Discrimination between Single Protein Conformations Using Dynamic SERS

Multidimensional Investigations of Single Molecule Unfolding of Bovine Serum Albumin Using Plasmonic Nanopores

Direct detection of proteins, especially their conformation and configuration information, at the single molecule level, is challenging in various biotechnological fields. Plasmonic nanopores have raised attention as multidimensional biosensors with single molecule (SM) sensitivity. Here, we employ a gold plasmonic nanopore to monitor the unfolding of SM bovine serum albumin (BSA). The gradual collapse of the BSA structure induced by high bias voltages is demonstrated through an increase in the fraction current blockade. Surface-enhanced Raman scattering (SERS) spectra provide structural evidence for protein unfolding, while the optical force is verified as an additional factor contributing to BSA deformation. The effect of the optical force on the dwell time of BSA in a nanopore is also investigated. The present study reveals that plasmonic nanopores offer multidimensional observations on the structure and conformation of SM proteins, which will drive further innovations in protein detection and analysis.

Multiwavelength Surface-Enhanced Raman Scattering Fingerprints of Human Urine for Cancer Diagnosis

Label-free surface-enhanced Raman spectroscopy (SERS) is capable of capturing rich compositional information from complex biosamples by providing vibrational spectra that are crucial for biosample identification. However, increasing complexity and subtle variations in biological media can diminish the discrimination accuracy of traditional SERS excited by a single laser wavelength. Herein, we introduce a multiwavelength SERS approach combined with machine learning (ML)-based classification to improve the discrimination accuracy of human urine specimens for bladder cancer (BCa) diagnosis. This strategy leverages the excitation-wavelength-dependent SERS spectral profiles of complex matrices, which are mainly attributed to wavelength-related vibrational changes in individual analytes and differences in the variation ratios of SERS intensity across different wavelengths among various analytes. By capturing SERS fingerprints under multiple excitation wavelengths, we can acquire more comprehensive and unique chemical information on complex samples. Further experimental examinations with clinical urine specimens, supported by ML algorithms, demonstrate the effectiveness of this multiwavelength strategy and improve the diagnostic accuracy of BCa and staging of its invasion with SERS spectra from increasing numbers of wavelengths. The multiwavelength SERS holds promise as a convenient, cost-effective, and broadly applicable technique for the precise identification of complex matrices and diagnosis of diseases based on body fluids.

Surface-Enhanced Raman Scattering Nanosensing and Imaging in Neuroscience

Monitoring neurochemicals and imaging the molecular content of brain tissues in vitro, ex vivo, and in vivo is essential for enhancing our understanding of neurochemistry and the causes of brain disorders. This review explores the potential applications of surface-enhanced Raman scattering (SERS) nanosensors in neurosciences, where their adoption could lead to significant progress in the field. These applications encompass detecting neurotransmitters or brain disorders biomarkers in biofluids with SERS nanosensors, and imaging normal and pathological brain tissues with SERS labeling. Specific studies highlighting in vitro, ex vivo, and in vivo analysis of brain disorders using fit-for-purpose SERS nanosensors will be detailed, with an emphasis on the ability of SERS to detect clinically pertinent levels of neurochemicals. Recent advancements in designing SERS-active nanomaterials, improving experimentation in biofluids, and increasing the usage of machine learning for interpreting SERS spectra will also be discussed. Furthermore, we will address the tagging of tissues presenting pathologies with nanoparticles for SERS imaging, a burgeoning domain of neuroscience that has been demonstrated to be effective in guiding tumor removal during brain surgery. The review also explores future research applications for SERS nanosensors in neuroscience, including monitoring neurochemistry in vivo with greater penetration using surface-enhanced spatially offset Raman scattering (SESORS), near-infrared lasers, and 2-photon techniques. The article concludes by discussing the potential of SERS for investigating the effectiveness of therapies for brain disorders and for integrating conventional neurochemistry techniques with SERS sensing.

Trace Detection of Adulterants in Illicit Opioid Samples Using Surface-Enhanced Raman Scattering and Random Forest Classification

The detection of trace adulterants in opioid samples is an important aspect of drug checking, a harm reduction measure that is required as a result of the variability and unpredictability of the illicit drug supply. While many analytical methods are suitable for such analysis, community-based approaches require techniques that are amenable to point-of-care applications with minimal sample preparation and automated analysis. We demonstrate that surface-enhanced Raman spectroscopy (SERS), combined with a random forest classifier, is able to detect the presence of two common sedatives, bromazolam (0.32-36% w/w) and xylazine (0.15-15% w/w), found in street opioid samples collected as a part of a community drug checking service. The Raman predictions, benchmarked against mass spectrometry results, exhibited high specificity (88% for bromazolam, 96% for xylazine) and sensitivity (88% for bromazolam, 92% for xylazine) for the compounds of interest. We additionally provide evidence that this exceeds the performance of a more conventional approach using infrared spectral data acquired on the same samples. This demonstrates the feasibility of SERS for point-of-care analysis of challenging multicomponent samples containing trace adulterants.

Surface enhanced Raman scattering for probing cellular biochemistry

Surface enhanced Raman scattering (SERS) from biomolecules in living cells enables the sensitive, but also very selective, probing of their biochemical composition. This minireview discusses the developments of SERS probing in cells over the past years from the proof-of-principle to observe a biochemical status to the characterization of molecule-nanostructure and molecule-molecule interactions and cellular processes that involve a wide variety of biomolecules and cellular compartments. Progress in applying SERS as a bioanalytical tool in living cells, to gain a better understanding of cellular physiology and to harness the selectivity of SERS, has been achieved by a combination of live cell SERS with several different approaches. They range from organelle targeting, spectroscopy of relevant molecular models, and the optimization of plasmonic nanostructures to the application of machine learning and help us to unify the information from defined biomolecules and from the cell as an extremely complex system.

Biosensing Using SERS Active Gold Nanostructures

Surface-enhanced Raman spectroscopy (SERS) has become a powerful tool for biosensing applications owing to its fingerprint recognition, high sensitivity, multiplex detection, and biocompatibility. This review provides an overview of the most significant aspects of SERS for biomedical and biosensing applications. We first introduced the mechanisms at the basis of the SERS amplifications: electromagnetic and chemical enhancement. We then illustrated several types of substrates and fabrication methods, with a focus on gold-based nanostructures. We further analyzed the relevant factors for the characterization of the SERS sensor performances, including sensitivity, reproducibility, stability, sensor configuration (direct or indirect), and nanotoxicity. Finally, a representative selection of applications in the biomedical field is provided.

Vibrational Spectra of Nucleotides in the Presence of the Au Cluster Enhancer in MD Simulation of a SERS Sensor

Surface-enhanced Raman scattering (SERS) nanoprobes have shown tremendous potential in in vivo imaging. The development of single oligomer resolution in the SERS promotes experiments on DNA and protein identification using SERS as a nanobiosensor. As Raman scanners rely on a multiple spectrum acquisition, faster imaging in real-time is required. SERS weak signal requires averaging of the acquired spectra that erases information on conformation and interaction. To build spectral libraries, the simulation of measurement conditions and conformational variations for the nucleotides relative to enhancer nanostructures would be desirable. In the molecular dynamic (MD) model of a sensing system, we simulate vibrational spectra of the cytosine nucleotide in FF2/FF3 potential in the dynamic interaction with the Au20 nanoparticles (NP) (EAM potential). Fourier transfer of the density of states (DOS) was performed to obtain the spectra of bonds in reaction coordinates for nucleotides at a resolution of 20 to 40 cm-1. The Au20 was optimized by ab initio density functional theory with generalized gradient approximation (DFT GGA) and relaxed by MD. The optimal localization of nucleotide vs. NP was defined and the spectral modes of both components vs. interaction studied. Bond-dependent spectral maps of nucleotide and NP have shown response to interaction. The marker frequencies of the Au20-nucleotide interaction have been evaluated.

Raman spectroscopy and neuroscience: from fundamental understanding to disease diagnostics and imaging

Neuroscience would directly benefit from more effective detection techniques, leading to earlier diagnosis of disease. The specificity of Raman spectroscopy is unparalleled, given that a molecular fingerprint is attained for each species. It also allows for label-free detection with relatively inexpensive instrumentation, minimal sample preparation, and rapid sample analysis. This review summarizes Raman spectroscopy-based techniques that have been used to advance the field of neuroscience in recent years.

Surface Enhanced Raman Spectroscopy for Single Molecule Protein Detection

A two-step process of protein detection at a single molecule level using SERS was developed as a proof-of-concept platform for medical diagnostics. First, a protein molecule was bound to a linker in the bulk solution and then this adduct was chemically reacted with the SERS substrate. Traut’s Reagent (TR) was used to thiolate Bovine serum albumin (BSA) in solution followed by chemical cross linking to a gold surface through a sulfhydryl group. A Glycine-TR adduct was used as a control sample to identify the protein contribution to the SER spectra. Gold SERS substrates were manufactured by electrochemical deposition. Solutions at an ultralow concentration were used for attaching the TR adducts to the SERS substrate. Samples showed the typical behavior of a single molecule SERS including spectral fluctuations, blinking and Raman signal being generated from only selected points on the substrate. The fluctuating SER spectra were examined using Principle Component Analysis. This unsupervised statistics allowed for the selecting of spectral contribution from protein moiety indicating that the method was capable of detecting a single protein molecule. Thus we have demonstrated, that the developed two-step methodology has the potential as a new platform for medical diagnostics.

Advances in surface-enhanced Raman spectroscopy (SERS) substrates for lipid and protein characterization: sensing and beyond

Surface-enhanced Raman spectroscopy (SERS) has become an essential ultrasensitive analytical tool for biomolecular analysis of small molecules, macromolecular proteins, and even cells. SERS enables label-free, direct detection of molecules through their intrinsic Raman fingerprint. In particular, protein and lipid bilayers are dynamic three-dimensional structures that necessitate label-free methods of characterization. Beyond direct detection and quantitation, the structural information contained in SERS spectra also enables deeper biophysical characterization of biomolecules near metallic surfaces. Therefore, SERS offers enormous potential for such systems, although making measurements in a nonperturbative manner that captures the full range of interactions and activity remains a challenge. Many of these challenges have been overcome through advances in SERS substrate development, which have expanded the applications and targets of SERS for direct biomolecular quantitation and biophysical characterization. In this review, we will first discuss different categories of SERS substrates including solution-phase, solid-supported, tip-enhanced Raman spectroscopy (TERS), and single-molecule substrates for biomolecular analysis. We then discuss detection of protein and biological lipid membranes. Lastly, biophysical insights into proteins, lipids and live cells gained through SERS measurements of these systems are reviewed.

SERS Probing of Proteins in Gold Nanoparticle Agglomerates

The collection of surface-enhanced Raman scattering (SERS) spectra of proteins and other biomolecules in complex biological samples such as animal cells has been achieved with gold nanoparticles that are introduced to the sample. As a model for such a situation, SERS spectra were measured in protein solutions using gold nanoparticles in the absence of aggregating agents, allowing for the free formation of a protein corona. The SERS spectra indicate a varied interaction of the protein molecule with the gold nanoparticles, depending on protein concentration. The concentration-dependent optical properties of the formed agglomerates result in strong variation in SERS enhancement. At protein concentrations that correspond to those inside cells, SERS signals are found to be very low. The results suggest that in living cells the successful collection of SERS spectra must be due to the positioning of the aggregates rather than the crowded biomolecular environment inside the cells. Experiments with DNA suggest the suitability of the applied sample preparation approach for an improved understanding of SERS nanoprobes and nanoparticle-biomolecule interactions in general.

Different binding sites of serum albumins in the protein corona of gold nanoparticles

Binding sites of albumins on gold nanoparticles were characterized by surface-enhanced Raman scattering.

Hand-Held Femtogram Detection of Hazardous Picric Acid with Hydrophobic Ag Nanopillar SERS Substrates and Mechanism of Elasto-Capillarity

Picric acid (PA) is a severe environmental and security risk due to its unstable, toxic, and explosive properties. It is also challenging to detect in trace amounts and in situ because of its highly acidic and anionic character. Here, we assess sensing of PA under nonlaboratory conditions using surface-enhanced Raman scattering (SERS) silver nanopillar substrates and hand-held Raman spectroscopy equipment. The advancing elasto-capillarity effects are explained by molecular dynamics simulations. We obtain a SERS PA detection limit on the order of 20 ppt, corresponding attomole amounts, which together with the simple analysis methodology demonstrates that the presented approach is highly competitive for ultrasensitive analysis in the field.