, dynamics of conformational changes, binding and reaction kinetics, and interactions with the neighboring molecule and environment. Despite the richness in information on individual molecules and potential of SM-SERS in various detection targets, including large and complex biomolecules, several issues and practical considerations remain to be addressed, such as the requirement of long integration time, challenges in forming reliable and controllable interfaces between nanostructures and biomolecules, difficulty in determining hotspot size and shape, and most importantly, insufficient signal reproducibility and stability. Moreover, utilizing and interpreting SERS spectra is challenging, mainly because of the complexity and dynamic nature of molecular fingerprint Raman spectra, and this leads to fragmentary analysis and incomplete understanding of the spectra. In this Perspective, we discuss the current challenges and future opportunities of SM-SERS in views of system approaches by integrating molecules of interest, Raman dyes, plasmonic nanostructures, and artificial intelligence, particularly for detecting and analyzing biomolecules to realize the validation and expansion of information space in SM-SERS.

Rapid Fingerprinting of Urinary Volatile Metabolites and Point-of-Care Diagnosis of Phenylketonuria on a Patterned Nanorod Sensor Array with Multiplexed Surface-Enhanced Raman Scattering Readouts

Phenylketonuria (PKU) is one of the most common genetic metabolic diseases, especially among newborns. Traditional clinical examination of newborn blood samples for PKU is invasive, laborious, and limited to hospitals and healthcare facilities. We reported herein a SERS-based sensor array with three thiophenolic nanoreceptors built on a patterned nanorod vertical array for rapid and inexpensive detection of characteristic volatile biomarkers indicative of PKU in the urine and accurate classification of newborn baby patients all performed on a hand-held SERS spectrophotometer. The well-ordered array was generated from the volatility-driven assembly of gold nanorods (AuNRs) into an upright and closely packed hexagonal configuration. The uniformly distributed nanowells between AuNRs offered an intense and aspect-ratio-dependent plasmonic field for the molecular enhancement of SERS outputs. The SERS-based detector was integrated into a test chip for regular monitoring of volatile phenylketone bodies in the spiked solution or patients' urine within 5 min, allowing the quantification of a wide variety of normal or abnormal metabolites at their physiologically relevant concentration range. The detection limits for common biomarkers of PKU, including phenylpyruvic acid, 4-hydroxyphenylacetic acid, and phenylacetic acid, were at a few μM and well below the diagnostic thresholds. Moreover, the volatile headspace mixtures from a given urine sample could be fingerprinted by the sensor array and discriminated using machine-learning algorithms. Ultimately, the discrimination of baby patients among 26 cases of mild and classic PKU phenotypes and 17 cases of healthy volunteers could be realized with an overall accuracy of 97%. This hand-held SERS platform plays a pivotal role in advancing healthcare applications in quick screening of neonatal PKU through a facile urinary vapor test.

Toward Modeling the Complexity of the Chemical Mechanism in SERS

Surface-enhanced Raman scattering (SERS) provides detailed information about the binding of molecules at interfaces and their interactions with the local environment due to the large enhancement of Raman scattering. This enhancement arises from a combination of the electromagnetic mechanism (EM) and chemical mechanism (CM). While it is commonly accepted that EM gives rise to most of the enhancement, large spectral changes originate from CM. To elucidate the rich information contained in SERS spectra about molecules at interfaces, a comprehensive understanding of the enhancement mechanisms is necessary. In this Perspective, we discuss the current understanding of the enhancement mechanisms and highlight their interplay in complex local environments. We will also discuss emerging areas where the development of computational and theoretical models is needed with specific attention given to how the CM contributes to the spectral changes. Future efforts in modeling should focus on overcoming the challenges presented in this review in order to capture the complexity of CM in SERS.

Advanced Vibrational Spectroscopy and Bacteriophages Team Up: Dynamic Synergy for Medical and Environmental Applications

Bacteriophages are emerging as a promising alternative in combating antibiotic-resistant bacteria amidst the escalating global antimicrobial resistance crisis. Recently, there has been a notable resurgence of interest in phages, prompting extensive research into their therapeutic potential. Beyond conventional microbiology and virology techniques, such as genomics and proteomics, novel phenotypic and chemical characterization methods are being explored. Among these, there is a growing interest in vibrational spectroscopy, especially in advanced modalities such as surface-enhanced Raman spectroscopy (SERS), tip-enhanced Raman spectroscopy (TERS), and atomic force microscopy-infrared spectroscopy (AFM-IR), which offer improved sensitivity and spatial resolution. This review explores the spectrum of uses of vibrational spectroscopy for bacteriophages, including its role in diagnostics, biosensing, phage detection, assistance in phage-based therapy, and advancing basic research.

DOX-DNA Interactions on the Nanoscale: In Situ Studies Using Tip-Enhanced Raman Scattering

Chemotherapeutic anthracyclines, like doxorubicin (DOX), are drugs endowed with cytostatic activity and are widely used in antitumor therapy. Their molecular mechanism of action involves the formation of a stable anthracycline-DNA complex, which prevents cell division and results in cell death. It is known that elevated DOX concentrations induce DNA chain loops and overlaps. Here, for the first time, tip-enhanced Raman scattering was used to identify and localize intercalated DOX in isolated double-stranded calf thymus DNA, and the correlated near-field spectroscopic and morphologic experiments locate the DOX molecules in the DNA and provide further information regarding specific DOX-nucleobase interactions. Thus, the study provides a tool specifically for identifying intercalation markers and generally analyzing drug-DNA interactions. The structure of such complexes down to the molecular level provides mechanistic information about cytotoxicity and the development of potential anticancer drugs.

Surface-Area Enhanced Raman Spectroscopy of DNA in Porous Silica: A Quantitative and Reproducible Alternative to Plasmonic-Based SERS

Despite the success of surface-enhanced Raman spectroscopy (SERS) for detecting DNA immobilized on plasmonic metal surfaces, its quantitative response is limited by the rapid falloff of enhancement with distance from the metal surface and variations in sensitivity that depend on orientation and proximity to plasmonic "hot spots". In this work, we assess an alternative approach for enhancing detection by immobilizing DNA on the interior surfaces of porous silica particles. These substrates provide over a 1000-fold greater surface area for detection compared to a planar support. The porous silica substrate is a purely dielectric material with randomly oriented internal surfaces, where scattering is independent of proximity and orientation of oligonucleotides relative to the silica surface. We characterize the quantitative response of Raman scattering from DNA in porous silica particles with sequences used in previous SERS investigations of DNA for comparison. The results show that Raman scattering of DNA in porous silica is independent of distance of nucleotides from the silica surface, allowing detection of longer DNA strands with constant sensitivity. The surface area enhancement within particles is reproducible (<4% particle-to-particle variation) owing to the uniform internal pore structure and surface chemistry of the silica support. DNA immobilization with a bis-thiosuccinimide linker provides a Raman-active internal standard for quantitative interpretation of Raman scattering results. Despite the high (30 mM) concentrations of immobilized DNA within porous silica particles, they can be used to measure nanomolar binding affinities of target molecules to DNA by equilibrating a very small number of particles with a sufficiently large volume of low-concentration solution of target molecules.

Electro-optical properties of a graphene device on a tip-enhanced Raman spectroscopy system

This paper investigates the impact of graphene on tip-enhanced Raman spectroscopy (TERS) by developing an electromagnetic characterization of the TERS-graphene device system. The study focuses on the interaction between the tip, the gate voltage, and the sample, specifically examining the electromagnetic effects in the system. Employing a finite element method (FEM)-based simulation model, we meticulously dissect the electric field distribution and the Raman amplification when graphene is introduced into the system. Our findings reveal that including graphene results in a marginal reduction in Raman amplification and a negligible variation in the induced charges within the system. To reinforce our simulations, we employ a simplified capacitor model, which corroborates our results, showcasing negligible induced charges and validating the obtained capacitance values. In this manuscript, we also explore the influence of the setup on the electro-optical properties of graphene, revealing a slight variation in conductivity despite strong changes in chemical potential. Overall, this work contributes to understanding TERS's electromagnetic aspects in the presence of graphene.

Remote Excitation of Tip-Enhanced Photoluminescence with a Parallel AgNW Coupler

Tip-enhanced photoluminescence (TEPL) microscopy allows for the correlation of scanning probe microscopic images and photoluminescent spectra at the nanoscale level in a similar way to tip-enhanced Raman scattering (TERS) microscopy. However, due to the higher cross-section of fluorescence compared to Raman scattering, the diffraction-limited background signal generated by far-field excitation is a limiting factor in the achievable spatial resolution of TEPL. Here, we demonstrate a way to overcome this drawback by using remote excitation TEPL (RE-TEPL). With this approach, the excitation and detection positions are spatially separated, minimizing the far-field contribution. Two probe designs are evaluated, both experimentally and via simulations. The first system consists of gold nanoparticles (AuNPs) through photoinduced deposition on a silver nanowire (AgNW), and the second system consists of two offset parallel AgNWs. This latter coupler system shows a higher coupling efficiency and is used to successfully demonstrate RE-TEPL spectral mapping on a MoSe2/WSe2 lateral heterostructure to reveal spatial heterogeneity at the heterojunction.

Probing Local Optical Fields via Ultralow Frequency Raman Scattering from a Corrugated Probe

We revisit nanoscale local optical field imaging via tip-enhanced Raman scattering (TERS). Rather than taking advantage of molecular reporters to probe different aspects of the local fields, we show how ultralow frequency Raman (ULF) scattering from the (nanocorrugated) metallic probe itself can be used for the same purpose. The bright ULF-TERS response we record allows non-invasive (tapping mode feedback) local field imaging, enables visualization of the local fields of small (≥20 nm) isolated plasmonic particles, and can also be exploited to distinguish between Si and SiO2 domains with 5 nm spatial resolution. We describe our approach and its limitations, particularly when it comes to using all-metallic versus molecular reporters.

A Full Quantum Mechanical Approach Assessing the Chemical and Electromagnetic Effect in TERS

Tip-enhanced Raman spectroscopy (TERS) is a valuable method for surface analysis with nanometer to angstrom-scale resolution; however, the accurate simulation of particular TERS signals remains a computational challenge. We approach this challenge by combining the two main contributors to plasmon-enhanced Raman spectroscopy and to the high resolution in TERS, in particular, the electromagnetic and the chemical effect, into one quantum mechanical simulation. The electromagnetic effect describes the sample's interaction with the strong, highly localized, and inhomogeneous electric fields associated with the plasmonic tip and is typically the thematic focus for most mechanistic studies. On the other hand, the chemical effect covers the different responses to the extremely close-range and highly position-sensitive chemical interaction between the apex tip atom(s) and the sample, and, as we could show in previous works, plays an often underestimated role. Starting from a (time-dependent) density functional theory description of the chemical model system, comprised of a tin(II) phthalocyanine sample molecule and a single silver atom as the tip, we introduce the electromagnetic effect through a series of static point charges that recreate the electric field in the vicinity of the plasmonic Ag nanoparticle. By scanning the tip over the molecule along a 3D grid, we can investigate the system's Raman response on each position for nonresonant and resonant illumination. Simulating both effects on their own already hints at the achievable signal enhancement and resolution, but the combination of both creates even stronger evidence that TERS is capable of resolving submolecular features.

Tip-enhanced photoluminescence of monolayer MoS2 increased and spectrally shifted by injection of electrons

Using tip-enhanced photoluminescence (TEPL), we investigate micron-size monolayer MoS2 flakes. In a sequence of studies, we apply various voltages between the Ag-coated nano-tip and the MoS2 flakes and observe an intriguing result. During the TEPL measurement, we observe that the photoluminescence spectrum is blue shifted and the overall signal intensity is increased. We attribute this behavior to plasmon-induced electron injection into MoS2. Additionally, when the tip is negatively biased with respect to the sample during the TEPL measurement, the nonuniform TEPL images of MoS2 monolayer flakes containing defects are gradually changed to be uniform that reach saturation. We verify that this saturation state in TEPL can last over half a year.

Nano-biosensor for SARS-CoV-2/COVID-19 detection: methods, mechanism and interface design

The epidemic of coronavirus disease 2019 (COVID-19) was a huge disaster to human society. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which led to COVID-19, has resulted in a large number of deaths. Even though the reverse transcription-polymerase chain reaction (RT-PCR) is the most efficient method for the detection of SARS-CoV-2, the disadvantages (such as long detection time, professional operators, expensive instruments, and laboratory equipment) limit its application. In this review, the different kinds of nano-biosensors based on surface-enhanced Raman scattering (SERS), surface plasmon resonance (SPR), field-effect transistor (FET), fluorescence methods, and electrochemical methods are summarized, starting with a concise description of their sensing mechanism. The different bioprobes (such as ACE2, S protein-antibody, IgG antibody, IgM antibody, and SARS-CoV-2 DNA probes) with different bio-principles are introduced. The key structural components of the biosensors are briefly introduced to give readers an understanding of the principles behind the testing methods. In particular, SARS-CoV-2-related RNA mutation detection and its challenges are also briefly described. We hope that this review will encourage readers with different research backgrounds to design SARS-CoV-2 nano-biosensors with high selectivity and sensitivity.

Inside Block Copolymer Micelles-Tracing Interfacial Influences on Crosslinking Efficiency in Nanoscale Confined Spaces

Recently, several studies have demonstrated the excellent capabilities of tip-enhanced Raman spectroscopyfor in-depth investigations of structural properties of matter with unprecedented resolution and chemical specificity. These capabilities are utilized here to study the internal structure of core-crosslinked micelles, which are formed by self-assembly of the diblock terpolymer poly(ethylene oxide)-block-poly(furfuryl glycidylether-co-tert-butylglycidyl ether). Supplementing force-volume atomic force microscopy experiments address additionally the nanomechanical properties. Particularly, TERS enables investigating the underlying principles influencing the homogeneity and efficiency of the Diels-Alder core-crosslinking process in the confined hydrophobic core. While the central core region is homogenously crosslinked, a breakdown of the crosslinking reaction is observed in the core-corona interfacial region. The results corroborate that a strong crosslinking efficiency is directly correlated to the formation of a mixed zone of the glycidyl ether and PEO corona blocks reaching ≈5 nm into the core region. Concomitantly a strong exclusion of the encapsulated bismaleimide crosslinker from the interfacial region is observed. It is conceivable that a changed structure, chemical composition and altered nanomechanical properties of this interfacial region may also influence the crosslinking efficiency across the entire core region by a modification of the solubility of the crosslinker in the interfacial core-corona region.

Regioselective Tip-Enhanced Raman Spectroscopy of Lipid Membranes with Sub-Nanometer Axial Resolution

Noninvasive and label-free analysis of cell membranes at the nanoscale is essential to comprehend vital cellular processes. However, conventional analytical tools generally fail to meet this challenge due to the lack of required sensitivity and/or spatial resolution. Herein, we demonstrate that tip-enhanced Raman spectroscopy (TERS) is a powerful nanoanalytical tool to analyze dipalmitoylphosphatidylcholine (DPPC) bilayers and human cell membranes with submolecular resolution in the vertical direction. Unlike the far-field Raman measurements, TERS spectra of the DPPC bilayers reproducibly exhibited a uniquely shaped C-H band. These unique spectral features were also reproducibly observed in the TERS spectrum of human pancreatic cancer cells. Spectral deconvolution and DFT simulations confirmed that the TERS signal primarily originated from vibrations of the CH₃ groups in the choline headgroup of the lipids. The reproducible TERS results obtained in this study unequivocally demonstrate the ultrahigh sensitivity of TERS for nanoanalysis of lipid membranes under ambient conditions.

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.

Ambient Tip-Enhanced Two Photon Photoluminescence from CdSe/ZnS Quantum Dots

Nonlinear nano-optical measurements that combine ultrafast spectroscopy with tools of scanning probe microscopy are scarce. This is particularly the case when high spatial resolution on the order of a few nanometers is sought after in experiments performed under ambient laboratory conditions. In this work, we demonstrate the latter through measurements that track two-photon photoluminescence from aggregates of CdSe/ZnS quantum dots with sub-5 nm spatial resolution. Our proof-of-principle measurements that only take advantage of a plasmonic probe (as opposed to a gap mode) pave the way for nonlinear photoluminescence-based spectral nanoimaging of realistic/heterogeneous (bio) molecular and (bio) material systems.

Infrared nanospectroscopic imaging of DNA molecules on mica surface

Significant efforts have been done in last two decades to develop nanoscale spectroscopy techniques owning to their great potential for single-molecule structural detection and in addition, to resolve open questions in heterogeneous biological systems, such as protein-DNA complexes. Applying IR-AFM technique has become a powerful leverage for obtaining simultaneous absorption spectra with a nanoscale spatial resolution for studied proteins, however the AFM-IR investigation of DNA molecules on surface, as a benchmark for a nucleoprotein complexes nanocharacterization, has remained elusive. Herein, we demonstrate methodological approach for acquisition of AFM-IR mapping modalities with corresponding absorption spectra based on two different DNA deposition protocols on spermidine and Ni²⁺ pretreated mica surface. The nanoscale IR absorbance of distinctly formed DNA morphologies on mica are demonstrated through series of AFM-IR absorption maps with corresponding IR spectrum. Our results thus demonstrate the sensitivity of AFM-IR nanospectroscopy for a nucleic acid research with an open potential to be employed in further investigation of nucleoprotein complexes.

Microlens-assisted microscopy for biology and medicine

The addition of dielectric transparent microlens in the optical scheme is an effective and at the same time simple and inexpensive way to increase the resolution of a light microscope. For these purposes, spherical and cylindrical microlenses with a diameter of 1-100 μm are usually used. The microlens focuses the light into a narrow beam called a photonic nanojet. An enlarged virtual image is formed, which is captured by the objective of the light microscope. In addition to microscopy, the microlenses are successfully applied to amplify optical signals, increase the trapping force of optical tweezers and are used in microsurgery. This review considers the design and principle of microlens-assisted microscopes. Taking into account the advantages of the super-resolution optical methods for research in life science, the examples of the use of the microlenses in biomedical practice are discussed in detail.

Multimodal (Non)Linear Optical Nanoimaging and Nanospectroscopy

This Perspective highlights recent advances in linear and nonlinear spectral nanoimaging. The described developments are motivated by the need to characterize molecular and material systems noninvasively with nanometer spatial and femtosecond temporal resolution. Indeed, the ability to image and chemically characterize heterogeneous interfaces with joint nano-femto resolution is a prerequisite to advancing our fundamental understanding of processes as diverse as heterogeneous catalysis, microbial communication, and energy flow in pristine/defect-containing low-dimensional quantum materials, to name a few. We describe pioneering work and recent demonstrations of (non)linear optical nanoimaging and nanospectroscopy, with an emphasis on high spatial resolution measurements conducted under ambient laboratory conditions.

Single-Molecule Surface-Enhanced Raman Spectroscopy

Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) has the potential to detect single molecules in a non-invasive, label-free manner with high-throughput. SM-SERS can detect chemical information of single molecules without statistical averaging and has wide application in chemical analysis, nanoelectronics, biochemical sensing, etc. Recently, a series of unprecedented advances have been realized in science and application by SM-SERS, which has attracted the interest of various fields. In this review, we first elucidate the key concepts of SM-SERS, including enhancement factor (EF), spectral fluctuation, and experimental evidence of single-molecule events. Next, we systematically discuss advanced implementations of SM-SERS, including substrates with ultra-high EF and reproducibility, strategies to improve the probability of molecules being localized in hotspots, and nonmetallic and hybrid substrates. Then, several examples for the application of SM-SERS are proposed, including catalysis, nanoelectronics, and sensing. Finally, we summarize the challenges and future of SM-SERS. We hope this literature review will inspire the interest of researchers in more fields.

Molecular vibrational imaging at nanoscale

The demand to visualize the spatial distribution of chemical species based on vibrational spectra is rapidly increasing. Driven by such a need, various Raman and infrared spectro-microscopies with a nanometric spatial resolution have been developed over the last two decades. Despite rapid progress, a large gap still exists between the general needs and what these techniques can achieve. This Perspective highlights the key challenges and recent breakthroughs of the two vibrational nano-imaging techniques, scattering-type scanning near-field optical microscopy and tip-enhanced Raman scattering.

Raman Microspectroscopy Identifies Biochemical Activation Fingerprints in THP-1- and PBMC-Derived Macrophages

(1) The monocytic leukemia cell line THP-1 and primary monocyte-derived macrophages (MDMs) are popular in vitro model systems to study human innate immunity, wound healing, and tissue regeneration. However, both cell types differ significantly in their origin and response to activation stimuli. (2) Resting THP-1 and MDMs were stimulated with lipopolysaccharide (LPS) and interferon γ (IFNγ) and analyzed by Raman microspectroscopy (RM) before and 48 h after activation. Raman data were subsequently analyzed using principal component analysis. (3) We were able to resolve and analyze the spatial distribution and molecular composition of proteins, nucleic acids, and lipids in resting and activated THP-1 and MDMs. Our findings reveal that proinflammatory activation-induced significant spectral alterations at protein and phospholipid levels in THP-1. In MDMs, we identified that nucleic acid and non-membrane-associated intracellular lipid composition were also affected. (4) Our results show that it is crucial to carefully choose the right cell type for an in vitro model as the nature of the cells itself may impact immune cell polarization or activation results. Moreover, we demonstrated that RM is a sensitive tool for investigating cell-specific responses to activation stimuli and monitoring molecular changes in subcellular structures.

Progress of tip-enhanced Raman scattering for the last two decades and its challenges in very recent years

Tip-enhanced Raman scattering (TERS) has recently attracted remarkable attention as a novel nano-spectroscopy technique. TERS, which provides site-specific information, can be performed on any material surface regardless of morphology. Moreover, it can be applied in various environments, such as ambient air, ultrahigh vacuum (UHV), solutions, and electrochemical environments. This review reports on one hand progress of TERS for the last two decades, and on the other hand, its challenges in very recent years. Part of the progress of TERS starts with the prehistory and history of TERS, and then, the characteristics and advantages of TERS are described. Significant emphasis is put on the development of TERS instrumentation and equipment such as ultrahigh vacuum TERS, liquid TERS, electrochemical-TERS, and tip-preparations. Applications of TERS, particularly those with nanocarbons, biological materials, and surface and interface analysis, are mentioned in some detail. In the part on challenges, we focus on the very recent advances in TERS; progress in spatial resolution to the angstrom scale is the hottest topic. Recent TERS studies performed under UHV, for example chemical imaging at the angstrom scale and Raman detection of bond breaking and making of a chemisorbed up-standing single molecules at single-bond level, are reviewed. Of course, there is no clear border between the two parts. In the last part the perspective of TERS is discussed.

Nanoscale chemical characterization of biomolecules using tip-enhanced Raman spectroscopy

Nanoscale chemical and structural characterization of single biomolecules and assemblies is of paramount importance for applications in biology and medicine. It aims to describe the molecular structure of biomolecules and their interaction with unprecedented spatial resolution to better comprehend underlying molecular mechanisms of biological processes involved in cell activity and diseases. Tip-enhanced Raman scattering (TERS) spectroscopy appears particularly appealing to reach these objectives. This state-of-the-art TERS technique is as versatile as it is ultrasensitive. To perform a successful TERS experiment, special care and a thorough methodology for the preparation of the TERS system, the TERS probe tip, and sample are needed. Intense efforts have been deployed to characterize nucleic acids, proteins and peptides, lipid membranes, and more complex systems such as cells and viruses using TERS. Although the vast majority of studies have first been performed in dry conditions, they have allowed for several scientific breakthroughs. These include DNA and RNA sequencing, and the determination of relationships between protein structure and biological function by the use of increasingly exploitative chemometric tools for spectral data analysis. The nanoscale determination of the secondary structure of amyloid fibrils, protofibrils and oligomers implicated in neurodegenerative diseases could, for instance, be connected with the toxicity of these species, amyloid formation pathways, and their interaction with phospholipids. Single particles of different viral strains could be distinguished from one another by comparison of their protein and lipid contents. In addition, TERS has allowed for the evermore accurate description of the molecular organization of lipid membranes. Very recent advances also demonstrated the possibility to carry out TERS in aqueous medium, which opens thrilling perspectives for the TERS technique in biological, biomedical, and potential clinical applications.

Advanced plasmonic technologies for multi-scale biomedical imaging

Plasmonic technologies are available for multi-scale biomedical imaging ranging from micrometre to angstrom level.

Tip-Enhanced Raman Scattering on Both Sides of the Schrödinger Equation

Historically, molecular spectroscopists have focused their attention to the right-hand side of the Schrödinger equation. Our major goal had and still has to do with determining a (bio)molecular system's Hamiltonian operator. From a theoretical spectroscopist's perspective, this entails varying the parameters of a model Hamiltonian until the predicted observables agree with their experimental analogues. In this context, less emphasis has been put on the left-hand side of the equation, where the interplay between a system and its immediate local environment is described. The latter is particularly meaningful and informative in modern applications of optical microscopy and spectroscopy that take advantage of surface plasmons to enhance molecular scattering cross-sections and to increase the attainable spatial resolution that is classically limited by diffraction. Indeed, the manipulation of light near the apex of a metallic nanotip has enabled single molecule detection, identification, and imaging. The distinct advantages of the so-called tip-enhanced optical nanospectroscopy/nanoimaging approaches are self-evident: ultrahigh spatial resolution (nanometer or better) and ultimate sensitivity (down to yoctomolar) are both attainable, all while retaining the ability to chemically fingerprint one molecule at a time (e.g., through Raman scattering). An equally interesting aspect of the same approach stems from using the properties of a single molecule to characterize the local environment in which it resides. This concept of single molecule spectroscopy on the left-hand side of the Schrödinger equation is certainly not novel and has been discussed in pioneering single molecule studies that ultimately led to a Nobel prize in chemistry. That said, local environment mapping through ultrasensitive optical spectroscopy acquires a unique flavor when executed using tip-enhanced Raman scattering (TERS). This is the subject of this Account.In a series of recent reports, our group utilized TERS to characterize different properties of nanolocalized and enhanced optical fields. The platforms that were used to this end consist of chemically functionalized plasmonic nanostructures and nanoparticles imaged using visible-light-irradiated gold- or silver-coated probes of an atomic force microscope. Through a detailed analysis of the recorded spectral nanoimages, we found that molecular Raman spectra may be used to track the magnitudes, resonances, spatiotemporal gradients, and even vector components of optical fields with nanometer spatial resolution under ambient conditions. On the other side of the equation, understanding how spatially varying optical fields modulate molecular nano-Raman spectra is of utmost importance to emerging areas of nanophotonics. For instance, tracking plasmon-enhanced chemical transformations via TERS necessitates a deeper fundamental understanding of the optical signatures of molecular reorientation and multipolar Raman scattering, both of which may be driven by local optical field gradients that are operative in TERS. We illustrate these concepts and introduce the readers to the generally less appreciated and equally exciting world of TERS on the left-hand side of the Schrödinger equation.

Molecular Perturbation Effects in AFM-Based Tip-Enhanced Raman Spectroscopy: Contact versus Tapping Mode

Tip-enhanced Raman spectroscopy (TERS) is a powerful tool for nondestructive and label-free surface chemical characterization at nanometer length scales. However, despite being considered nondestructive, the interaction of the TERS probe used in the analysis can alter the molecular organization of the sample. In this study, we investigate the role of the atomic force microscopy (AFM) feedback (contact mode and tapping mode) on molecular perturbation in TERS analysis of soft samples using a self-assembled monolayer (SAM) of 2-chloro-4-nitrobenzene-1-thiol (Cl-NBT) as a test sample. Surprisingly, the tapping mode shows a consistently higher TERS signal resulting from a minimal perturbation of the Cl-NBT SAM compared to the contact mode. This study provides novel insights into the choice of the correct AFM-TERS operation mode for nanoscale chemical analysis of soft and delicate samples and is expected to expedite the growing application of TERS in this area.

Revealing DNA Structure at Liquid/Solid Interfaces by AFM-Based High-Resolution Imaging and Molecular Spectroscopy

DNA covers the genetic information in all living organisms. Numerous intrinsic and extrinsic factors may influence the local structure of the DNA molecule or compromise its integrity. Detailed understanding of structural modifications of DNA resulting from interactions with other molecules and surrounding environment is of central importance for the future development of medicine and pharmacology. In this paper, we review the recent achievements in research on DNA structure at nanoscale. In particular, we focused on the molecular structure of DNA revealed by high-resolution AFM (Atomic Force Microscopy) imaging at liquid/solid interfaces. Such detailed structural studies were driven by the technical developments made in SPM (Scanning Probe Microscopy) techniques. Therefore, we describe here the working principles of AFM modes allowing high-resolution visualization of DNA structure under native (liquid) environment. While AFM provides well-resolved structure of molecules at nanoscale, it does not reveal the chemical structure and composition of studied samples. The simultaneous information combining the structural and chemical details of studied analyte allows achieve a comprehensive picture of investigated phenomenon. Therefore, we also summarize recent molecular spectroscopy studies, including Tip-Enhanced Raman Spectroscopy (TERS), on the DNA structure and its structural rearrangements.

DNA Studies: Latest Spectroscopic and Structural Approaches

This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

Unveiling the interaction of protein fibrils with gold nanoparticles by plasmon enhanced nano-spectroscopy

The development of various degenerative diseases is suggested to be triggered by the uncontrolled organisation and aggregation of proteins into amyloid fibrils. For this reason, there are ongoing efforts to develop novel agents and approaches, including metal nanoparticle-based colloids, that dissolve amyloid structures and prevent pathogenic protein aggregation. In this contribution, the role of gold nanoparticles (AuNPs) in degrading amyloid fibrils of the model protein lysozyme is investigated. The amino acid composition of fibril surfaces before and after the incubation with AuNPs is determined at the single fibril level by exploiting the high spatial resolution and sensitivity provided by tip-enhanced and surface-enhanced Raman spectroscopies. This combined spectroscopic approach allows to reveal the molecular mechanisms driving the interaction between fibrils and AuNPs. Our results provide an important input for the understanding of amyloid fibrils and could have a potential translational impact on the development of strategies for the prevention and treatment of amyloid-related diseases.

Challenges and Opportunities for Clustered Regularly Interspaced Short Palindromic Repeats Based Molecular Biosensing

Clustered regularly interspaced short palindromic repeats, CRISPR, has recently emerged as a powerful molecular biosensing tool for nucleic acids and other biomarkers due to its unique properties such as collateral cleavage nature, room temperature reaction conditions, and high target-recognition specificity. Numerous platforms have been developed to leverage the CRISPR assay for ultrasensitive biosensing applications. However, to be considered as a new gold standard, several key challenges for CRISPR molecular biosensing must be addressed. In this paper, we briefly review the history of biosensors, followed by the current status of nucleic acid-based detection methods. We then discuss the current challenges pertaining to CRISPR-based nucleic acid detection, followed by the recent breakthroughs addressing these challenges. We focus upon future advancements required to enable rapid, simple, sensitive, specific, multiplexed, amplification-free, and shelf-stable CRISPR-based molecular biosensors.

Probing the plasmon-driven Suzuki-Miyaura coupling reactions with cargo-TERS towards tailored catalysis

We present a label-free approach that is based on tip-enhanced Raman spectroscopy (TERS) for a direct in situ assessment of the molecular reactivity in plasmon-driven reactions. Using this analytical approach, named cargo-TERS, we investigate the relationship between the chemical structure of aromatic halides and the catalytic probability of the Suzuki-Miyaura coupling reaction on gold-palladium bimetallic nanoplates (Au@PdNPs). We demonstrate that cargo-TERS can be used to quantify the yield of biphenyl-4,4'-dithiol (BPDT), the product of the coupling reaction. Our results also show that the halide reactivity decreases from bromo through chloro to fluorohalides. Finally, we employ this novel imaging technique to unravel the nanoscale reactivity and selectivity of Au@PdNPs. We find that the edges and corners of these nanostructures exhibit the highest catalytic reactivity, while the flat terraces of Au@PdNPs remain catalytically inactive.

Recent developments in Raman spectral analysis of microbial single cells: Techniques and applications

The conventional microbial cell analyses are mostly population-averaged methods that conceal the characteristics of single-cell in the community. Single-cell analysis can provide information on the functional and structural variation of each cell, resulting in the elimination of long and tedious microbial cultivation techniques. Raman spectroscopy is a label-free, noninvasive, and in-vivo method ideal for single-cell measurement to obtain spatially resolved chemical information. In the current review, recent developments in Raman spectroscopic techniques for microbial characterization at the single-cell level are presented, focusing on Raman imaging of single cells to study the intracellular distribution of different components. The review also discusses the limitation and challenges of each technique and put forward some future outlook for improving Raman spectroscopy-based techniques for single-cell analysis. Raman spectroscopic methods at the single-cell level have potential in precision measurements, metabolic analysis, antibiotic susceptibility testing, resuscitation capability, and correlating phenotypic information to genomics for cells, the integration of Raman spectroscopy with other techniques such as microfluidics, stable isotope probing (SIP), and atomic force microscope can further improve the resolution and provide extensive information. Future focuses should be given to advance algorithms for data analysis, standardized reference libraries, and automated cell isolation techniques in future.

Low-Background Tip-Enhanced Raman Spectroscopy Enabled by a Plasmon Thin-Film Waveguide Probe

Tip-enhanced Raman spectroscopy (TERS) is a nano-optical approach to extract spatially resolved chemical information with nanometer precision. However, in the case of direct-illumination TERS, which is often employed in commercial TERS instruments, strong fluorescence or far-field Raman signals from the illuminated areas may be excited as a background. They may overwhelm the near-field TERS signal and dramatically decrease the near-field to far-field signal contrast of TERS spectra. It is still challenging for TERS to study the surface of fluorescent materials or a bulk sample that cannot be placed on an Au/Ag substrate. In this study, we developed an indirect-illumination TERS probe that allows a laser to be focused on a flat interface of a thin-film waveguide located far away from the region generating the TERS signal. Surface plasmon polaritons are generated stably on the waveguide and eventually accumulated at the tip apex, thereby producing a spatially and energetically confined hotspot to ensure stable and high-resolution TERS measurements with a low background. With this thin-film waveguide probe, TERS spectra with obvious contrast from a diamond plate can be acquired. Furthermore, the TERS technique based on this probe exhibits excellent TERS signal stability, a long lifetime, and good spatial resolution. This technique is expected to have commercial potential and enable further popularization and development of TERS technology as a powerful analytical method.

Atomic Point Contact Raman Spectroscopy of a Si(111)-7 × 7 Surface

Tip-enhanced Raman scattering (TERS) has recently demonstrated the exceptional sensitivity to observe vibrational structures on the atomic scale. However, it strongly relies on electromagnetic enhancement in plasmonic nanogaps. Here, we demonstrate that atomic point contact (APC) formation between a plasmonic tip and the surface of a bulk Si sample can lead to a dramatic enhancement of Raman scattering and consequently the phonons of the reconstructed Si(111)-7 × 7 surface can be detected. Furthermore, we demonstrate the chemical sensitivity of APC-TERS by probing local vibrations resulting from Si-O bonds on the partially oxidized Si(111)-7 × 7 surface. This approach will expand the applicability of ultrasensitive TERS, exceeding the previous measurement strategies that exploit intense gap-mode plasmons, typically requiring a plasmonic substrate.

Light-Nucleotide versus Ion-Nucleotide Interactions for Single-Nucleotide Resolution

Several parallel reads of ionic currents through multiple CsgG nanopores provide information about ion-nucleotide interactions for sequencing single-stranded DNA (ss-DNA) using base-calling algorithms. However, the information in ion-nucleotide interactions seems insufficient for single-read nanopore DNA sequencing. Here we report discriminative light-nucleotide interactions calculated from density functional theory (DFT), which are compared with ionic currents obtained from molecular dynamics (MD) simulations. The MD simulations were performed on a system containing a transverse nanochannel and a longitudinal solid state nanopore. We show that both of the transverse and longitudinal ionic currents during the translocation of A₁₆, G₁₆, T₁₆, and C₁₆ through the nanopore, overlapped widely. On the other hand, the UV-vis and Raman spectra of different types of single nucleotides, nucleosides, and nucleobases show relatively higher resolution than the ionic currents. Light-nucleotide interactions provide better information for characterizing the nucleotides in comparison to ion-nucleotide interactions for nanopore DNA sequencing. This can be realized by using optical techniques including surface-enhanced Raman spectroscopy (SERS) or tip-enhanced Raman spectroscopy (TERS), while plasmon excitation can be used to localize light and control the rate of nucleotide flow.

Investigations of Shape, Material and Excitation Wavelength Effects on Field Enhancement in SERS Advanced Tips

This article, a part of the larger research project of Surface-Enhanced Raman Scattering (SERS), describes an advanced study focusing on the shapes and materials of Tip-Enhanced Raman Scattering (TERS) designated to serve as part of a novel imager device. The initial aim was to define the optimal shape of the "probe": tip or cavity, round or sharp. The investigations focused on the effect of shape (hemi-sphere, hemispheroid, ellipsoidal cavity, ellipsoidal rod, nano-cone), and the effect of material (Ag, Au, Al) on enhancement, as well as the effect of excitation wavelengths on the electric field. Complementary results were collected: numerical simulations consolidated with analytical models, based on solid assumptions. Preliminary experimental results of fabrication and structural characterization are also presented. Thorough analyses were performed around critical parameters, such as the plasmonic metal-Silver, Aluminium or Gold-using Rakic model, the tip geometry-sphere, spheroid, ellipsoid, nano-cone, nano-shell, rod, cavity-and the geometry of the plasmonic array: cross-talk in multiple nanostructures. These combined outcomes result in an optimized TERS design for a large number of applications.

From SERS to TERS and Beyond: Molecules as Probes of Nanoscopic Optical Fields

A detailed understanding of the interaction between molecules and plasmonic nanostructures is important for several exciting developments in (bio)molecular sensing and imaging, catalysis, as well as energy conversion. While much of the focus has been on the nanostructures that generate enhanced and nano-confined optical fields, we herein highlight recent work from our groups that uses the molecular response in surface and tip enhanced Raman scattering (SERS and TERS, respectively) to investigate different aspects of the local fields. TERS provides access to ultra-confined volumes, and as a result can further explore and explain ensemble-averaged SERS measurements. Exciting and distinct molecular behaviors are observed in the quantum limit of plasmons, including molecular charging, chemical conversion, and optical rectification. Evidence of multipolar Raman scattering from molecules additionally provides insights into the inhomogeneous electric fields that drive SERS and TERS and their spatial and temporal gradients. The time scales of these processes show evidence of cooperative nanoscale phenomena that altogether contribute to SERS and TERS.

Ångström- and Nano-scale Pore-Based Nucleic Acid Sequencing of Current and Emergent Pathogens

State-of-the-art nanopore sequencing enables rapid and real-time identification of novel pathogens, which has wide application in various research areas and is an emerging diagnostic tool for infectious diseases including COVID-19. Nanopore translocation enables de novo sequencing with long reads (> 10 kb) of novel genomes, which has advantages over existing short-read sequencing technologies. Biological nanopore sequencing has already achieved success as a technology platform but it is sensitive to empirical factors such as pH and temperature. Alternatively, ångström- and nano-scale solid-state nanopores, especially those based on two-dimensional (2D) membranes, are promising next-generation technologies as they can surpass biological nanopores in the variety of membrane materials, ease of defining pore morphology, higher nucleotide detection sensitivity, and facilitation of novel and hybrid sequencing modalities. Since the discovery of graphene, atomically-thin 2D materials have shown immense potential for the fabrication of nanopores with well-defined geometry, rendering them viable candidates for nanopore sequencing membranes. Here, we review recent progress and future development trends of 2D materials and their ångström- and nano-scale pore-based nucleic acid (NA) sequencing including fabrication techniques and current and emerging sequencing modalities. In addition, we discuss the current challenges of translocation-based nanopore sequencing and provide an outlook on promising future research directions.