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

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.

Accurate categorization and rapid pathological diagnosis correction with Micro-Raman technique in human lung adenocarcinoma infiltration level

Background

In the context of surgical interventions for lung adenocarcinoma (LADC), precise determination of the extent of LADC infiltration plays a pivotal role in shaping the surgeon's strategic approach to the procedure. The prevailing diagnostic standard involves the expeditious intraoperative pathological diagnosis of areas infiltrated by LADC. Nevertheless, current methodologies rely on the visual interpretation of tissue images by proficient pathologists, introducing an error margin of up to 15.6%.

Methods

In this study, we investigated the utilization of Micro-Raman technique on isolated specimens of human LADC with the objective of formulating and validating a workflow for the pathological diagnosis of LADC featuring diverse degrees of infiltration. Our strategy encompasses a thorough pathological characterization of LADC, spanning different tissue types and levels of infiltration. Through the integration of Raman spectroscopy with advanced deep learning models for simultaneous diagnosis, this approach offers a swift, precise, and clinically relevant means of analysis.

Results

The diagnostic performance of the convolutional neural network (CNN) model, coupled with the microscopic Raman technique, was found to be exceptional and consistent, surpassing the traditional support vector machine (SVM) model. The CNN model exhibited an area under the curve (AUC) value of 96.1% for effectively distinguishing normal tissue from LADC and an impressive 99.0% for discerning varying degrees of infiltration in LADCs. To comprehensively assess its clinical utility, Raman datasets from patients with intraoperative rapid pathologic diagnostic errors were utilized as test subjects and input into the established CNN model. The results underscored the substantial corrective capacity of the Micro-Raman technique, revealing a misdiagnosis correction rate exceeding 96% in all cases.

Conclusions

Ultimately, our discoveries highlight the Micro-Raman technique's potential to augment the intraoperative diagnostic precision of LADC with varying levels of infiltration. And compared to the traditional SVM model, the CNN model has better generalization ability in diagnosing different infiltration levels. This method furnishes surgeons with an objective groundwork for making well-informed decisions concerning subsequent surgical plans.

Deciphering biomolecular complexities: the indispensable role of surface-enhanced Raman spectroscopy in modern bioanalytical research

Surface-enhanced Raman spectroscopy (SERS) has emerged as an indispensable analytical tool in biomolecular research, providing unmatched sensitivity critical for the elucidation of biomolecular structures. This review presents a thorough examination of SERS, outlining its fundamental principles, cataloging its varied applications within the biomolecular sphere, and contemplating its future developmental trajectories. We begin with a detailed analysis of SERS's mechanistic principles, emphasizing both the phenomena of surface enhancement and the complexities inherent in Raman scattering spectroscopy. Subsequently, we delve into the pivotal role of SERS in the structural analysis of diverse biomolecules, including proteins, nucleic acids, lipids, carbohydrates, and biochromes. The remarkable capabilities of SERS extend beyond mere detection, offering profound insights into biomolecular configurations and interactions, thereby enriching our comprehension of intricate biological processes. This review also sheds light on the application of SERS in real-time monitoring of various bio-relevant compounds, from enzymes and coenzymes to metal ion-chelate complexes and cellular organelles, thereby providing a holistic view and empowering researchers to unravel the complexities of biological systems. We also address the current challenges faced by SERS, such as enhancing sensitivity and resolution, developing stable and reproducible substrates, and conducting thorough analyses in complex biological matrices. Nonetheless, the continual advancements in nanotechnology and spectroscopy solidify the standing of SERS as a formidable force in biomolecular research. In conclusion, the versatility and robustness of SERS not only deepen our understanding of biomolecular intricacies but also pave the way for significant developments in medical research, therapeutic innovation, and diagnostic approaches.

Activatable Probes for Ratiometric Imaging of Endogenous Biomarkers In Vivo

Dynamic variations in the concentration and abnormal distribution of endogenous biomarkers are strongly associated with multiple physiological and pathological states. Therefore, it is crucial to design imaging systems capable of real-time detection of dynamic changes in biomarkers for the accurate diagnosis and effective treatment of diseases. Recently, ratiometric imaging has emerged as a widely used technique for sensing and imaging of biomarkers due to its advantage of circumventing the limitations inherent to conventional intensity-dependent signal readout methods while also providing built-in self-calibration for signal correction. Here, the recent progress of ratiometric probes and their applications in sensing and imaging of biomarkers are outlined. Ratiometric probes are classified according to their imaging mechanisms, and ratiometric photoacoustic imaging, ratiometric optical imaging including photoluminescence imaging and self-luminescence imaging, ratiometric magnetic resonance imaging, and dual-modal ratiometric imaging are discussed. The applications of ratiometric probes in the sensing and imaging of biomarkers such as pH, reactive oxygen species (ROS), reactive nitrogen species (RNS), glutathione (GSH), gas molecules, enzymes, metal ions, and hypoxia are discussed in detail. Additionally, this Review presents an overview of challenges faced in this field along with future research directions.

SERS and MRS signals engineered dual-mode aptasensor for simultaneous distinguishment of aflatoxin subtypes

The accurate monitoring of aflatoxin subtypes is vitally important for food safety. Herein, a dual-mode aptasensor with surface-enhanced Raman scattering (SERS) and magnetic relaxation switching (MRS) signals is developed for the detection of aflatoxin B1, B2 and M1 (i.e. AFB1, AFB2 and AFM1). Au-Ag Janus NPs and Au-mushroom NPs are prepared and show intense and non-interfering SERS peaks without the additional modification of Raman molecules, and are utilized as SERS nanotags for the distinguishment of AFB1 and AFB2. Fe3O4@Au NPs functionalized by AFM1 aptamers are applied as MRS nanoprobes for the monitoring of AFM1. Aptamers engineered SERS nanotags and MRS nanoprobes are assembled, and show strong SERS performances and high transverse relaxation time (T2). AFB1, AFB2 and AFM1 induce the separation of SERS nanotags from the assemblies and the dispersion of Fe3O4@Au NPs, resulting in the decrease of SERS signals at 1278 cm-1 and 1000 cm-1 as well as the reduction of T2 values. The dual-mode but three kinds of detection signals don't interfere with each other and exhibit a significant linear relationship with the concentration of targets. This platform provides a high throughput monitoring strategy for the simultaneous analysis of different subtypes of mycotoxin.

CRISPR/Cas-Powered Amplification-Free Detection of Nucleic Acids: Current State of the Art, Challenges, and Futuristic Perspectives

CRISPR/Cas system is becoming an increasingly influential technology that has been repositioned in nucleic acid detection. A preamplification step is usually required to improve the sensitivity of CRISPR/Cas-based detection. The striking biological features of CRISPR/Cas, including programmability, high sensitivity and sequence specificity, and single-base resolution. More strikingly, the target-activated trans-cleavage could act as a biocatalytic signal transductor and amplifier, thereby empowering it to potentially perform nucleic acid detection without a preamplification step. The reports of such work are on the rise, which is not only scientifically significant but also promising for futuristic end-user applications. This review started with the introduction of the detection methods of nucleic acids and the CRISPR/Cas-based diagnostics (CRISPR-Dx). Next, we objectively discussed the pros and cons of preamplification steps for CRISPR-Dx. We then illustrated and highlighted the recently developed strategies for CRISPR/Cas-powered amplification-free detection that can be realized through the uses of ultralocalized reactors, cascade reactions, ultrasensitive detection systems, or others. Lastly, the challenges and futuristic perspectives were proposed. It can be expected that this work not only makes the researchers better understand the current strategies for this emerging field, but also provides insight for designing novel CRISPR-Dx without a preamplification step to win practicable use in the near future.

Rapidly determining the 3D structure of proteins by surface-enhanced Raman spectroscopy

Despite great advances in protein structure analysis, label-free and ultrasensitive methods to obtain the natural and dynamic three-dimensional (3D) structures are still urgently needed. Surface-enhanced Raman spectroscopy (SERS) can be a good candidate, whereas the complexity originated from the interactions between the protein and the gradient surface electric field makes it extremely challenging to determine the protein structure. Here, we propose a deciphering strategy for accurate determination of 3D protein structure from experimental SERS spectra in seconds by simply summing SERS spectra of isolated amino acids in electric fields of different strength with their orientations in protein. The 3D protein structure can be reconstructed by comparing the experimental spectra obtained in a well-defined gap-mode SERS configuration with the simulated spectra. The gradient electric field endows SERS with a unique advantage to section biomolecules with atomic precision, which makes SERS a competent tool for monitoring biomolecular events under physiological conditions.

Efficient optical plasmonic tweezer-controlled single-molecule SERS characterization of pH-dependent amylin species in aqueous milieus

It is challenging to characterize single or a few biomolecules in physiological milieus without excluding the influences of surrounding environment. Here we utilize optical plasmonic trapping to construct a dynamic nanocavity, which reduces the diffraction-limited detection volume and provides reproducible electromagnetic field enhancements to achieve high-throughput single-molecule surface-enhanced Raman spectroscopy (SERS) characterizations in aqueous environments. Specifically, we study human Islet Amyloid Polypeptide (amylin, hIAPP) under different physiological pH conditions by combining spectroscopic experiments and molecular dynamics (MD) simulations. Based on a statistically significant amount of time-dependent SERS spectra, two types of low-populated transient species of hIAPP containing either turn or β-sheet structure among its predominant helix-coil monomers are characterized during the early-stage incubation at neutral condition, which play a crucial role in driving irreversible amyloid fibril developments even after a subsequent adjustment of pH to continue the prolonged incubation at acidic condition. Our results might provide profound mechanistic insight into the pH-regulated amyloidogenesis and introduce an alternative approach for investigating complex biological processes at the single-molecule level.

Einstein Model of a Graph to Characterize Protein Folded/Unfolded States

The folded structures of proteins can be accurately predicted by deep learning algorithms from their amino-acid sequences. By contrast, in spite of decades of research studies, the prediction of folding pathways and the unfolded and misfolded states of proteins, which are intimately related to diseases, remains challenging. A two-state (folded/unfolded) description of protein folding dynamics hides the complexity of the unfolded and misfolded microstates. Here, we focus on the development of simplified order parameters to decipher the complexity of disordered protein structures. First, we show that any connected, undirected, and simple graph can be associated with a linear chain of atoms in thermal equilibrium. This analogy provides an interpretation of the usual topological descriptors of a graph, namely the Kirchhoff index and Randić resistance, in terms of effective force constants of a linear chain. We derive an exact relation between the Kirchhoff index and the average shortest path length for a linear graph and define the free energies of a graph using an Einstein model. Second, we represent the three-dimensional protein structures by connected, undirected, and simple graphs. As a proof of concept, we compute the topological descriptors and the graph free energies for an all-atom molecular dynamics trajectory of folding/unfolding events of the proteins Trp-cage and HP-36 and for the ensemble of experimental NMR models of Trp-cage. The present work shows that the local, nonlocal, and global force constants and free energies of a graph are promising tools to quantify unfolded/disordered protein states and folding/unfolding dynamics. In particular, they allow the detection of transient misfolded rigid states.

Hot-Electron Dynamics Mediated Medical Diagnosis and Therapy

Surface plasmon resonance excitation significantly enhances the absorption of light and increases the generation of "hot" electrons, i.e., conducting electrons that are raised from their steady states to excited states. These excited electrons rapidly decay and equilibrate via radiative and nonradiative damping over several hundred femtoseconds. During the hot-electron dynamics, from their generation to the ultimate nonradiative decay, the electromagnetic field enhancement, hot electron density increase, and local heating effect are sequentially induced. Over the past decade, these physical phenomena have attracted considerable attention in the biomedical field, e.g., the rapid and accurate identification of biomolecules, precise synthesis and release of drugs, and elimination of tumors. This review highlights the recent developments in the application of hot-electron dynamics in medical diagnosis and therapy, particularly fully integrated device techniques with good application prospects. In addition, we discuss the latest experimental and theoretical studies of underlying mechanisms. From a practical standpoint, the pioneering modeling analyses and quantitative measurements in the extreme near field are summarized to illustrate the quantification of hot-electron dynamics. Finally, the prospects and remaining challenges associated with biomedical engineering based on hot-electron dynamics are presented.

SERS-Based Optical Nanobiosensors for the Detection of Alzheimer's Disease

Alzheimer's disease (AD) is a leading cause of dementia, impacting millions worldwide. However, its complex neuropathologic features and heterogeneous pathophysiology present significant challenges for diagnosis and treatment. To address the urgent need for early AD diagnosis, this review focuses on surface-enhanced Raman scattering (SERS)-based biosensors, leveraging the excellent optical properties of nanomaterials to enhance detection performance. These highly sensitive and noninvasive biosensors offer opportunities for biomarker-driven clinical diagnostics and precision medicine. The review highlights various types of SERS-based biosensors targeting AD biomarkers, discussing their potential applications and contributions to AD diagnosis. Specific details about nanomaterials and targeted AD biomarkers are provided. Furthermore, the future research directions and challenges for improving AD marker detection using SERS sensors are outlined.

Optofluidic Tweezers: Efficient and Versatile Micro/Nano-Manipulation Tools

Optical tweezers (OTs) can transfer light momentum to particles, achieving the precise manipulation of particles through optical forces. Due to the properties of non-contact and precise control, OTs have provided a gateway for exploring the mysteries behind nonlinear optics, soft-condensed-matter physics, molecular biology, and analytical chemistry. In recent years, OTs have been combined with microfluidic chips to overcome their limitations in, for instance, speed and efficiency, creating a technology known as "optofluidic tweezers." This paper describes static OTs briefly first. Next, we overview recent developments in optofluidic tweezers, summarizing advancements in capture, manipulation, sorting, and measurement based on different technologies. The focus is on various kinds of optofluidic tweezers, such as holographic optical tweezers, photonic-crystal optical tweezers, and waveguide optical tweezers. Moreover, there is a continuing trend of combining optofluidic tweezers with other techniques to achieve greater functionality, such as antigen-antibody interactions and Raman tweezers. We conclude by summarizing the main challenges and future directions in this research field.

Development of a micro-Raman system for in vivo studying the mechanism of laser biological effects

The laser irradiation on organism will produce a series of biological effects, which can be used for basic medical research, diagnosis and treatments of diseases. However, the mechanism of this biological effects is still unclear. As a sensitive molecular monitoring technique, Raman spectroscopy has became a very popular detection method in biomedical research especially in vivo study. In this paper, we present a compact and flexible micro-Raman system for in vivo studying the mechanism of laser biological effects. The system has the two functions of laser induction and Raman measurement, which can realize the micro-area radiation of laser and simultaneously collect the corresponding Raman spectra in vivo. The detection method provided by this home-built system is able to deepen the understanding of laser biological effects mechanism at molecular level, so it is expected that the system is significant for the treatments and diagnosis of diseases in the near future.

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.

Real-time SERS monitoring anticancer drug release along with SERS/MR imaging for pH-sensitive chemo-phototherapy

In situ and real-time monitoring of responsive drug release is critical for the assessment of pharmacodynamics in chemotherapy. In this study, a novel pH-responsive nanosystem is proposed for real-time monitoring of drug release and chemo-phototherapy by surface-enhanced Raman spectroscopy (SERS). The Fe3O4@Au@Ag nanoparticles (NPs) deposited graphene oxide (GO) nanocomposites with a high SERS activity and stability are synthesized and labeled with a Raman reporter 4-mercaptophenylboronic acid (4-MPBA) to form SERS probes (GO-Fe3O4@Au@Ag-MPBA). Furthermore, doxorubicin (DOX) is attached to SERS probes through a pH-responsive linker boronic ester (GO-Fe3O4@Au@Ag-MPBA-DOX), accompanying the 4-MPBA signal change in SERS. After the entry into tumor, the breakage of boronic ester in the acidic environment gives rise to the release of DOX and the recovery of 4-MPBA SERS signal. Thus, the DOX dynamic release can be monitored by the real-time changes of 4-MPBA SERS spectra. Additionally, the strong T2 magnetic resonance (MR) signal and NIR photothermal transduction efficiency of the nanocomposites make it available for MR imaging and photothermal therapy (PTT). Altogether, this GO-Fe3O4@Au@Ag-MPBA-DOX can simultaneously fulfill the synergistic combination of cancer cell targeting, pH-sensitive drug release, SERS-traceable detection and MR imaging, endowing it great potential for SERS/MR imaging-guided efficient chemo-phototherapy on cancer treatment.

Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers

Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.

Solvent-driven biotoxin into nano-units as a versatile and sensitive SERS strategy

In recent years, marine biotoxins have posed a great threat to fishermen, human security and military prevention and control due to their diverse, complex, toxic and widespread nature, and the development of rapid and sensitive methods is essential. Surface-enhanced Raman spectroscopy (SERS) is a promising technique for the rapid and sensitive in situ detection of marine biotoxins due to its advantages of rapid, high sensitivity, and fingerprinting information. However, the complex structure of toxin molecules, small Raman scattering cross-section and low affinity to conventional substrates make it difficult to achieve direct and sensitive SERS detection. Here, we generate a large number of active hotspot structures by constructing monolayer nanoparticle films with high density hotspots, which have good target molecules that can actively access the hotspot structures using nanocapillaries. In addition, the efficient and stable signal can be achieved during dynamic detection, increasing the practicality and operability of the method. This versatile SERS method achieves highly sensitive detection of marine biotoxins GTX and NOD, providing good prospects for convenient, rapid and sensitive SERS detection of marine biotoxins.

Amplification-free CRISPR/Cas detection technology: challenges, strategies, and perspectives

Rapid and accurate molecular diagnosis is a prerequisite for precision medicine, food safety, and environmental monitoring. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)-based detection, as a cutting-edged technique, has become an immensely effective tool for molecular diagnosis because of its outstanding advantages including attomolar level sensitivity, sequence-targeted single-base specificity, and rapid turnover time. However, the CRISPR/Cas-based detection methods typically require a pre-amplification step to elevate the concentration of the analyte, which may produce non-specific amplicons, prolong the detection time, and raise the risk of carryover contamination. Hence, various strategies for target amplification-free CRISPR/Cas-based detection have been developed, aiming to minimize the sensitivity loss due to lack of pre-amplification, enable detection for non-nucleic acid targets, and facilitate integration in portable devices. In this review, the current status and challenges of target amplification-free CRISPR/Cas-based detection are first summarized, followed by highlighting the four main strategies to promote the performance of target amplification-free CRISPR/Cas-based technology. Furthermore, we discuss future perspectives that will contribute to developing more efficient amplification-free CRISPR/Cas detection systems.

Raman Spectroscopy on Brain Disorders: Transition from Fundamental Research to Clinical Applications

Brain disorders such as brain tumors and neurodegenerative diseases (NDs) are accompanied by chemical alterations in the tissues. Early diagnosis of these diseases will provide key benefits for patients and opportunities for preventive treatments. To detect these sophisticated diseases, various imaging modalities have been developed such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). However, they provide inadequate molecule-specific information. In comparison, Raman spectroscopy (RS) is an analytical tool that provides rich information about molecular fingerprints. It is also inexpensive and rapid compared to CT, MRI, and PET. While intrinsic RS suffers from low yield, in recent years, through the adoption of Raman enhancement technologies and advanced data analysis approaches, RS has undergone significant advancements in its ability to probe biological tissues, including the brain. This review discusses recent clinical and biomedical applications of RS and related techniques applicable to brain tumors and NDs.

One-click investigation of shape influence of silver nanostructures on SERS performance for sensitive detection of COVID-19

Sensitive and accurate detection of SARS-CoV-2 methods is meaningful for preventing and controlling the novel coronavirus. The detection techniques supporting portable, onsite, in-time, and online data transfer are urgently needed. Here, we one-click investigated the shape influence of silver nanostructures on SERS performance and their applications in the sensitive detection of SARS-CoV-2. Such investigation is achieved by adjusting multiple parameters (concentration, potential, and time) on the integrated electrochemical array, thus various morphologies (e.g., bulk, dendritic, globular, and spiky) can be one-click synthesized. The SERS performance results indicated that dendritic nanostructures are superior to the other three with an order of magnitude signal enhancement. Such on-electrode dendritic silver substrate also represents high sensitivity (LOD = 7.42 × 10⁻¹⁴ M) and high reproducibility (RSD = 3.67%) toward the SARS-CoV-2 RNA sequence detection. Such approach provides great potentials for rapid diagnosis and prevention of diverse infectious diseases.

Optical trapping of multiple particles based on a rotationally-symmetric power-exponent-phase vortex beam

In this paper, the optical trapping of multiple particles based on a rotationally-symmetric power-exponent-phase vortex beam (RSPEPVB) was introduced and demonstrated. Based on the theories of tight focusing and optical force, the optical force model of RSPEPVB was established to analyze the optical trapping force of tightly focused RSPEPVB. Then, an experimental setup of optical tweezer, by utilizing the RSPEPVB, was built to demonstrate that the optical tweezer of RSPEPVBs can achieve the optical trapping of multiple particles, and the number of captured particles is equal to the topological charge l of RSPEPVB, which shows that the RSPEPVBs can achieve multi-particles trapping with controllable number. Moreover, compared to vortex beam, the captured particles by RSPEPVB will not rotate around the circular light intensity distribution. The results will provide a new option for optical trapping of multiple particles in biomedicine, laser cooling and so on.

Influence of TiO2 and ZnO Nanoparticles on α-Synuclein and β-Amyloid Aggregation and Formation of Protein Fibrils

The most common neurological disorders, i.e., Parkinson's disease (PD) and Alzheimer's disease (AD), are characterized by degeneration of cognitive functions due to the loss of neurons in the central nervous system. The aggregation of amyloid proteins is an important pathological feature of neurological disorders.The aggregation process involves a series of complex structural transitions from monomeric to the formation of fibrils. Despite its potential importance in understanding the pathobiology of PD and AD diseases, the details of the aggregation process are still unclear. Nanoparticles (NPs) absorbed by the human circulatory system can interact with amyloid proteins in the human brain and cause PD. In this work, we report the study of the interaction between TiO₂ nanoparticles (TiO₂-NPs) and ZnO nanoparticles (ZnO-NPs) on the aggregation kinetics of β-amyloid fragment 1-40 (βA) and α-synuclein protein using surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS). The characterizations of ZnO-NPs and TiO₂-NPs were evaluated by X-ray diffraction (XRD) spectrum, atomic force microscopy (AFM), and UV-Vis spectroscopy. The interaction of nanoparticles with amyloid proteins was investigated by SERS. Our study showed that exposure of amyloid protein molecules to TiO₂-NPs and ZnO-NPs after incubation at 37 °C caused morphological changes and stimulated aggregation and fibrillation. In addition, significant differences in the intensity and location of active Raman frequencies in the amide I domain were found. The principal component analysis (PCA) results show that the effect of NPs after incubation at 4 °C does not cause changes in βA structure.

Single-cell stable isotope probing in microbial ecology

Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.

Wild-Type α-Synuclein and Variants Occur in Different Disordered Dimers and Pre-Fibrillar Conformations in Early Stage of Aggregation

α-Synuclein is a 140 amino-acid intrinsically disordered protein mainly found in the brain. Toxic α-synuclein aggregates are the molecular hallmarks of Parkinson’s disease. In vitro studies showed that α-synuclein aggregates in oligomeric structures of several 10th of monomers and into cylindrical structures (fibrils), comprising hundred to thousands of proteins, with polymorphic cross-β-sheet conformations. Oligomeric species, formed at the early stage of aggregation remain, however, poorly understood and are hypothezised to be the most toxic aggregates. Here, we studied the formation of wild-type (WT) and mutant (A30P, A53T, and E46K) dimers of α-synuclein using coarse-grained molecular dynamics. We identified two principal segments of the sequence with a higher propensity to aggregate in the early stage of dimerization: residues 36–55 and residues 66–95. The transient α-helices (residues 53–65 and 73–82) of α-synuclein monomers are destabilized by A53T and E46K mutations, which favors the formation of fibril native contacts in the N-terminal region, whereas the helix 53–65 prevents the propagation of fibril native contacts along the sequence for the WT in the early stages of dimerization. The present results indicate that dimers do not adopt the Greek key motif of the monomer fold in fibrils but form a majority of disordered aggregates and a minority (9–15%) of pre-fibrillar dimers both with intra-molecular and intermolecular β-sheets. The percentage of residues in parallel β-sheets is by increasing order monomer < disordered dimers < pre-fibrillar dimers. Native fibril contacts between the two monomers are present in the NAC domain for WT, A30P, and A53T and in the N-domain for A53T and E46K. Structural properties of pre-fibrillar dimers agree with rupture-force atomic force microscopy and single-molecule Förster resonance energy transfer available data. This suggests that the pre-fibrillar dimers might correspond to the smallest type B toxic oligomers. The probability density of the dimer gyration radius is multi-peaks with an average radius that is 10 Å larger than the one of the monomers for all proteins. The present results indicate that even the elementary α-synuclein aggregation step, the dimerization, is a complicated phenomenon that does not only involve the NAC region.

Controlling synthetic membraneless organelles by a red-light-dependent singlet oxygen-generating protein

Membraneless organelles (MLOs) formed via protein phase separation have great implications for both physiological and pathological processes. However, the inability to precisely control the bioactivities of MLOs has hindered our understanding of their roles in biology, not to mention their translational applications. Here, by combining intrinsically disordered domains such as RGG and mussel-foot proteins, we create an in cellulo protein phase separation system, of which various biological activities can be introduced via metal-mediated protein immobilization and further controlled by the water-soluble chlorophyll protein (WSCP)—a remarkably stable, red-light-responsive singlet oxygen generator. The WSCP-laden protein condensates undergo a liquid-to-solid phase transition on light exposure, due to oxidative crosslinking, providing a means to control catalysis within synthetic MLOs. Moreover, these photoresponsive condensates, which retain the light-induced phase-transition behavior in living cells, exhibit marked membrane localization, reminiscent of the semi-membrane-bound compartments like postsynaptic densities in nervous systems. Together, this engineered system provides an approach toward controllable synthetic MLOs and, alongside its light-induced phase transition, may well serve to emulate and explore the aging process at the subcellular or even molecular level.

Membraneless organelles play vital cellular roles, and control over their formation and state could have varied applications. Here, the authors develop photoresponsive synthetic condensates whose activity can be controlled through the use of light to trigger liquid-to-solid phase transition.

Highly sensitive SERS detection in a non-volatile liquid-phase system with nanocluster-patterned optical fiber SERS probes

The use of surface-enhanced Raman scattering (SERS) spectroscopy for the detection of substances in non-volatile systems, such as edible oil and biological cells, is an important issue in the fields of food safety and biomedicine. However, traditional dry-state SERS detection with planar SERS substrates is not suitable for highly sensitive and rapid SERS detection in non-volatile liquid-phase systems. In this paper, we take contaminant in edible oil as an example and propose an in situ SERS detection method for non-volatile complex liquid-phase systems with high-performance optical fiber SERS probes. Au-nanorod clusters are successfully prepared on optical fiber facet by a laboratory-developed laser-induced dynamic dip-coating method, and relatively high detection sensitivity (LOD of 2.4 × 10^-6 mol/L for Sudan red and 3.6 × 10^-7 mol/L for thiram in sunflower oil) and good reproducibility (RSD less than 10%) are achieved with a portable Raman spectrometer and short spectral integration time of 10 s even in complex edible oil systems. Additionally, the recovery rate experiment indicates the reliability and capability of this method for quantitative detection applications. This work provides a new insight for highly sensitive and rapid SERS detection in non-volatile liquid-phase systems with optical fiber SERS probes and may find important practical applications in food safety and biomedicine.

Tunable particle/cell separation across aqueous two-phase system interface by electric pulse in microfluidics

HYPOTHESIS

Separations of particles and cells are indispensable in many microfluidic systems and have numerous applications in chemistry and biomedicine. The interface of aqueous two-phase system (ATPS) can act as a liquid filter. Under electric field stimuli, the selective transfer of targets across the liquid-liquid interface are expected for particles and cells separation.

EXPERIMENTS

The separations of particles and cells based on ATPS electrophoresis in a microfluidic chip were investigated. A systematical study of the mechanism of ATPS electrophoresis was performed first by employing polystyrene (PS) particles. Subsequently, the separations of particles and microalgae cells were demonstrated.

FINDINGS

The electrophoretic transfer of particles across the interface of ATPS is determined by multi-parameters, including the strength of electric pulse, particle size, zeta potential, and hydrophobicity of the particle. The continuous separations of particles/cells can be achieved through the controllable transfer of target particles/cells across the interface under electric pulses in a microfluidic chip. By simply turning the magnitude of the applied electric pulse, the technique is suitable for different purposes, for example, the separations of particles and cells, purification of cells, and viability identification of cells. This tunable separation approach opens opportunities in multidimensional particle and cell sorting for the fields of seed selection of microorganisms, environmental assessment, and biomedical research.

Directivity-Enhanced Detection of a Single Nanoparticle Using a Plasmonic Slot Antenna

In situ refractive index sensors integrated with nanoaperture-based optical tweezers possess stable and sensitive responsivity to single nanoparticles. In most existing works, detection events are only identified using the total light intensity with directivity information ignored, leading to a low signal-to-noise ratio. Here, we propose to detect an optically trapped 20 nm silica particle by monitoring directivity of a plasmonic antenna. The main and secondary radiation lobes of the antenna reverse upon trapping because the particle-induced perturbation negates the relative phase between two antenna elements, leading to a significant change of the antenna front-to-back ratio. As a result, we obtain a signal-to-noise ratio of 20, with an order-of-magnitude improvement as compared to the intensity-only detection scheme.

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.

Controllable Nanoparticle Aggregation through a Superhydrophobic Laser-Induced Graphene Dynamic System for Surface-Enhanced Raman Scattering Detection

Surface-enhanced Raman scattering (SERS) is widely used for low-concentration molecular detection; however, challenges related to detection uniformity and repeatability are bottlenecks for practical application, especially as regards ultrasensitive detection. Here, through the coupling of bionics and fluid mechanics, a lotus-leaf effect and rose-petal effect (LLE-RPE)-integrated superhydrophobic chip is facilely developed using laser-induced graphene (LIG) fabricated on a polyimide film. Dense and uniform aggregation of gold nanoparticles (AuNPs) in droplets is realized through a constant contact angle (CCA) evaporation mode in the dynamic enrichment process, facilitating reliable ultrasensitive detection. The detection chip consists of two components: an LLE zone containing an ethanol-treated LIG superhydrophobic surface with a low-adhesive property, which functions as an AuNP-controllable aggregation zone, and an RPE zone containing an as-fabricated LIG superhydrophobic surface with water-solution pinning ability, which functions as a droplet solvent evaporation and a AuNP blending zone. AuNPs realize uniform aggregation during rolling on the LLE zone, and then get immobilized on the RPE zone to complete evaporation of the solvent, followed by Raman detection. Here, based on dense and uniform AuNP aggregation, the detection system achieves high-efficiency (242 s/18 μL) and ultralow-concentration (10^-17 M) detection of a target analyte (rhodamine 6G). The proposed system constitutes a simple approach toward high-performance detection for chemical analysis, environmental monitoring, biological analysis, and medical diagnosis.

Metal coordination induced SERS nanoprobe for sensitive and selective detection of histamine in serum

Sensitivity and credibility detecting histamine (HA) as an important neurotransmitter in biofluids is of importance in analytical science and physiology. Surface-enhanced Raman spectroscopy (SERS) is able to realize the high sensitivity with single molecules level, but providing the high sensitivity for HA with a small cross section remains a challenge. Here we develop the metal complex-based SERS nanoprobe nitrilotriacetic acid-Ni²⁺ (NTA-Ni²⁺) combined with self-assemble Au NPs active substrates for sensitive detection of HA. The NTA-Ni²⁺ can capture the HA molecules close to Au NPs substrates and then amplify the Raman signals of HA owing to the formation of a complex of NTA-Ni²⁺-HA. The self-assemble Au film through the evaporation-driven method can provide the high-density hot spots substrate with high stability and reproducibility. The NTA-Ni²⁺ decorated Au NPs as nanoprobe responds to HA with 1 μM level of sensitivity. More importantly, the developed SERS nanoprobe composing of NTA-Ni²⁺ and self-assemble Au NPs can be utilized to detect and monitor the HA spiked into serum, indicating the potential prospect in analysis of HA in complex specimen.

Attomolar Sensitive Magnetic Microparticles and a Surface-Enhanced Raman Scattering-Based Assay for Detecting SARS-CoV-2 Nucleic Acid Targets

Highly sensitive, reliable assays with strong multiplexing capability for detecting nucleic acid targets are significantly important for diagnosing various diseases, particularly severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The nanomaterial-based assay platforms suffer from several critical issues such as non-specific binding and highly false-positive results. In this paper, to overcome such limitations, we reported sensitive and remarkably reproducible magnetic microparticles (MMPs) and a surface-enhanced Raman scattering (SERS)-based assay using stable silver nanoparticle clusters for detecting viral nucleic acids. The MMP-SERS-based assay exhibited a sensitivity of 1.0 fM, which is superior to the MMP-fluorescence-based assay. In addition, in the presence of anisotropic Ag nanostructures (nanostars and triangular nanoplates), the assay exhibited greatly enhanced sensitivity (10 aM) and excellent signal reproducibility. This assay platform intrinsically eliminated the non-specific binding that occurs in the target detection step, and the controlled formation of stable silver nanoparticle clusters in solution enabled the remarkable reproducibility of the results. These findings indicate that this assay can be employed for future practical bioanalytical applications.

Missense Mutations Modify the Conformational Ensemble of the α-Synuclein Monomer Which Exhibits a Two-Phase Characteristic

α-Synuclein is an intrinsically disordered protein occurring in different conformations and prone to aggregate in β-sheet structures, which are the hallmark of the Parkinson disease. Missense mutations are associated with familial forms of this neuropathy. How these single amino-acid substitutions modify the conformations of wild-type α-synuclein is unclear. Here, using coarse-grained molecular dynamics simulations, we sampled the conformational space of the wild type and mutants (A30P, A53P, and E46K) of α-synuclein monomers for an effective time scale of 29.7 ms. To characterize the structures, we developed an algorithm, CUTABI (CUrvature and Torsion based of Alpha-helix and Beta-sheet Identification), to identify residues in the α-helix and β-sheet from C^α-coordinates. CUTABI was built from the results of the analysis of 14,652 selected protein structures using the Dictionary of Secondary Structure of Proteins (DSSP) algorithm. DSSP results are reproduced with 93% of success for 10 times lower computational cost. A two-dimensional probability density map of α-synuclein as a function of the number of residues in the α-helix and β-sheet is computed for wild-type and mutated proteins from molecular dynamics trajectories. The density of conformational states reveals a two-phase characteristic with a homogeneous phase (state B, β-sheets) and a heterogeneous phase (state HB, mixture of α-helices and β-sheets). The B state represents 40% of the conformations for the wild-type, A30P, and E46K and only 25% for A53T. The density of conformational states of the B state for A53T and A30P mutants differs from the wild-type one. In addition, the mutant A53T has a larger propensity to form helices than the others. These findings indicate that the equilibrium between the different conformations of the α-synuclein monomer is modified by the missense mutations in a subtle way. The α-helix and β-sheet contents are promising order parameters for intrinsically disordered proteins, whereas other structural properties such as average gyration radius, R_g, or probability distribution of R_g cannot discriminate significantly the conformational ensembles of the wild type and mutants. When separated in states B and HB, the distributions of R_g are more significantly different, indicating that global structural parameters alone are insufficient to characterize the conformational ensembles of the α-synuclein monomer.

Toward Sensitive and Reliable Surface-Enhanced Raman Scattering Imaging: From Rational Design to Biomedical Applications

Early specific detection through indicative biomarkers and precise visualization of lesion sites are urgent requirements for clinical disease diagnosis. However, current detection and optical imaging methods are insufficient for these demands. Molecular imaging technologies are being intensely studied for reliable medical diagnosis. In the past several decades, molecular imaging with surface-enhanced Raman scattering (SERS) has significant advances from analytical chemistry to medical science. SERS is the inelastic scattering generated from the interaction between photons and substances, presenting molecular structure information. The outstanding SERS virtues of high sensitivity, high specificity, and resistance to biointerference are highly advantageous for biomarker detection in a complex biological matrix. In this work, we review recent progress on the applications of SERS imaging in clinical diagnostics. With the assistance of SERS imaging, the detection of disease-related proteins, nucleic acids, small molecules, and pH of the cellular microenvironment can be implemented for adjuvant medical diagnosis. Moreover, multimodal imaging integrates the high penetration and high speed of other imaging modalities and imaging precision of SERS imaging, resulting in final complete and accurate imaging outcomes and exhibiting robust potential in the discrimination of pathological tissues and surgical navigation. As a promising molecular imaging technology, SERS imaging has achieved remarkable performance in clinical diagnostics and the biomedical realm. It is expected that this review will provide insights for further development of SERS imaging and promote the rapid progress and successful translation of advanced molecular imaging with clinical diagnostics.