Nanoscale Discrimination between Toxic and Nontoxic Protein Misfolded Oligomers with Tip-Enhanced Raman Spectroscopy

Impact of seed amplification assay and surface-enhanced Raman spectroscopy combined approach on the clinical diagnosis of Alzheimer's disease

BACKGROUND

The current diagnosis of Alzheimer's disease (AD) is based on a series of analyses which involve clinical, instrumental and laboratory findings. However, signs, symptoms and biomarker alterations observed in AD might overlap with other dementias, resulting in misdiagnosis.

METHODS

Here we describe a new diagnostic approach for AD which takes advantage of the boosted sensitivity in biomolecular detection, as allowed by seed amplification assay (SAA), combined with the unique specificity in biomolecular recognition, as provided by surface-enhanced Raman spectroscopy (SERS).

RESULTS

The SAA-SERS approach supported by machine learning data analysis allowed efficient identification of pathological Aβ oligomers in the cerebrospinal fluid of patients with a clinical diagnosis of AD or mild cognitive impairment due to AD.

CONCLUSIONS

Such analytical approach can be used to recognize disease features, thus allowing early stratification and selection of patients, which is fundamental in clinical treatments and pharmacological trials.

Apex-Confined Plasmonic Tip for High Resolution Tip-Enhanced Raman Spectroscopic Imaging of Carbon Nanotubes

This paper reports a handy technical scheme to decorate atomic force microscopy (AFM) tips toward tip-enhanced Raman spectroscopy (TERS) applications. The major attraction of these homemade tips lies in that silver decoration can be confined at the apex of commercial tips by the means of an AFM-controlled electrochemical reaction. The reduction of Ag⁺ occurs in a highly sealed environment to secure the metal coating efficiency. Key factors include silver nitrate solution to provide Ag⁺, ambient relative humidity and temperature in a humidity cell, electric potential bias, and tip-surface distance. Subsequently, these silver-coated tips are evaluated for TERS measurement of carbon nanotubes (CNTs) so that both morphological and chemical characteristics of CNTs are concurrently obtained. The Raman spectra reveal that our plasmonic tip competently possesses an ∼30-fold local field signal increase and the corresponding TERS image laterally resolves at the single-pixel level.

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

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

Total Internal Reflection Tip-Enhanced Raman Spectroscopy of Tau Fibrils

Total internal reflection tip-enhanced Raman spectroscopy (TIR-TERS) has recently emerged as a promising technique for noninvasive nanoscale chemical characterization of biomolecules. We demonstrate that the TERS enhancement achieved in this experimental configuration is nearly 30 times higher than that in linear polarization and 8 times higher than that in radial polarization using traditional bottom-illumination geometry. TIR-TERS is applied to the study of Tau amyloid fibrils formed with the human full-length Tau protein mixed with heparin. This technique reveals the possibility to perform TERS imaging with 1-4 nm axial and 5-10 nm lateral spatial optical resolution. In these Tau/heparin fibrils, spectral signatures assigned to aromatic amino acid residues (phenylalanine, histidine, and tyrosine) and nonaromatic ones (e.g., cysteine, lysine, arginine, asparagine, and glutamine) are distinctly observed. Amide I and amide III bands can also be detected. In a fibril portion, it is shown that antiparallel β-sheets and fibril core β-sheets are abundant and are often localized in amino acid-rich regions where parallel β-sheets and random coils are present in lower proportions. This first TIR-TERS study on a nonresonant biological sample paves the way for future nanoscale chemical and structural characterization of biomolecules using this performant and original technique.

Comparing Commercial Metal-Coated AFM Tips and Home-Made Bulk Gold Tips for Tip-Enhanced Raman Spectroscopy of Polymer Functionalized Multiwalled Carbon Nanotubes

Tip-enhanced Raman spectroscopy (TERS) combines the high specificity and sensitivity of plasmon-enhanced Raman spectroscopy with the high spatial resolution of scanning probe microscopy. TERS has gained a lot of attention from many nanoscience fields, since this technique can provide chemical and structural information of surfaces and interfaces with nanometric spatial resolution. Multiwalled carbon nanotubes (MWCNTs) are very versatile nanostructures that can be dispersed in organic solvents or polymeric matrices, giving rise to new nanocomposite materials, showing improved mechanical, electrical and thermal properties. Moreover, MWCNTs can be easily functionalized with polymers in order to be employed as specific chemical sensors. In this context, TERS is strategic, since it can provide useful information on the cooperation of the two components at the nanoscale for the optimization of the macroscopic properties of the hybrid material. Nevertheless, efficient TERS characterization relies on the geometrical features and material composition of the plasmonic tip used. In this work, after comparing the TERS performance of commercial Ag coated nanotips and home-made bulk Au tips on bare MWCNTs, we show how TERS can be exploited for characterizing MWCNTs mixed with conjugated fluorene copolymers, thus contributing to the understanding of the polymer/CNT interaction process at the local scale.

Molecular and plasmonic resonances on tip-enhanced Raman spectroscopy

Plasmon has been widely investigated and applied, because it can greatly enhance molecular Raman spectral intensity. In this study, the resonance Raman effect of the tetra-tert-butylnaphthalocyanine (TTBN) is analyzed, including the Raman wave number shift and enhancement factor, resulting from light of different incident wavelengths. Furthermore, the optical properties of TTBN are obtained, such as charge transfer, the electronic circular dichroism (ECD) spectrum, etc. Lastly, we study the tip-enhanced Raman spectroscopy (TERS) by adjusting the parameters of the metal tip to achieve the highest electromagnetic enhancement at different incident wavelengths. Combining the resonance excitation effect and the tip enhanced Raman effect, the enhancement factor of TERS can reach up to 10⁸-10⁹. This study provides significant help for a profound understanding of the TERS mechanism.

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.

The Progress of Label-Free Optical Imaging in Alzheimer's Disease Screening and Diagnosis

As the major neurodegenerative disease of dementia, Alzheimer's disease (AD) has caused an enormous social and economic burden on society. Currently, AD has neither clear pathogenesis nor effective treatments. Positron emission tomography (PET) and magnetic resonance imaging (MRI) have been verified as potential tools for diagnosing and monitoring Alzheimer's disease. However, the high costs, low spatial resolution, and long acquisition time limit their broad clinical utilization. The gold standard of AD diagnosis routinely used in research is imaging AD biomarkers with dyes or other reagents, which are unsuitable for in vivo studies owing to their potential toxicity and prolonged and costly process of the U.S. Food and Drug Administration (FDA) approval for human use. Furthermore, these exogenous reagents might bring unwarranted interference to mechanistic studies, causing unreliable results. Several label-free optical imaging techniques, such as infrared spectroscopic imaging (IRSI), Raman spectroscopic imaging (RSI), optical coherence tomography (OCT), autofluorescence imaging (AFI), optical harmonic generation imaging (OHGI), etc., have been developed to circumvent this issue and made it possible to offer an accurate and detailed analysis of AD biomarkers. In this review, we present the emerging label-free optical imaging techniques and their applications in AD, along with their potential and challenges in AD diagnosis.

Ion-exchanged glass microrods as hybrid SERS/fluorescence substrates for molecular beacon-based DNA detection

Ion-exchange in molten nitrate salts containing metal ions (i.e. silver, copper, etc.) represents a well-established technique able to modify the chemical-physical properties of glass materials. It is widely used not only in the field of integrated optics (IO) but also, more recently, in plasmonics due to the possibility to induce the formation of metal nanoparticles in the glass matrix by an ad hoc thermal post-process. In this work, the application of this technology for the realisation of low-cost and stable surface-enhanced Raman scattering (SERS) active substrates, based on soda-lime glass microrods, is reported. The microrods, with a radius of a few tens of microns, were obtained by cutting the end of an ion-exchanged soda-lime fibre for a length less than 1 cm. As ion source, silver nitrate was selected due to the outstanding SERS properties of silver. The ion-exchange and thermal annealing post-process parameters were tuned to expose the embedded silver nanoparticles on the surface of the glass microrods, avoiding the use of any further chemical etching step. In order to test the combined SERS/fluorescence response of these substrates, labelled molecular beacons (MBs) were immobilised on their surface for deoxyribonucleic acid (DNA) detection. Our experiments confirm that target DNA is attached on the silver nanoparticles and its presence is revealed by both SERS and fluorescence measurements. These results pave the way towards the development of low-cost and stable hybrid fibres, in which SERS and fluorescence interrogation techniques are combined in the same optical device.

Probing the Structure of Toxic Amyloid-β Oligomers with Electron Spin Resonance and Molecular Modeling

Structural models of the toxic species involved in the development of Alzheimer's disease are of utmost importance to understand the molecular mechanism and to describe early biomarkers of the disease. Among toxic species, soluble oligomers of amyloid-β (Aβ) peptides are particularly important, because they are responsible for spreading cell damages over brain regions, thus rapidly impairing brain functions. In this work we obtain structural information on a carefully prepared Aβ(1-42) sample, representing a toxic state for cell cultures, by combining electron spin resonance spectroscopy and computational models. We exploited the binding of Cu²⁺ to Aβ(1-42) and used copper as a probe for estimating Cu-Cu distances in the oligomers by applying double electron-electron resonance (DEER) pulse sequence. The DEER trace of this sample displays a unique feature that fits well with structural models of oligomers formed by Cu-cross-linked peptide dimers. Because Cu is bound to the Aβ(1-42) N-terminus, for the first time structural constraints that are missing in reported studies are provided at physiological conditions for the Aβ N-termini. These constraints suggest the Aβ(1-42) dimer as the building block of soluble oligomers, thus changing the scenario for any kinetic model of Aβ(1-42) aggregation.

Full-length TDP-43 and its C-terminal domain form filaments in vitro having non-amyloid properties

Accumulation of ubiquitin-positive, tau- and α-synuclein-negative intracellular inclusions of TDP-43 in the central nervous system represents the major hallmark correlated to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U). Such inclusions have variably been described as amorphous aggregates or more structured deposits having amyloid properties. Here we have purified full-length TDP-43 (FL TDP-43) and its C-terminal domain (Ct TDP-43) to investigate the morphological, structural and tinctorial features of aggregates formed in vitro by them at pH 7.4 and 37 °C. AFM images indicate that both protein variants show a tendency to form filaments. Moreover, we show that both FL TDP-43 and Ct TDP-43 filaments possess a largely disordered secondary structure, as ascertained by far-UV circular dichroism and Fourier transform infra-red spectroscopy, do not bind Congo red and induce a very weak increase of thioflavin T fluorescence, indicating the absence of a clear amyloid-like signature.

Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study

Amyloid-β (Aβ) peptides form assemblies that are pathological hallmarks of Alzheimer's disease. Aβ oligomers are soluble, mobile, and toxic forms of the peptide that act in the extracellular space before assembling into protofibrils and fibrils. Therefore, oligomers play an important role in the mechanism of Alzheimer's disease. Since it is difficult to determine by experiment the atomic structures of oligomers, which accumulate fast and are polymorphic, computer simulation is a useful tool to investigate elusive oligomers' structures. In this work, we report extended all-atom molecular dynamics simulations, both canonical and replica exchange, of Aβ(1-42) trimer starting from two different initial conformations: (i) the pose produced by the best docking of a monomer aside of a dimer (simulation 1), representing oligomers freshly formed by assembling monomers, and (ii) a configuration extracted from an experimental mature fibril structure (simulation 2), representing settled oligomers in equilibrium with extended fibrils. We showed that in simulation 1, regions with small β-barrels are populated, indicating the chance of spontaneous formation of domains resembling channel-like structures. These structural domains are alternative to those more representative of mature fibrils (simulation 2), the latter showing a stable bundle of C-termini that is not sampled in simulation 1. Moreover, trimer of Aβ(1-42) can form internal pores that are large enough to be accessed by water molecules and Ca2+ ions.

Label-free SERS detection of proteins based on machine learning classification of chemo-structural determinants

Establishing standardized methods for a consistent analysis of spectral data remains a largely underexplored aspect in surface-enhanced Raman spectroscopy (SERS), particularly applied to biological and biomedical research. Here we propose an effective machine learning classification of protein species with closely resembled spectral profiles by a mixed data processing based on principal component analysis (PCA) applied to multipeak fitting on SERS spectra. This strategy simultaneously assures a successful discrimination of proteins and a thorough characterization of the chemostructural differences among them, ultimately opening up new routes for SERS evolution toward sensing applications and diagnostics of interest in life sciences.

Contributions of Molecular and Optical Techniques to the Clinical Diagnosis of Alzheimer's Disease

Alzheimer's disease (AD) is the most common neurodegenerative disorder worldwide. The distinctive neuropathological feature of AD is the intracerebral accumulation of two abnormally folded proteins: β-amyloid (Aβ) in the form of extracellular plaques, and tau in the form of intracellular neurofibrillary tangles. These proteins are considered disease-specific biomarkers, and the definite diagnosis of AD relies on their post-mortem identification in the brain. The clinical diagnosis of AD is challenging, especially in the early stages. The disease is highly heterogeneous in terms of clinical presentation and neuropathological features. This phenotypic variability seems to be partially due to the presence of distinct Aβ conformers, referred to as strains. With the development of an innovative technique named Real-Time Quaking-Induced Conversion (RT-QuIC), traces of Aβ strains were found in the cerebrospinal fluid of AD patients. Emerging evidence suggests that different conformers may transmit their strain signature to the RT-QuIC reaction products. In this review, we describe the current challenges for the clinical diagnosis of AD and describe how the RT-QuIC products could be analyzed by a surface-enhanced Raman spectroscopy (SERS)-based systems to reveal the presence of strain signatures, eventually leading to early diagnosis of AD with the recognition of individual disease phenotype.

Advances in nanomedicines for diagnosis of central nervous system disorders

In spite of a great improvement in medical health services and an increase in lifespan, we have witnessed a skyrocket increase in the incidence of central nervous system (CNS) disorders including brain tumors, neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, Huntington's disease), ischemic stroke, and epilepsy, which have seriously undermined the quality of life and substantially increased economic and societal burdens. Development of diagnostic methods for CNS disorders is still in the early stage, and the clinical outcomes suggest these methods are not ready for the challenges associated with diagnosis of CNS disorders, such as early detection, specific binding, sharp contrast, and continuous monitoring of therapeutic interventions. Another challenge is to overcome various barrier structures during delivery of diagnostic agents, especially the blood-brain barrier (BBB). Fortunately, utilization of nanomaterials has been pursued as a potential and promising strategy to address these challenges. This review will discuss anatomical and functional structures of BBB and transport mechanisms of nanomaterials across the BBB, and special emphases will be placed on the state-of-the-art advances in the development of nanomedicines from a variety of nanomaterials for diagnosis of CNS disorders. Meanwhile, current challenges and future perspectives in this field are also highlighted.

Hollow core photonic crystal fiber-assisted Raman spectroscopy as a tool for the detection of Alzheimer's disease biomarkers

SIGNIFICANCE

Alzheimer's disease (AD) is an irreversible and progressive disorder that damages brain cells and impairs the cognitive abilities of the affected. Developing a sensitive and cost-effective method to detect Alzheimer's biomarkers appears vital in both a diagnostic and therapeutic perspective.

AIM

Our goal is to develop a sensitive and reliable tool for detection of amyloid β (1-42) peptide (Aβ42), a major AD biomarker, using fiber-enhanced Raman spectroscopy (FERS).

APPROACH

A hollow core photonic crystal fiber (HCPCF) was integrated with a conventional Raman spectroscopic setup to perform FERS measurements. FERS was then coupled with surface-enhanced Raman spectroscopy (SERS) to further amplify the Raman signal thanks to a combined FERS-SERS assay.

RESULTS

A minimum 20-fold enhancement of the Raman signal of Aβ42 as compared to a conventional Raman spectroscopy scheme was observed using the HCPCF-based light delivery system. The signal was further boosted by decorating the fiber core with gold bipyramids generating an additional SERS effect, resulting in an overall 200 times amplification.

CONCLUSIONS

The results demonstrate that the use of an HCPCF-based platform can provide sharp and intense Raman signals of Aβ42, in turn paving the way toward the development of a sensitive label-free detection tool for early diagnosis of AD.

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.

Nanoscopic insights into the surface conformation of neurotoxic amyloid β oligomers

Raman spectroscopy assisted by localized plasmon resonances generating effective hot spots at the gaps between intertwined silver nanowires is herein adopted to unravel characteristic molecular motifs on the surface of Aβ₄₂ misfolded oligomers that are critical in driving intermolecular interactions in neurodegeneration.

Unraveling characteristic structural determinants at the basis of Aβ₄₂ oligomers' neurotoxicity by a sub-molecular SERS investigation of their surface.

Conformational Evolution of Molecular Signatures during Amyloidogenic Protein Aggregation

Aggregation is a pathological hallmark of proteinopathies such as Alzheimer's disease and results in the deposition of β-sheet-rich amyloidogenic protein aggregates. Such proteinopathies can be classified by the identity of one or more aggregated proteins, with recent evidence also suggesting that distinct molecular conformers (strains) of the same protein can be observed in different diseases, as well is in subtypes of the same disease. Therefore, methods for the quantification of pathological changes in protein conformation are central to understanding and treating proteinopathies. In this work, the evolution of Raman spectroscopic molecular signatures of three conformationally distinct proteins, bovine serum albumin (α-helical-rich), β2-microglobulin (β-sheet-rich), and tau (natively disordered), was assessed during aggregation into oligomers and fibrils. The morphological evolution was tracked using atomic force microscopy and corresponding conformational changes were assessed by their Raman signatures acquired in both wet and dried conditions. A deconvolution model was developed which allowed us to quantify the conformation of the nonregular protein tau, as well as for the oligomeric and fibrillar species of each of the proteins. Principle component analysis of the fingerprint region allowed further identification of the distinguishing spectral features and unsupervised distinction. While an increase in β-sheet is seen on aggregation, crucially, however, each protein also retains a significant proportion of its native monomeric structure after aggregation. Thus, spectral analysis of each aggregated species, oligomeric, as well as fibrillar, for each protein resulted in a unique and quantitative "conformational fingerprint". This approach allowed us to provide the first differential detection of both oligomers and fibrils of the three different amyloidogenic proteins, including tau, whose aggregates have never before been interrogated using spontaneous Raman spectroscopy. Quantitative "conformational fingerprinting" by Raman spectroscopy thus demonstrates its huge potential and utility in understanding proteinopathic disease mechanisms and for providing strain-specific early diagnostic markers and targets for disease-modifying therapies.

Fractal Silver Dendrites as 3D SERS Platform for Highly Sensitive Detection of Biomolecules in Hydration Conditions

In this paper, we report on the realization of a highly sensitive and low cost 3D surface-enhanced Raman scattering (SERS) platform. The structural features of the Ag dendrite network that characterize the SERS material were exploited, attesting a remarked self-similarity and scale invariance over a broad range of length scales that are typical of fractal systems. Additional structural and optical investigations confirmed the purity of the metal network, which was characterized by low oxygen contamination and by broad optical resonances introduced by the fractal behavior. The SERS performances of the 3D fractal Ag dendrites were tested for the detection of lysozyme as probe molecule, attesting an enhancement factor of ~2.4 × 10⁶. Experimental results assessed the dendrite material as a suitable SERS detection platform for biomolecules investigations in hydration conditions.

Nanoscopic Portrait of an Amyloidogenic Pathway Visualized through Tip-Enhanced Raman Spectroscopy

Inroads into understanding the process by which amyloid proteins become toxic have been hampered by the lack of experimental techniques that adequately resolve the process. Recently, tip-enhanced Raman spectroscopy, with its unique capability to spectroscopically image and chemically identify reaction mixtures with nanoscale precision, was used to obtain a high-resolution roadmap of the soluble-to-toxic conversion of amyloid beta. This technique opens the door for studying the toxic aggregation pathways of other amyloid proteins and spurs efforts devoted to prophylactic and therapeutic intervention in neurodegenerative and protein-misfolding-related disorders.

Low cost tips for tip-enhanced Raman spectroscopy fabricated by two-step electrochemical etching of 125 µm diameter gold wires

Tip-enhanced Raman spectroscopy (TERS) has become a well-applied technique for nanospectroscopy, allowing for single molecule sensitivity with sub-nanometer spatial resolution. The demand for efficient, reproducible and cost-effective probes for TERS is increasing. Here we report on a new electrochemical etching protocol to fabricate TERS tips starting from 125 µm diameter gold wires in a reproducible way. The process is reliable (50% of the tips have radius of curvature <35 nm, 66% <80 nm), fast (less than 2 min) and 2.5 times cheaper than the etching of standard 250 µm diameter wires. The TERS performance of the tips is tested on dyes, pigments and biomolecules and enhancement factors higher than 10⁵ are observed. TERS mapping with a spatial resolution of 5 nm is demonstrated.