Imaging secondary structure of individual amyloid fibrils of a β2-microglobulin fragment using near-field infrared spectroscopy

Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features

This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of 13C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of 13C-13C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.

Infrared nanoimaging of neuronal ultrastructure and nanoparticle interaction with cells

Here we introduce scattering-type scanning near-field optical microscopy (s-SNOM) as a novel tool for nanoscale chemical-imaging of sub-cellular organelles, nanomaterials and of the interactions between them. Our setup uses a tuneable mid-infrared laser and a sharp scanning probe to image at a resolution substantially surpassing the diffraction limit. The laser can be tuned to excite vibrational modes of functional groups in biomolecules, (e.g. amide moieties), in a way that enables direct chemical mapping without the need for labelling. We, for the first time, chemically image neuronal ultrastructure, identify neuronal organelles and sub-organelle structures as small as 10 nm and validate our findings using transmission electron microscopy (TEM). We produce chemical and morphological maps of neurons treated with gold nanospheres and characterize nanoparticle size and intracellular location, and their interaction with the plasma membrane. Our results show that the label-free nature of s-SNOM means it has a 'true' chemical resolution of up to 20 nm which can be further improved. We argue that it offers significant potential in nanomedicine for nanoscale chemical imaging of cell ultrastructure and the subcellular distribution of nanomaterials within tissues.

The Evolution of MXenes Conductivity and Optical Properties Upon Heating in Air

MXenes, a family of 2D transition-metal carbides and nitrides, have excellent electrical conductivity and unique optical properties. However, MXenes oxidize in ambient conditions, which is accelerated upon heating. Intercalation of water also causes hydrolysis accelerating oxidation. Developing new tools to readily characterize MXenes' thermal stability can enable deeper insights into their structure-property relationships. Here, in situ spectroscopic ellipsometry (SE) is employed to characterize the optical properties of three types of MXenes (Ti3 C2 Tx , Mo2 TiC2 Tx , and Ti2 CTx ) with varied composition and atomistic structures to investigate their thermal degradation upon heating under ambient environment. It is demonstrated that changes in MXene extinction and optical conductivity in the visible and near-IR regions correlate well with the amount of intercalated water and hydroxyl termination groups and the degree of oxidation, measured using thermogravimetric analysis. Among the three MXenes, Ti3 C2 Tx and Ti2 CTx , respectively, have the highest and lowest thermal stability, indicating the role of transition-metal type, synthesis route, and the number of atomic layers in MXene flakes. These findings demonstrate the utility of SE as a powerful in situ technique for rapid structure-property relationship studies paving the way for the further design, fabrication, and property optimization of novel MXene materials.

Label-free nanoscale mapping of intracellular organelle chemistry

The ability to image cell chemistry at the nanoscale is key for understanding cell biology, but many optical microscopies are restricted by the ~(200-250)nm diffraction limit. Electron microscopy and super-resolution fluorescence techniques beat this limit, but rely on staining and specialised labelling to generate image contrast. It is challenging, therefore, to obtain information about the functional chemistry of intracellular components. Here we demonstrate a technique for intracellular label-free chemical mapping with nanoscale (~30 nm) resolution. We use a probe-based optical microscope illuminated with a mid-infrared laser whose wavelengths excite vibrational modes of functional groups occurring within biological molecules. As a demonstration, we chemically map intracellular structures in human multiple myeloma cells and compare the morphologies with electron micrographs of the same cell line. We also demonstrate label-free mapping at wavelengths chosen to target the chemical signatures of proteins and nucleic acids, in a way that can be used to identify biochemical markers in the study of disease and pharmacology.

Diversity at the nanoscale: laser-oxidation of single-layer graphene affects Fmoc-phenylalanine surface-mediated self-assembly

We report the effects of a laser-oxidized single layer graphene (SLG) surface on the self-assembly of amphiphilic gelator N-fluorenylmethoxycarbonyl-L-phenylalanine (Fmoc-Phe) towards an gel-SLG interface. Laser oxidation modulates the levels of hydrophobicity/hydrophilicity on the SLG surface. Atomic force, scanning electron, helium ion and scattering scanning nearfield optical microscopies (AFM, SEM, HIM, s-SNOM) were employed to assess the effects of surface properties on the secondary and tertiary organization of the formed Fmoc-Phe fibres at the SLG-gel interface. S-SNOM shows sheet-like secondary structures on both hydrophobic/hydrophilic areas of SLG and helical or disordered structures mainly on the hydrophilic oxidized surface. The gel network heterogeneity on pristine graphene was observed at the scale of single fibres by s-SNOM, demonstrating its power as a unique tool to study supramolecular assemblies and interfaces at nanoscale. Our findings underline the sensitivity of assembled structures to surface properties, while our characterization approach is a step forward in assessing surface-gel interfaces for the development of bionic devices.

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.

Unsaturation in the Fatty Acids of Phospholipids Drastically Alters the Structure and Toxicity of Insulin Aggregates Grown in Their Presence

Lipid bilayers play an important role in the pathological assembly of amyloidogenic proteins and peptides. This assembly yields oligomers and fibrils, which are highly toxic protein aggregates. In this study, we investigated the role of saturation in fatty acids of two phospholipids that are present in cell membranes. We found that unsaturated cardiolipin (CL) drastically shortened the lag phase of insulin aggregation. Furthermore, structurally and morphologically different aggregates were formed in the presence of unsaturated CL vs saturated CL. These aggregates exerted drastically different cell toxicity. Both saturated and unsaturated phosphatidylcholine (PC) were able to inhibit insulin aggregation equally efficiently. Similar to CL, structurally different aggregates were formed in the presence of saturated and unsaturated PC. These aggregates exerted different cell toxicities. These results show that unsaturated phospholipids catalyze the formation of more toxic amyloid aggregates comparing to those formed in the presence of saturated lipids.

Super-resolution mid-infrared spectro-microscopy of biological applications through tapping mode and peak force tapping mode atomic force microscope

Small biomolecules at the subcellular level are building blocks for the manifestation of complex biological activities. However, non-intrusive in situ investigation of biological systems has been long daunted by the low spatial resolution and poor sensitivity of conventional light microscopies. Traditional infrared (IR) spectro-microscopy can enable label-free visualization of chemical bonds without extrinsic labeling but is still bound by Abbe's diffraction limit. This review article introduces a way to bypass the optical diffraction limit and improve the sensitivity for mid-IR methods - using tip-enhanced light nearfield in atomic force microscopy (AFM) operated in tapping and peak force tapping modes. Working principles of well-established scattering-type scanning near-field optical microscopy (s-SNOM) and two relatively new techniques, namely, photo-induced force microscopy (PiFM) and peak force infrared (PFIR) microscopy, will be briefly presented. With ∼ 10-20 nm spatial resolution and monolayer sensitivity, their recent applications in revealing nanoscale chemical heterogeneities in a wide range of biological systems, including biomolecules, cells, tissues, and biomaterials, will be reviewed and discussed. We also envision several future improvements of AFM-based tapping and peak force tapping mode nano-IR methods that permit them to better serve as a versatile platform for uncovering biological mechanisms at the fundamental level.

Infrared nanoscopy and tomography of intracellular structures

Although techniques such as fluorescence-based super-resolution imaging or confocal microscopy simultaneously gather both morphological and chemical data, these techniques often rely on the use of localized and chemically specific markers. To eliminate this flaw, we have developed a method of examining cellular cross sections using the imaging power of scattering-type scanning near-field optical microscopy and Fourier-transform infrared spectroscopy at a spatial resolution far beyond the diffraction limit. Herewith, nanoscale surface and volumetric chemical imaging is performed using the intrinsic contrast generated by the characteristic absorption of mid-infrared radiation by the covalent bonds. We employ infrared nanoscopy to study the subcellular structures of eukaryotic (Chlamydomonas reinhardtii) and prokaryotic (Escherichia coli) species, revealing chemically distinct regions within each cell such as the microtubular structure of the flagellum. Serial 100 nm-thick cellular cross-sections were compiled into a tomogram yielding a three-dimensional infrared image of subcellular structure distribution at 20 nm resolution. The presented methodology is able to image biological samples complementing current fluorescence nanoscopy but at less interference due to the low energy of infrared radiation and the absence of labeling.

Low terahertz-band scanning near-field microscope with 155-nm resolution

We report on the design and implementation of a scattering-type scanning near-field microscope working in the low terahertz-band under ambient conditions for nanoscopic investigations of physical properties and characteristics at sample surfaces and interfaces in the microwave and millimeter wave bands. Employing a nano-tip that oscillates vertically at a frequency Ω as the antenna, and a subharmonic mixer as the receiver, and corresponding demodulation algorithms, the back-scattered light carrying tip-sample interaction information is effectively extracted, while excluding almost all of the background noises. The amplitude and phase images constructed from signals demodulated at various harmonics (nΩ, n = 1 - 4) are obtained while scanning an Au-Si step structure with the newly developed microscope, and a resolution of 155 nm (~λ/20,000) has been demonstrated at the fourth harmonic frequency (4Ω) working at 110 GHz, with signal-to-noise ratio (SNR) equal to 44.4 dB on the Au surface and 36.2 dB on the Si surface, demonstrating the power of this new instrument for micro/nano-resolution studies in the millimeter wave band.

SSNOMBACTER: A collection of scattering-type scanning near-field optical microscopy and atomic force microscopy images of bacterial cells

BACKGROUND

In recent years, a variety of imaging techniques operating at nanoscale resolution have been reported. These techniques have the potential to enrich our understanding of bacterial species relevant to human health, such as antibiotic-resistant pathogens. However, owing to the novelty of these techniques, their use is still confined to addressing very particular applications, and their availability is limited owing to associated costs and required expertise. Among these, scattering-type scanning near field optical microscopy (s-SNOM) has been demonstrated as a powerful tool for exploring important optical properties at nanoscale resolution, depending only on the size of a sharp tip. Despite its huge potential to resolve aspects that cannot be tackled otherwise, the penetration of s-SNOM into the life sciences is still proceeding at a slow pace for the aforementioned reasons.

RESULTS

In this work we introduce SSNOMBACTER, a set of s-SNOM images collected on 15 bacterial species. These come accompanied by registered Atomic Force Microscopy images, which are useful for placing nanoscale optical information in a relevant topographic context.

CONCLUSIONS

The proposed dataset aims to augment the popularity of s-SNOM and for accelerating its penetration in life sciences. Furthermore, we consider this dataset to be useful for the development and benchmarking of image analysis tools dedicated to s-SNOM imaging, which are scarce, despite the high need. In this latter context we discuss a series of image processing and analysis applications where SSNOMBACTER could be of help.

FTIR Nanospectroscopy Shows Molecular Structures of Plant Biominerals and Cell Walls

Plant tissues are complex composite structures of organic and inorganic components whose function relies on molecular heterogeneity at the nanometer scale. Scattering-type near-field optical microscopy (s-SNOM) in the mid-infrared (IR) region is used here to collect IR nanospectra from both fixed and native plant samples. We compared structures of chemically extracted silica bodies (phytoliths) to silicified and nonsilicified cell walls prepared as a flat block of epoxy-embedded awns of wheat (Triticum turgidum), thin sections of native epidermis cells from sorghum (Sorghum bicolor) comprising silica phytoliths, and isolated cells from awns of oats (Avena sterilis). The correlation of the scanning-probe IR images and the mechanical phase image enables a combined probing of mechanical material properties together with the chemical composition and structure of both the cell walls and the phytolith structures. The data reveal a structural heterogeneity of the different silica bodies in situ, as well as different compositions and crystallinities of cell wall components. In conclusion, IR nanospectroscopy is suggested as an ideal tool for studies of native plant materials of varied origins and preparations and could be applied to other inorganic-organic hybrid materials.

Electric field stimulates production of highly conductive microbial OmcZ nanowires

Multifunctional living materials are attractive due to their powerful ability to self-repair and replicate. However, most natural materials lack electronic functionality. Here we show that an electric field, applied to electricity-producing Geobacter sulfurreducens biofilms, stimulates production of previously unknown cytochrome OmcZ nanowires with 1,000-fold higher conductivity (30 S/cm), and 3-fold higher stiffness (1.5 GPa), than the cytochrome OmcS nanowires that are important in natural environments. Using chemical imaging-based multimodal nanospectroscopy, we correlate protein structure with function, and observe pH-induced conformational switching to β-sheets in individual nanowires, which increases their stiffness and conductivity by 100-fold due to enhanced π-stacking of heme groups; this was further confirmed by computational modelling and bulk spectroscopic studies. These nanowires can transduce mechanical and chemical stimuli into electrical signals to perform sensing, synthesis and energy production. These findings of biologically-produced, highly-conductive protein nanowires may help to guide the development of seamless, bidirectional interfaces between biological and electronic systems.

Dark-field hyperspectral imaging for label free detection of nano-bio-materials

Nanomaterials are playing an increasingly important role in cancer diagnosis and treatment. Nanoparticle (NP)-based technologies have been utilized for targeted drug delivery during chemotherapies, photodynamic therapy, and immunotherapy. Another active area of research is the toxicity studies of these nanomaterials to understand the cellular uptake and transport of these materials in cells, tissues, and environment. Traditional techniques such as transmission electron microscopy, and mass spectrometry to analyze NP-based cellular transport or toxicity effect are expensive, require extensive sample preparation, and are low-throughput. Dark-field hyperspectral imaging (DF-HSI), an integration of spectroscopy and microscopy/imaging, provides the ability to investigate cellular transport of these NPs and to quantify the distribution of them within bio-materials. DF-HSI also offers versatility in non-invasively monitoring microorganisms, single cell, and proteins. DF-HSI is a low-cost, label-free technique that is minimally invasive and is a viable choice for obtaining high-throughput quantitative molecular analyses. Multimodal imaging modalities such as Fourier transform infrared and Raman spectroscopy are also being integrated with HSI systems to enable chemical imaging of the samples. HSI technology is being applied in surgeries to obtain molecular information about the tissues in real-time. This article provides brief overview of fundamental principles of DF-HSI and its application for nanomaterials, protein-detection, single-cell analysis, microbiology, surgical procedures along with technical challenges and future integrative approach with other imaging and measurement modalities. This article is categorized under: Diagnostic Tools > in vitro Nanoparticle-Based Sensing Diagnostic Tools > in vivo Nanodiagnostics and Imaging Implantable Materials and Surgical Technologies > Nanoscale Tools and Techniques in Surgery.

Subsurface chemical nanoidentification by nano-FTIR spectroscopy

Nano-FTIR spectroscopy based on Fourier transform infrared near-field spectroscopy allows for label-free chemical nanocharacterization of organic and inorganic composite surfaces. The potential capability for subsurface material analysis, however, is largely unexplored terrain. Here, we demonstrate nano-FTIR spectroscopy of subsurface organic layers, revealing that nano-FTIR spectra from thin surface layers differ from that of subsurface layers of the same organic material. Further, we study the correlation of various nano-FTIR peak characteristics and establish a simple and robust method for distinguishing surface from subsurface layers without the need of theoretical modeling or simulations (provided that chemically induced spectral modifications are not present). Our experimental findings are confirmed and explained by a semi-analytical model for calculating nano-FTIR spectra of multilayered organic samples. Our results are critically important for the interpretation of nano-FTIR spectra of multilayer samples, particularly to avoid that geometry-induced spectral peak shifts are explained by chemical effects.

Nano-FTIR spectroscopy allows chemical characterization of composite surfaces, but its capability in subsurface analysis is not much explored. The authors show that spectra from thin surface layers differ from those of subsurface layers of the same organic material, and establish a method for distinguishing them in experiments.

Infrared Spectroscopy Reveals the Preferred Motif Size and Local Disorder in Parallel Stranded DNA G-Quadruplexes

Infrared spectroscopy detects the formation of G-quadruplexes in guanine-rich nucleic acid sequences through shifts in the guanine C=O stretch mode. Here, we use ultrafast 2D infrared (IR) spectroscopy and isotope substitution to show that these shifts arise from vibrational delocalization among stacked G-quartets. This provides a direct measure of the sizes of locally ordered motifs in heterogeneous samples with substantial disordered regions. We find that parallel-stranded, potassium-bound DNA G-quadruplexes are limited to five consecutive G-quartets and 3-4 consecutive layers are preferred for longer polyguanine tracts. The resulting potassium-dependent G-quadruplex assembly landscape reflects the polyguanine tract lengths found in genomes, the ionic conditions prevalent in healthy mammalian cells, and the onset of structural disorder in disease states. Our study describes spectral markers that can be used to probe other G-quadruplex structures and provides insight into the fundamental limits of their formation in biological and artificial systems.

Identifying Polymorphs of Amyloid-β (1-40) Fibrils Using High-Resolution Atomic Force Microscopy

Many amyloid-β fibril preparations are highly polymorphic, and the conditions under which they are formed determine their morphology. This report describes the application of high-resolution atomic force microscopy (HR-AFM), combined with volume-per-length analysis, to define, identify, and quantify the structural components of polymorphic Aβ fibril preparations. Volume-per-length analysis confirms that they are composed of discrete cross-β filaments, and the analysis of HR-AFM images yields the number of striations in each fibril. Compared to mass-per-length analysis by electron microscopy, HR-AFM analysis yields narrower distributions, facilitating rapid and label-free quantitative morphological characterization of Aβ fibril preparations.

Modern Scattering-Type Scanning Near-Field Optical Microscopy for Advanced Material Research

Infrared and optical spectroscopy represents one of the most informative methods in advanced materials research. As an important branch of modern optical techniques that has blossomed in the past decade, scattering-type scanning near-field optical microscopy (s-SNOM) promises deterministic characterization of optical properties over a broad spectral range at the nanoscale. It allows ultrabroadband optical (0.5-3000 µm) nanoimaging, and nanospectroscopy with fine spatial (<10 nm), spectral (<1 cm^-1 ), and temporal (<10 fs) resolution. The history of s-SNOM is briefly introduced and recent advances which broaden the horizons of this technique in novel material research are summarized. In particular, this includes the pioneering efforts to study the nanoscale electrodynamic properties of plasmonic metamaterials, strongly correlated quantum materials, and polaritonic systems at room or cryogenic temperatures. Technical details, theoretical modeling, and new experimental methods are also discussed extensively, aiming to identify clear technology trends and unsolved challenges in this exciting field of research.

Nano-spectroscopic imaging of proteins with near-field scanning optical microscopy (NSOM)

Understanding the hierarchical structure of proteins at their fundamental length scales is essential to get insights into their functions and roles in fundamental biological processes. Near-field scanning optical microscopy (NSOM), which overcomes the diffraction limits of conventional optics, provides a powerful analytical tool to image target proteins at nanoscale resolution. Especially, by combining NSOM with infrared (IR) or Raman spectroscopy, near-field nanospectroscopic imaging of a single protein is achieved. In this review, we present the recent technical progress of NSOM setup for nanospectroscopic imaging of proteins, and its application to nanospectroscopic analysis of protein structures is highlighted and critically reviewed. Finally, current challenges and perspectives on application of NSOM in emerging areas of industrial, environmental and medical biotechnology are discussed.

Potential Artifacts in Sample Preparation Methods Used for Imaging Amyloid Oligomers and Protofibrils due to Surface-Mediated Fibril Formation

Accurate imaging of nanometer-sized structures and morphologies is essential to characterizing amyloid species formed at various stages of amyloid aggregation. In this article, we examine the effect of different drying procedures on the final morphology of surface-mediated fibrils formed during the incubation period, which may then be mistaken as oligomers or protofibrils intentionally formed in solution for a particular study. Atomic force microscopy results show that some artifacts, such as globules, flakelike structures, and even micrometer-long fibrils, can be produced under various drying conditions. We also demonstrate that one can prevent drying artifacts by using an appropriate spin-coating procedure to dry amyloid samples. This procedure can bypass the wetting/dewetting transition of the liquid layer during the drying process and preserve the structure of interest on the substrate without generating drying artifacts.

Scattering-type scanning near-field optical microscopy with reconstruction of vertical interaction

Scattering-type scanning near-field optical microscopy provides access to super-resolution spectroscopic imaging of the surfaces of a variety of materials and nanostructures. In addition to chemical identification, it enables observations of nano-optical phenomena, such as mid-infrared plasmons in graphene and phonon polaritons in boron nitride. Despite the high lateral spatial resolution, scattering-type near-field optical microscopy is not able to provide characteristics of near-field responses in the vertical dimension, normal to the sample surface. Here, we present an accurate and fast reconstruction method to obtain vertical characteristics of near-field interactions. For its first application, we investigated the bound electromagnetic field component of surface phonon polaritons on the surface of boron nitride nanotubes and found that it decays within 20 nm with a considerable phase change in the near-field signal. The method is expected to provide characterization of the vertical field distribution of a wide range of nano-optical materials and structures.

Conventionally, scattering-type scanning near-field optical microscopy does not provide information on the vertical characteristic of near-field responses. Here, Xu et al. develop a method to reconstruct the vertical interaction response between the tip and the sample using this near-field technique.

Magnitude and phase-resolved infrared vibrational nanospectroscopy with a swept quantum cascade laser

We demonstrate a method of rapidly acquiring background-free infrared near-field spectra by combining magnitude and phase resolved scattering-type scanning near-field optical microscopy (s-SNOM) with a wavelength-swept quantum cascade laser (QCL). Background-free measurement of both near-field magnitude and phase allows for direct comparison with far-field absorption spectra, making the technique particularly useful for rapid and straightforward nanoscale material identification. Our experimental setup is based on the commonly used pseudo-heterodyne detection scheme, which we modify by operating the interferometer in the white light position; we show this adjustment to be critical for measurement repeatability. As a proof-of-principle experiment we measure the near-field spectrum between 1690 and 1750 cm(-1) of a PMMA disc with a spectral resolution of 1.5 cm(-1). We finish by chemically identifying two fibers on a sample surface by gathering their spectra between 1570 and 1750 cm(-1), each with a measurement time of less than 2.5 minutes. Our method offers the possibility of performing both nanoscale-resolved point spectroscopy and monochromatic imaging with a single laser that is capable of wavelength-sweeping.

Surface effects mediate self-assembly of amyloid-β peptides

Here we present a label-free method for studying the mechanism of surface effects on amyloid aggregation. In this method, spin-coating is used to rapidly dry samples, in a homogeneous manner, after various incubation times. This technique allows the control of important parameters for self-assembly, such as the surface concentration. Atomic force microscopy is then used to obtain high-resolution images of the morphology. While imaging under dry conditions, we show that the morphologies of self-assembled aggregates of a model amyloid-β peptide, Aβ(12-28), are strongly influenced by the local surface concentration. On mica surfaces, where the peptides can freely diffuse, homogeneous, self-assembled protofibrils formed spontaneously and grew longer with longer subsequent incubation. The surface fibrillization rate was much faster than the rates of fibril formation observed in solution, with initiation occurring at much lower concentrations. These data suggest an alternative pathway for amyloid formation on surfaces where the nucleation stage is either bypassed entirely or too fast to measure. This simple preparation procedure for high-resolution atomic force microscopy imaging of amyloid oligomers and protofibrils should be applicable to any amyloidogenic protein species.

Characterization of semiconductor materials using synchrotron radiation-based near-field infrared microscopy and nano-FTIR spectroscopy

We describe the application of scattering-type near-field optical microscopy to characterize various semiconducting materials using the electron storage ring Metrology Light Source (MLS) as a broadband synchrotron radiation source. For verifying high-resolution imaging and nano-FTIR spectroscopy we performed scans across nanoscale Si-based surface structures. The obtained results demonstrate that a spatial resolution below 40 nm can be achieved, despite the use of a radiation source with an extremely broad emission spectrum. This approach allows not only for the collection of optical information but also enables the acquisition of near-field spectral data in the mid-infrared range. The high sensitivity for spectroscopic material discrimination using synchrotron radiation is presented by recording near-field spectra from thin films composed of different materials used in semiconductor technology, such as SiO2, SiC, SixNy, and TiO2.

Structural analysis and mapping of individual protein complexes by infrared nanospectroscopy

Mid-infrared spectroscopy is a widely used tool for material identification and secondary structure analysis in chemistry, biology and biochemistry. However, the diffraction limit prevents nanoscale protein studies. Here we introduce mapping of protein structure with 30 nm lateral resolution and sensitivity to individual protein complexes by Fourier transform infrared nanospectroscopy (nano-FTIR). We present local broadband spectra of one virus, ferritin complexes, purple membranes and insulin aggregates, which can be interpreted in terms of their α-helical and/or β-sheet structure. Applying nano-FTIR for studying insulin fibrils—a model system widely used in neurodegenerative disease research—we find clear evidence that 3-nm-thin amyloid-like fibrils contain a large amount of α-helical structure. This reveals the surprisingly high level of protein organization in the fibril’s periphery, which might explain why fibrils associate. We envision a wide application potential of nano-FTIR, including cellular receptor in vitro mapping and analysis of proteins within quaternary structures.

Mid-infrared spectroscopy offers important chemical and structural information about biological samples but diffraction prevents nanoscale studies. Amenabar et al. demonstrate Fourier transform infrared nanospectroscopy for analysing the secondary structure of protein complexes with 30 nm spatial resolution.

Thermal-sensitive viscosity transition of elongated micelles induced by breaking intermolecular hydrogen bonding of amide groups

A heat-induced viscosity transition of novel worm-like micelles of a long alkyl-chain amidoamine derivative (C18AA) bearing intermolecular hydrogen-bonding group was investigated by cryo-TEM, FT-IR, and rheological measurements. At lower temperature, C18AA forms straight elongated micelles with a length on the order of micrometers due to strong intermolecular hydrogen-bonded packing of the amide groups, although the micelles rarely entangle and have low value of zero-shear viscosity. The straight elongated micelles likely became flexible and underwent a morphological transition from straight structure to worm-like structure at a certain temperature, which caused a drastic increase in viscosity due to entanglement of the micelles. This morphological transition was caused by a defect of intermolecular hydrogen bonding between the amide groups on heating. Furthermore, addition of LiCl, which acts as hydrogen-bond breaker, also promoted the viscosity transition, leading to a lowering of the transition temperature.

IR spectroscopic analyses of amyloid fibril formation of β2-microglobulin using a simplified procedure for its in vitro generation at neutral pH

β2-microglobulin (β2m) is known to be the major component of fibrillar deposits in the joints of patients suffering from dialysis-related amyloidosis. We have developed a simplified procedure to convert monomeric recombinant β2m into amyloid fibrils at physiological pH by a combination of stirring and heating, enabling us to follow conformational changes associated with the assembly by infrared spectroscopy and electron microscopy. Our studies reveal that fibrillogenesis begins with the formation of relatively large aggregates, with secondary structure not significantly altered by the stirring-induced association. In contrast, the conversion of the amorphous aggregates into amyloid fibrils is associated with a profound re-organization at the level of the secondary and tertiary structures, leading to non-native like parallel arrangements of the β-strands in the fully formed amyloid structure of β2m. This study highlights the power of an approach to investigate the formation of β2m fibrils by a combination of biophysical techniques including IR spectroscopy.

Quantitative Measurement of Local Infrared Absorption and Dielectric Function with Tip-Enhanced Near-Field Microscopy

Scattering-type scanning near-field optical microscopy (s-SNOM) and Fourier transform infrared nanospectroscopy (nano-FTIR) are emerging tools for nanoscale chemical material identification. Here, we push s-SNOM and nano-FTIR one important step further by enabling them to quantitatively measure local dielectric constants and infrared absorption. Our technique is based on an analytical model, which allows for a simple inversion of the near-field scattering problem. It yields the dielectric permittivity and absorption of samples with 2 orders of magnitude improved spatial resolution compared to far-field measurements and is applicable to a large class of samples including polymers and biological matter. We verify the capabilities by determining the local dielectric permittivity of a PMMA film from nano-FTIR measurements, which is in excellent agreement with far-field ellipsometric data. We further obtain local infrared absorption spectra with unprecedented accuracy in peak position and shape, which is the key to quantitative chemometrics on the nanometer scale.

Super-resolved FT-IR spectroscopy: Strategies, challenges, and opportunities for membrane biophysics

Direct correlation of molecular conformation with local structure is critical to studies of protein- and peptide-membrane interactions, particularly in the context of membrane-facilitated aggregation, and disruption or disordering. Infrared spectroscopy has long been a mainstay for determining molecular conformation, following folding dynamics, and characterizing reactions. While tremendous advances have been made in improving the spectral and temporal resolution of infrared spectroscopy, it has only been with the introduction of scanned-probe techniques that exploit the raster-scanning tip as either a source, scattering tool, or measurement probe that researchers have been able to obtain sub-diffraction limit IR spectra. This review will examine the history of correlated scanned-probe IR spectroscopies, from their inception to their use in studies of molecular aggregates, membrane domains, and cellular structures. The challenges and opportunities that these platforms present for examining dynamic phenomena will be discussed. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.

Resonant antenna probes for tip-enhanced infrared near-field microscopy

We report the development of infrared-resonant antenna probes for tip-enhanced optical microscopy. We employ focused-ion-beam machining to fabricate high-aspect ratio gold cones, which replace the standard tip of a commercial Si-based atomic force microscopy cantilever. Calculations show large field enhancements at the tip apex due to geometrical antenna resonances in the cones, which can be precisely tuned throughout a broad spectral range from visible to terahertz frequencies by adjusting the cone length. Spectroscopic analysis of these probes by electron energy loss spectroscopy, Fourier transform infrared spectroscopy, and Fourier transform infrared near-field spectroscopy corroborates their functionality as resonant antennas and verifies the broad tunability. By employing the novel probes in a scattering-type near-field microscope and imaging a single tobacco mosaic virus (TMV), we experimentally demonstrate high-performance mid-infrared nanoimaging of molecular absorption. Our probes offer excellent perspectives for optical nanoimaging and nanospectroscopy, pushing the detection and resolution limits in many applications, including nanoscale infrared mapping of organic, molecular, and biological materials, nanocomposites, or nanodevices.

Infrared spectroscopic imaging: the next generation

Infrared (IR) spectroscopic imaging seemingly matured as a technology in the mid-2000s, with commercially successful instrumentation and reports in numerous applications. Recent developments, however, have transformed our understanding of the recorded data, provided capability for new instrumentation, and greatly enhanced the ability to extract more useful information in less time. These developments are summarized here in three broad areas--data recording, interpretation of recorded data, and information extraction--and their critical review is employed to project emerging trends. Overall, the convergence of selected components from hardware, theory, algorithms, and applications is one trend. Instead of similar, general-purpose instrumentation, another trend is likely to be diverse and application-targeted designs of instrumentation driven by emerging component technologies. The recent renaissance in both fundamental science and instrumentation will likely spur investigations at the confluence of conventional spectroscopic analyses and optical physics for improved data interpretation. While chemometrics has dominated data processing, a trend will likely lie in the development of signal processing algorithms to optimally extract spectral and spatial information prior to conventional chemometric analyses. Finally, the sum of these recent advances is likely to provide unprecedented capability in measurement and scientific insight, which will present new opportunities for the applied spectroscopist.

Nano-FTIR absorption spectroscopy of molecular fingerprints at 20 nm spatial resolution

We demonstrate Fourier transform infrared nanospectroscopy (nano-FTIR) based on a scattering-type scanning near-field optical microscope (s-SNOM) equipped with a coherent-continuum infrared light source. We show that the method can straightforwardly determine the infrared absorption spectrum of organic samples with a spatial resolution of 20 nm, corresponding to a probed volume as small as 10 zeptoliter (10(-20) L). Corroborated by theory, the nano-FTIR absorption spectra correlate well with conventional FTIR absorption spectra, as experimentally demonstrated with poly(methyl methacrylate) (PMMA) samples. Nano-FTIR can thus make use of standard infrared databases of molecular vibrations to identify organic materials in ultrasmall quantities and at ultrahigh spatial resolution. As an application example we demonstrate the identification of a nanoscale PDMS contamination on a PMMA sample.

Nanoscale Fluorescence Imaging of Single Amyloid Fibrils

Amyloid formation is implicated in a variety of human diseases. It is important to perform high-resolution optical imaging of individual amyloid fibrils to delineate the structural basis of supramolecular protein assembly. However, amyloid fibrils do not lend themselves to the conventional microscopic resolution, which is hindered by the diffraction limit. Here we show super-resolution fluorescence imaging of fluorescently stained amyloid fibrils derived from disease-associated human β2-microglobulin using near-field scanning fluorescence microscopy. Using this technique, we were able to resolve the fibrils that were spatially separated by ∼75 nm. We have also been able to interrogate individual fibrils in a fibril-by-fibril manner by simultaneously monitoring both nanoscale topography and fluorescence brightness along the length of the fibrils. This method holds promise to detect conformational distributions and heterogeneity that are believed to correlate with the supramolecular packing of misfolded proteins within the fibrils in a diverse conformationally enciphered prion strains and amyloid polymorphs.

Phase in nanooptics

Quantitative phase measurements in imaging, microscopy, and nanooptics provide information not carried in amplitude measurements alone. In this issue of ACS Nano, Honigstein et al. present a new method in phase measurement. In this Perspective, we comment on this work and more broadly on the emerging role of phase and phase measurements in nanooptics.

Nucleation and growth of elastin-like peptide fibril multilayers: an in situ atomic force microscopy study

Controlling how molecules assemble into complex supramolecular architectures requires careful consideration of the subtle inter- and intra-molecular interactions that control their association. This is particularly crucial in the context of assembly at interfaces, where both surface chemistry and structure can play a role in directing structure formation. We report here the results of a study into the self-assembly of the elastin-like peptide EP I on structurally modified highly ordered pyrolytic graphite, including the role of spatial confinement on fibril nucleation and the growth of oriented fibril multilayers. In situ atomic force microscopy performed in fluid and at elevated temperature provided direct evidence of frustrated fibril nuclei and oriented growth of independent fibril domains. These results portend the application of this in situ strategy for studies of the nucleation and growth mechanisms of other fibril- and amyloid-forming proteins.

Nanoscale infrared absorption spectroscopy of individual nanoparticles enabled by scattering-type near-field microscopy

Infrared absorption spectroscopy is a powerful and widely used tool for analyzing the chemical composition and structure of materials. Because of the diffraction limit, however, it cannot be applied for studying individual nanostructures. Here we demonstrate that the phase contrast in substrate-enhanced scattering-type scanning near-field optical microscopy (s-SNOM) provides a map of the infrared absorption spectrum of individual nanoparticles with nanometer-scale spatial resolution. We succeeded in the chemical identification of silicon nitride nanoislands with heights well below 10 nm, by infrared near-field fingerprint spectroscopy of the Si-N stretching bond. Employing a novel theoretical model, we show that the near-field phase spectra of small particles correlate well with their far-field absorption spectra. On the other hand, the spectral near-field contrast does not scale with the volume of the particles. We find a nearly linear scaling law, which we can attribute to the near-field coupling between the near-field probe and the substrate. Our results provide fundamental insights into the spectral near-field contrast of nanoparticles and clearly demonstrate the capability of s-SNOM for nanoscale chemical mapping based on local infrared absorption.