Invited review article: combining scanning probe microscopy with optical spectroscopy for applications in biology and materials science

Conformational Changes in Surface-Immobilized Proteins Measured Using Combined Atomic Force and Fluorescence Microscopy

Biological organisms rely on proteins to perform the majority of their functions. Most protein functions are based on their physical motions (conformational changes), which can be described as transitions between different conformational states in a multidimensional free-energy landscape. A comprehensive understanding of this free-energy landscape is therefore of paramount importance for understanding the biological functions of proteins. Protein dynamics includes both equilibrium and nonequilibrium motions, which typically exhibit a wide range of characteristic length and time scales. The relative probabilities of various conformational states in the energy landscape, the energy barriers between them, their dependence on external parameters such as force and temperature, and their connection to the protein function remain largely unknown for most proteins. In this paper, we present a multimolecule approach in which the proteins are immobilized at well-defined locations on Au substrates using an atomic force microscope (AFM)-based patterning method called nanografting. This method enables precise control over the protein location and orientation on the substrate, as well as the creation of biologically active protein ensembles that self-assemble into well-defined nanoscale regions (protein patches) on the gold substrate. We performed AFM-force compression and fluorescence experiments on these protein patches and measured the fundamental dynamical parameters such as protein stiffness, elastic modulus, and transition energies between distinct conformational states. Our results provide new insights into the processes that govern protein dynamics and its connection to protein function.

Polarized tip-enhanced Raman spectroscopy at liquid He temperature in ultrahigh vacuum using an off-axis parabolic mirror

Tip-enhanced Raman spectroscopy (TERS) combines inelastic light scattering well below the diffraction limit down to the nanometer range and scanning probe microscopy and, possibly, spectroscopy. In this way, topographic and spectroscopic as well as single- and two-particle information may simultaneously be collected. While single molecules can now be studied successfully, bulk solids are still not meaningfully accessible. It is the purpose of the work presented here to outline approaches toward this objective. We describe a home-built, liquid helium cooled, ultrahigh vacuum TERS. The setup is based on a scanning tunneling microscope and, as an innovation, an off-axis parabolic mirror having a high numerical aperture of ∼0.85 and a large working distance. The system is equipped with a fast load-lock chamber, a chamber for the in situ preparation of tips, substrates, and samples, and a TERS chamber. Base pressure and temperature in the TERS chamber were ∼3 × 10-11 mbar and 15 K, respectively. Polarization dependent tip-enhanced Raman spectra of the vibration modes of carbon nanotubes were successfully acquired at cryogenic temperature. The new features described here including very low pressure and temperature and the external access to the light polarizations, thus the selection rules, may pave the way toward the investigation of bulk and surface materials.

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.

Detection techniques of biological and chemical Hall sensors

Integrated magnetic Hall effect sensors have been widely used in people's daily life over the past decades, and still are gaining enormous attention from researchers to establish novel applications, especially in biochemistry and biomedical healthcare. This paper reviews, classifies, compares and concludes state-of-the-art integrated Hall magnetic sensors in terms of cost, power, area, performance and application. Current applications of the Hall sensors such as detecting magnetic nanoparticles (MNPs) labeled on biomolecule, monitoring blood pulse wave velocity, characterizing soft biological materials, controlling syringe injection rate and eye surgery by training systems, and assisting magnetic resonance imaging (MRI) will be discussed comprehensively and future applications and trends will be highlighted. This review paper will introduce Hall sensor's advantages such as simple design and technology of manufacturing, low cost, low power consumption, possibility of the miniaturizing, noninvasive and room temperature measurement, with respect to the other magnetic sensing systems and methods.

Facilitating Hotspot Alignment in Tip-Enhanced Raman Spectroscopy via the Silver Photoluminescence of the Probe

A tip-enhanced Raman spectroscopy (TERS) system based on an atomic force microscope (AFM) and radially polarized laser beam was developed. A TERS probe with plasmon resonance wavelength matching the excitation wavelength was prepared with the help of dark-field micrographs. The intrinsic photoluminescence (PL) from the silver (Ag)-coated TERS probe induced by localized surface plasmon resonance contains information about the near-field enhanced electromagnetic field intensity of the probe. Therefore, we used the intensity change of Ag PL to evaluate the stability of the Ag-coated probe during TERS experiments. Tracking the Ag PL of the TERS probe was helpful to detect probe damage and hotspot alignment. Our setup was successfully used for the TERS imaging of single-walled carbon nanotubes, which demonstrated that the Ag PL of the TERS probe is a good criterion to assist in the hotspot alignment procedure required for TERS experiments. This method lowers the risk of contamination and damage of the precious TERS probe, making it worthwhile for wide adoption in TERS experiments.

A low-temperature scanning probe microscopy system with molecular beam epitaxy and optical access

A low-temperature ultra-high vacuum scanning probe microscopy (SPM) system with molecular beam epitaxy (MBE) capability and optical access was conceived, built, and tested in our lab. The design of the whole system is discussed here, with special emphasis on some critical parts. The SPM scanner head takes a modified Pan-type design with improved rigidity and compatible configuration to optical access and can accommodate both scanning tunneling microscope (STM) tips and tuning-fork based qPlus sensors. In the system, the scanner head is enclosed by a double-layer cold room under a bath type cryostat. Two piezo-actuated focus-lens stages are mounted on both sides of the cold room to couple light in and out. The optical design ensures the system's forward compatibility to the development of photo-assisted STM techniques. To test the system's performance, we conducted STM and spectroscopy studies. The herringbone reconstruction and atomic structure of an Au(111) surface were clearly resolved. The dI/dV spectra of an Au(111) surface were obtained at 5 K. In addition, a periodic 2D tellurium (Te) structure was grown on the Au(111) surface using MBE and the atomic structure is clearly resolved by using STM.

Tip in-light on: Advantages, challenges, and applications of combining AFM and Raman microscopy on biological samples

Scanning probe microscopies and spectroscopies, especially AFM and Confocal Raman microscopy are powerful tools to characterize biological materials. They are both non-destructive methods and reveal mechanical and chemical properties on the micro and nano-scale. In the last years the interest for increasing the lateral resolution of optical and spectral images has driven the development of new technologies that overcome the diffraction limit of light. The combination of AFM and Raman reaches resolutions of about 50-150 nm in near-field Raman and 1.7-50 nm in tip enhanced Raman spectroscopy (TERS) and both give a molecular information of the sample and the topography of the scanned surface. In this review, the mentioned approaches are introduced, the main advantages and problems for application on biological samples discussed and some examples for successful experiments given. Finally the potential of colocated AFM and Raman measurements is shown on a case study of cellulose-lignin films: the topography structures revealed by AFM can be related to a certain chemistry by the colocated Raman scan and additionally the mechanical properties be revealed by using the digital pulsed force mode. Microsc. Res. Tech. 80:30-40, 2017. © 2016 Wiley Periodicals, Inc.

A Microsystem for Magnetic Immunoassay Based on Planar Microcoil Array

This work focuses on the circuit and system implementation of a microsystem platform for magnetic immunoassay, which is a novel type of diagnostic method using magnetic beads as labels. Three main challenges facing this work-design of a high performance sensor, packaging technique and design of integrated circuits are discussed. Planar microcoil array are exploited as sensor of magnetic beads, whereas ultra thin bottom microplate in traditional ELISA is used for the assay. Main circuits blocks include bidirectional current supply circuit, magnetic field sensing circuit and on-chip temperature sensor. Experiments using mouse IgG with different densities were performed on the proposed platform, results show that a minimum density of 100 pg/mL can be detected, which is a comparable sensitivity to conventional optical ELISA, and a quantitative relationship can be acquired in the range from 1 ng/ml to 1 ug/ml, thus this platform is suitable for quantitative analysis in practical health and environment application and has potential for medical diagnostics, food pathogen detection or water analysis.

A new tribological experimental setup to study confined and sheared monolayers

We have developed an original experimental setup, coupling tribology, and velocimetry experiments together with a direct visualization of the contact. The significant interest of the setup is to measure simultaneously the apparent friction coefficient and the velocity of confined layers down to molecular scale. The major challenge of this experimental coupling is to catch information on a nanometer-thick sheared zone confined between a rigid spherical indenter of millimetric radius sliding on a flat surface at constant speed. In order to demonstrate the accuracy of this setup to investigate nanometer-scale sliding layers, we studied a model lipid monolayer deposited on glass slides. It shows that our experimental setup will, therefore, help to highlight the hydrodynamic of such sheared confined layers in lubrication, biolubrication, or friction on solid polymer.

A Smart CMOS Assay SoC for Rapid Blood Screening Test of Risk Prediction

A micro-controller unit (MCU) assisted immunoassay lab-on-a-chip is realized in 0.35 μm CMOS technology. The MCU automatically controls the detection procedure including blood filtration through a nonporous aluminum oxide membrane, bimolecular conjugation with antibodies attached to magnetic beads, electrolytic pumping, magnetic flushing and threshold detection based on Hall sensor array readout analysis. To verify the function of this chip, in-vitro Tumor necrosis factor- α (TNF-α) and N-terminal pro-brain natriuretic peptide (NT-proBNP) tests are performed by this 9 mm(2)-sized single chip. The cost, efficiency and portability are considerably improved compared to the prior art.

Opto-nanomechanical spectroscopic material characterization

The non-destructive, simultaneous chemical and physical characterization of materials at the nanoscale is an essential and highly sought-after capability. However, a combination of limitations imposed by Abbe diffraction, diffuse scattering, unknown subsurface, electromagnetic fluctuations and Brownian noise, for example, have made achieving this goal challenging. Here, we report a hybrid approach for nanoscale material characterization based on generalized nanomechanical force microscopy in conjunction with infrared photoacoustic spectroscopy. As an application, we tackle the outstanding problem of spatially and spectrally resolving plant cell walls. Nanoscale characterization of plant cell walls and the effect of complex phenotype treatments on biomass are challenging but necessary in the search for sustainable and renewable bioenergy. We present results that reveal both the morphological and compositional substructures of the cell walls. The measured biomolecular traits are in agreement with the lower-resolution chemical maps obtained with infrared and confocal Raman micro-spectroscopies of the same samples. These results should prove relevant in other fields such as cancer research, nanotoxicity, and energy storage and production, where morphological, chemical and subsurface studies of nanocomposites, nanoparticle uptake by cells and nanoscale quality control are in demand.

Novel imaging technologies for characterization of microbial extracellular polysaccharides

Understanding of biology is underpinned by the ability to observe structures at various length scales. This is so in a historical context and is also valid today. Evolution of novel insight often emerges from technological advancement. Recent developments in imaging technologies that is relevant for characterization of extraceullar microbiological polysaccharides are summarized. Emphasis is on scanning probe and optical based techniques since these tools offers imaging capabilities under aqueous conditions more closely resembling the physiological state than other ultramicroscopy imaging techniques. Following the demonstration of the scanning probe microscopy principle, novel operation modes to increase data capture speed toward video rate, exploitation of several cantilever frequencies, and advancement of utilization of specimen mechanical properties as contrast, also including their mode of operation in liquid, have been developed on this platform. Combined with steps in advancing light microscopy with resolution beyond the far field diffraction limit, non-linear methods, and combinations of the various imaging modalities, the potential ultramicroscopy toolbox available for characterization of exopolysaccharides (EPS) are richer than ever. Examples of application of such ultramicroscopy strategies range from imaging of isolated microbial polysaccharides, structures being observed when they are involved in polyelectrolyte complexes, aspects of their enzymatic degradation, and cell surface localization of secreted polysaccharides. These, and other examples, illustrate that the advancement in imaging technologies relevant for EPS characterization supports characterization of structural aspects.

Metal-carbonyl units for vibrational and luminescence imaging: towards multimodality

Metal-carbonyl complexes are attractive structures for bio-imaging. In addition to unique vibrational properties due to the CO moieties enabling IR and Raman cell imaging, the appropriate choice of ancillary ligands opens up the opportunity for luminescence detection. Through a classification by techniques, past and recent developments in the application of metal-carbonyl complexes for vibrational and luminescence bio-imaging are reviewed. Finally, their potential as bimodal IR and luminescent probes is addressed.

Evanescent-field-induced Raman scattering for bio-friendly fingerprinting at sub-cellular dimension

Evanescent field induced chemical imaging concept has been realized in analytical platform based on the µ-tip-enhanced Raman scattering spectroscopy (µ-TERS). The technique aimed to minimize thermal decomposition of dried biological sample as the result of huge concentration of optical field near the tip by increasing the size of an aperture-less "excitation source". µ-TERS technique is similar to classical biosensor systems based on propagating surface plasmon resonance phenomenon but with sensitive elements a few micrometers in size that can be targeted to the area of interest. The utility of the concept is exemplified by the analysis of dried single cell envelope of genetically modified Saccharomyces cerevisiae yeast cells, which do not have any heat-removing pathways, by water as in the case of the living cell. Practical excitation conditions effective for µ-TERS Raman observation of single layer dried biological samples without photodamage-related spectral distortion have been determined - the allowable limit is above 30s at 13 µW/µm(2). Finally, potential of µ-TERS spectroscopy as new bio-friendly instrumental platform for chemical fingerprinting and analytical characterization of buried nanoscale features is discussed.

Techniques for physicochemical characterization of nanomaterials

Advances in nanotechnology have opened up a new era of diagnosis, prevention and treatment of diseases and traumatic injuries. Nanomaterials, including those with potential for clinical applications, possess novel physicochemical properties that have an impact on their physiological interactions, from the molecular level to the systemic level. There is a lack of standardized methodologies or regulatory protocols for detection or characterization of nanomaterials. This review summarizes the techniques that are commonly used to study the size, shape, surface properties, composition, purity and stability of nanomaterials, along with their advantages and disadvantages. At present there are no FDA guidelines that have been developed specifically for nanomaterial based formulations for diagnostic or therapeutic use. There is an urgent need for standardized protocols and procedures for the characterization of nanoparticles, especially those that are intended for use as theranostics.

Tip-enhanced near-field optical microscopy

Tip-enhanced near-field optical microscopy (TENOM) is a scanning probe technique capable of providing a broad range of spectroscopic information on single objects and structured surfaces at nanometer spatial resolution and with highest detection sensitivity. In this review, we first illustrate the physical principle of TENOM that utilizes the antenna function of a sharp probe to efficiently couple light to excitations on nanometer length scales. We then discuss the antenna-induced enhancement of different optical sample responses including Raman scattering, fluorescence, generation of photocurrent and electroluminescence. Different experimental realizations are presented and several recent examples that demonstrate the capabilities of the technique are reviewed.

The hydrophobic force: measurements and methods

The hydrophobic force describes the attraction between water-hating molecules (and surfaces) that draws them together, causing aggregation, phase separation, protein folding and many other inherent physical phenomena.

Atomic force microscope controlled topographical imaging and proximal probe thermal desorption/ionization mass spectrometry imaging

This paper reports on the development of a hybrid atmospheric pressure atomic force microscopy/mass spectrometry imaging system utilizing nanothermal analysis probes for thermal desorption surface sampling with subsequent atmospheric pressure chemical ionization and mass analysis. The basic instrumental setup and the general operation of the system were discussed, and optimized performance metrics were presented. The ability to correlate topographic images of a surface with atomic force microscopy and a mass spectral chemical image of the same surface, utilizing the same probe without moving the sample from the system, was demonstrated. Co-registered mass spectral chemical images and atomic force microscopy topographical images were obtained from inked patterns on paper as well as from a living bacterial colony on an agar gel. Spatial resolution of the topography images based on pixel size (0.2 μm × 0.8 μm) was better than the resolution of the mass spectral images (2.5 μm × 2.0 μm), which were limited by current mass spectral data acquisition rate and system detection levels.

Tip-enhanced Raman imaging: an emergent tool for probing biology at the nanoscale

Typically limited by the diffraction of light, most optical spectroscopy methods cannot provide the spatial resolution necessary to characterize specimens at the nanoscale. An emerging exception to this rule is tip-enhanced Raman spectroscopy (TERS), which overcomes the diffraction limit through electromagnetic field localization at the end of a sharp metallic tip. As demonstrated by the Zenobi group in this issue of ACS Nano, TER imaging is an analytical technique capable of providing high-resolution chemical maps of biological samples. In this Perspective, we highlight recent advances and future applications of TER imaging as a technique for interrogating biology at the nanoscale.

Scanning near-field optical coherent anti-Stokes Raman microscopy (SNOM-CARS) with femtosecond laser pulses in vibrational and electronic resonance

Accessing ultrafast photoinduced molecular dynamics on a femtosecond time-scale with vibrational selectivity and at the same time sub-diffraction limited spatial resolution would help to gain important information about ultrafast processes in nanostructures. While nonlinear Raman techniques have been used to obtain highly resolved images in combination with near-field microscopy, the use of femtosecond laser pulses in electronic resonance still constitutes a big challenge. Here, we present our first results on coherent anti-Stokes Raman scattering (fs-CARS) with femtosecond laser pulses detected in the near-field using scanning near-field optical microscopy (SNOM). We demonstrate that highly spatially resolved images can be obtained from poly(3-hexylthiophene) (P3HT) nano-structures where the fs-CARS process was in resonance with the P3HT absorption and with characteristic P3HT vibrational modes without destruction of the samples. Sub-diffraction limited lateral resolution is achieved. Especially the height resolution clearly surpasses that obtained with standard microCARS. These results will be the basis for future investigations of mode-selective dynamics in the near field.

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.

Reflection-mode, confocal, tip-enhanced Raman spectroscopy system for scanning chemical microscopy of surfaces

A reflection-mode, confocal, tip-enhanced Raman spectroscopy system for nanoscale chemical imaging of surfaces is presented. The instrument is based on a beam-bounce atomic force microscope with a side-on Raman microscope with true confocal light illumination and collection. Localized vibrational (Raman) spectroscopy is demonstrated at length scales down to 20 nm on opaque samples. The design and validation of the instrument are discussed with quantitative emphasis on confocal microscope operation, plasmonic properties of the tip, point spectroscopy, and Raman imaging of SiGe nanowires.