Nanoscale Chemical Imaging Using Tip‐Enhanced Raman Spectroscopy: A Critical Review

Methods for chemical analysis at the nanometer scale are crucial for understanding and characterizing nanostructures of modern materials and biological systems. Tip‐enhanced Raman spectroscopy (TERS) combines the chemical information provided by Raman spectroscopy with the signal enhancement known from surface‐enhanced Raman scattering (SERS) and the high spatial resolution of atomic force microscopy (AFM) or scanning tunneling microscopy (STM). A metallic or metallized tip is illuminated by a focused laser beam and the resulting strongly enhanced electromagnetic field at the tip apex acts as a highly confined light source for Raman spectroscopic measurements. This Review focuses on the prerequisites for the efficient coupling of light to the tip as well as the shortcomings and pitfalls that have to be considered for TERS imaging, a fascinating but still challenging way to look at the nanoworld. Finally, examples from recent publications have been selected to demonstrate the potential of this technique for chemical imaging with a spatial resolution of approximately 10 nm and sensitivity down to the single‐molecule level for applications ranging from materials sciences to life sciences.     

Phosphorylation of Histone H2AX Generated by Linear Alkylbenzene Sulfonates and its Suppression by UVB Exposure

We previously demonstrated that the nonionic surfactants, nonylphenol polyethoxylates (NPEOs) induced the phosphorylation of histone H2AX (γ‐H2AX), accompanied by DNA double‐strand breaks (DSBs), and that exposure to ultraviolet (UV) degraded NPEOs, which sometimes enhanced their DNA‐damaging ability. In this study, we showed that linear alkylbenzene sulfonates (LAS), general anion surfactants, also generated DSBs with γ‐H2AX, and this ability was attenuated by UVB exposure. In the human breast adenocarcinoma cell line, MCF‐7, γ‐H2AX was generated in a dose‐dependent manner immediately after cells were treated with LAS, and this was attributed to the formation of DSBs and was independent of cell cycle phases. The ability to generate γ‐H2AX was markedly reduced in LAS exposed to UVB. HPLC analysis revealed that LAS were a mixture of various alkyl chain lengths, the peaks of which were detected at individual retention times. UVB evenly decreased all peaks of LAS, without migration of peaks to other retention times, which indicated that UVB may degrade the benzene ring of LAS, but did not shorten the alkyl chains. UVB is an important environmental factor in the degradation of LAS exhibiting the ability to induce DSBs, the most serious type of DNA damage.     

Nanoscale Chemical Imaging of Interfacial Monolayers by Tip‐Enhanced Raman Spectroscopy

We report an investigation of interfacial fluorinated hydrocarbon (carboxylic‐fantrip) monolayers by nanoscale imaging using tip‐enhanced Raman spectroscopy (TERS) and density functional theory (DFT) calculations. By comparing TERS images of a sub‐monolayer prepared by spin‐coating and a π–π‐stacked monolayer on Au(111) in which the molecular orientation is confined, specific Raman peaks shift and line widths narrow in the transferred LB monolayer. Based on DFT calculations that take into account dispersion corrections and surface selection rules, these specific effects are proposed to originate from π–π stacking and molecular orientation restriction. TERS shows the possibility to distinguish between a random and locked orientation with a spatial resolution of less than 10 nm. This work combines experimental TERS imaging with theoretical DFT calculations and opens up the possibility of studying molecular orientations and intermolecular interaction at the nanoscale and molecular level.     

Photoresponsive DNA Nanocapsule Having an Open/Close System for Capture and Release of Nanomaterials

A photofunctionalized square bipyramidal DNA nanocapsule (NC) was designed and prepared for the creation of a nanomaterial carrier. Photocontrollable open/close system and toehold system were introduced into the NC for the inclusion and release of a gold nanoparticle (AuNP) by photoirradiation and strand displacement. The reversible open and closed states were examined by gel electrophoresis and atomic force microscopy (AFM), and the open behavior was directly observed by high‐speed AFM. The encapsulation of the DNA‐modified AuNP within the NC was carried out by hybridization of a specific DNA strand (capture strand), and the release of the AuNP was examined by addition of toehold‐containing complementary DNA strand (release strand). The release of the AuNP from the NC was achieved by the opening of the NC and subsequent strand displacement.     

Fabrication of a Biocompatible Mica/Gold Surface for Tip-Enhanced Raman Spectroscopy

Tip-enhanced Raman spectroscopy (TERS) is a promising technique for structural studies of biological systems and biomolecules, owing to its ability to provide a chemical fingerprint with sub-diffraction-limit spatial resolution. This application of TERS has thus far been limited, due to difficulties in generating high field enhancements while maintaining biocompatibility. The high sensitivity achievable through TERS arises from the excitation of a localized surface plasmon resonance in a noble metal atomic force microscope (AFM) tip, which in combination with a metallic surface can produce huge enhancements in the local optical field. However, metals have poor biocompatibility, potentially introducing difficulties in characterizing native structure and conformation in biomolecules, whereas biocompatible surfaces have weak optical field enhancements. Herein, a novel, biocompatible, highly enhancing surface is designed and fabricated based on few-monolayer mica flakes, mechanically exfoliated on a metal surface. These surfaces allow the formation of coupled plasmon enhancements for TERS imaging, while maintaining the biocompatibility and atomic flatness of the mica surface for high resolution AFM. The capability of these substrates for TERS is confirmed numerically and experimentally. We demonstrate up to five orders of magnitude improvement in TERS signals over conventional mica surfaces, expanding the sensitivity of TERS to a wide range of non-resonant biomolecules with weak Raman cross-sections. The increase in sensitivity obtained through this approach also enables the collection of nanoscale spectra with short integration times, improving hyperspectral mapping for these applications. These mica/metal surfaces therefore have the potential to revolutionize spectromicroscopy of complex, heterogeneous biological systems such as DNA and protein complexes.     

Single‐Molecule Visualization of the Activity of a Zn2+‐Dependent DNAzyme

We demonstrate the single‐molecule imaging of the catalytic reaction of a Zn²⁺‐dependent DNAzyme in a DNA origami nanostructure. The single‐molecule catalytic activity of the DNAzyme was examined in the designed nanostructure, a DNA frame. The DNAzyme and a substrate strand attached to two supported dsDNA molecules were assembled in the DNA frame in two different configurations. The reaction was monitored by observing the configurational changes of the incorporated DNA strands in the DNA frame. This configurational changes were clearly observed in accordance with the progress of the reaction. The separation processes of the dsDNA molecules, as induced by the cleavage by the DNAzyme, were directly visualized by high‐speed atomic force microscopy (AFM). This nanostructure‐based AFM imaging technique is suitable for the monitoring of various chemical and biochemical catalytic reactions at the single‐molecule level.     

Distinguishing Individual DNA Bases in a Network by Non‐Resonant Tip‐Enhanced Raman Scattering

The importance of identifying DNA bases at the single‐molecule level is well recognized for many biological applications. Although such identification can be achieved by electrical measurements using special setups, it is still not possible to identify single bases in real space by optical means owing to the diffraction limit. Herein, we demonstrate the outstanding ability of scanning tunneling microscope (STM)‐controlled non‐resonant tip‐enhanced Raman scattering (TERS) to unambiguously distinguish two individual complementary DNA bases (adenine and thymine) with a spatial resolution down to 0.9 nm. The distinct Raman fingerprints identified for the two molecules allow to differentiate in real space individual DNA bases in coupled base pairs. The demonstrated ability of non‐resonant Raman scattering with super‐high spatial resolution will significantly extend the applicability of TERS, opening up new routes for single‐molecule DNA sequencing.     

Hierarchical Growth of Fluorescent Dye Aggregates in Water by Fusion of Segmented Nanostructures

Dye aggregates are becoming increasingly attractive for diverse applications, in particular as organic electronic and sensor materials. However, the growth processes of such aggregates from molecular to small assemblies up to nanostructures is still not properly understood, limiting the design of materials’ functional properties. Here we elucidate the supramolecular growth process for an outstanding class of functional dyes, perylene bisimides (PBIs), by transmission electron microscopy (TEM), cryogenic scanning electron microscopy (cryo‐SEM), and atomic force microscopy (AFM). Our studies reveal a sequential growth of amphiphilic PBI dyes from nanorods into nanoribbons in water by fusion and fission processes. More intriguingly, the fluorescence observed for higher hierarchical order nanoribbons was enhanced relative to that of nanorods. Our results provide insight into the relationship between molecular, morphological, and functional properties of self‐assembled organic materials.     

Narrow‐band UVB‐induced Externalization of Selected Nuclear Antigens in Keratinocytes: Implications for Lupus Erythematosus Pathogenesis†

The aim of this study was to analyze whether sera obtained from patients with lupus erythematosus (LE) react with membrane structures found on keratinocytes irradiated with narrow‐band ultraviolet B (NB‐UVB). We applied atomic force microscopy (AFM) to visualize cell surface structures expressing nuclear antigens upon apoptosis following NB‐UVB irradiation. Immortalized human keratinocytes (HaCaT) were cultured under standard conditions, irradiated with 800 mJ cm^?2 NB‐UVB light and imaged by AFM mounted on an inverted optical microscope. It was observed that NB‐UVB irradiation provoked significant alterations of the keratinocyte morphology and led to the membrane expression of antigens recognized by anti‐La and anti‐Ro 60 kDa sera but not by antidouble‐strand DNA sera. The presence of La and Ro 60 kDa antigens on keratinocyte surfaces after NB‐UVB irradiation was limited mainly to the small bleb‐like protrusions found on the keratinocytes by AFM. A closer investigation by AFM also revealed that some structures positively stained with anti‐Ro 60 kDa serum were also located submembranously. We hypothesize that the externalization of some nuclear antigens because of NB‐UVB exposure might be responsible for exacerbation of skin symptoms in patients suffering from LE.     

Induction of persistent double strand breaks following multiphoton irradiation of cycling and G1-arrested mammalian cells-replication-induced double strand breaks

DNA double strand breaks (DSBs) are amongst the most deleterious lesions induced within the cell following exposure to ionizing radiation. Mammalian cells repair these breaks predominantly via the nonhomologous end joining pathway which is active throughout the cell cycle and is error prone. The alternative pathway for repair of DSBs is homologous recombination (HR) which is error free and active during S- and G2/M-phases of the cell cycle. We have utilized near-infrared laser radiation to induce DNA damage in individual mammalian cells through multiphoton excitation processes to investigate the dynamics of single cell DNA damage processing. We have used immunofluorescent imaging of gamma-H2AX (a marker for DSBs) in mammalian cells and investigated the colocalization of this protein with ATM, p53 binding protein 1 and RAD51, an integral protein of the HR DNA repair pathway. We have observed persistent DSBs at later times postlaser irradiation which are indicative of DSBs arising at replication, presumably from UV photoproducts or clustered damage containing single strand breaks. Cell cycle studies have shown that in G1 cells, a significant fraction of multiphoton laser-induced prompt DSBs persists for > 4 h in addition to those induced at replication.     

Probing Adsorption Configurations of Small Molecules on Surfaces by Single-Molecule Tip-Enhanced Raman Spectroscopy

Determining the adsorption configurations of organic molecules on surfaces, especially for relatively small molecules, is a key issue for understanding the microscopic physical and chemical processes in surface science. In this work, we have applied low-temperature ultrahigh-vacuum tip-enhanced Raman scattering (TERS) technique to distinguish the configurations of small 4,4′-bipyridine (44BPY) molecules adsorbed on the Ag(111) surface. The observed Raman spectra exhibit notable differences in the spectral features which can be assigned to three different molecular orientations, each featuring a specific fingerprint pattern based on the TERS selection rule that determines the distribution of the relative intensities of different vibrational peaks. Furthermore, such a small molecule can in turn act as a local probe to provide information on the local electric field distribution at the tip apex. Our work showcases the capability of TERS technique for obtaining information on adsorption configurations of small molecules on surfaces down to the single-molecule level, which is of fundamental importance for many applications in the fields of molecular science and surface chemistry.     

TERS Detection of αVβ3 Integrins in Intact Cell Membranes

Integrins are important membrane receptors that form focal adhesions with the extracellular matrix and are transmembrane signaling proteins. We demonstrate that nanoparticles functionalized with c‐RGDfC ligands bind to intact cell membranes and selectively enhance the amino acid signals of the integrin receptor when coupled with tip‐enhanced Raman scattering (TERS) detection. Controlling the plasmonic interaction between the functionalized nanoparticle and the TERS tip provides a clear Raman signal from α_Vβ₃ integrins in the cell membrane that matches the signal of the purified integrin receptor. Random aggregation of nanoparticles on the cell does not provide the same spectral information. Chemical characterization of membrane receptors in intact cellular membranes is important for understanding membrane signaling and drug targeting. These results provide a new method to investigate the chemical interactions associated with ligand binding to membrane receptors in cells.     

Impact of Single Basepair Mismatches on Electron‐Transfer Processes at Fc‐PNA⋅DNA Modified Gold Surfaces

Gold‐surface grafted peptide nucleic acid (PNA) strands, which carry a redox‐active ferrocene tag, present unique tools to electrochemically investigate their mechanical bending elasticity based on the kinetics of electron‐transfer (ET) processes. A comparative study of the mechanical bending properties and the thermodynamic stability of a series of 12‐mer Fc‐PNA?DNA duplexes was carried out. A single basepair mismatch was integrated at all possible strand positions to provide nanoscopic insights into the physicochemical changes provoked by the presence of a single basepair mismatch with regard to its position within the strand. The ET processes at single mismatch Fc‐PNA?DNA modified surfaces were found to proceed with increasing diffusion limitation and decreasing standard ET rate constants k⁰ when the single basepair mismatch was dislocated along the strand towards its free‐dangling Fc‐modified end. The observed ET characteristics are considered to be due to a punctual increase in the strand elasticity at the mismatch position. The kinetic mismatch discrimination with respect to the fully‐complementary duplex presents a basis for an electrochemical DNA sensing strategy based on the Fc‐PNA?DNA bending dynamics for loosely packed monolayers. In a general sense, the strand elasticity presents a further physicochemical property which is affected by a single basepair mismatch which may possibly be used as a basis for future DNA sensing concepts for the specific detection of single basepair mismatches.     

Make them Blink: Probes for Super‐Resolution Microscopy

In recent years, a number of approaches have emerged that enable far‐field fluorescence imaging beyond the diffraction limit of light, namely super‐resolution microscopy. These techniques are beginning to profoundly alter our abilities to look at biological structures and dynamics and are bound to spread into conventional biological laboratories. Nowadays these approaches can be divided into two categories, one based on targeted switching and readout, and the other based on stochastic switching and readout of the fluorescence information. The main prerequisite for a successful implementation of both categories is the ability to prepare the fluorescent emitters in two distinct states, a bright and a dark state. Herein, we provide an overview of recent developments in super‐resolution microscopy techniques and outline the special requirements for the fluorescent probes used. In combination with the advances in understanding the photophysics and photochemistry of single fluorophores, we demonstrate how essentially any single‐molecule compatible fluorophore can be used for super‐resolution microscopy. We present examples for super‐resolution microscopy with standard organic fluorophores, discuss factors that influence resolution and present approaches for calibration samples for super‐resolution microscopes including AFM‐based single‐molecule assembly and DNA origami.     

Site‐Directed Spin‐Labeling of DNA by the Azide–Alkyne ‘Click’ Reaction: Nanometer Distance Measurements on 7‐Deaza‐2′‐deoxyadenosine and 2′‐Deoxyuridine Nitroxide Conjugates Spatially Separated or Linked to a ‘dA‐dT’ Base Pair

Nucleobase‐directed spin‐labeling by the azide‐alkyne ‘click’ (CuAAC) reaction has been performed for the first time with oligonucleotides. 7‐Deaza‐7‐ethynyl‐2′‐deoxyadenosine ( 1 ) and 5‐ethynyl‐2′‐deoxyuridine ( 2 ) were chosen to incorporate terminal triple bonds into DNA. Oligonucleotides containing 1 or 2 were synthesized on a solid phase and spin labeling with 4‐azido‐2,2,6,6‐tetramethylpiperidine 1‐oxyl (4‐azido‐TEMPO, 3 ) was performed by post‐modification in solution. Two spin labels ( 3 ) were incorporated with high efficiency into the DNA duplex at spatially separated positions or into a ‘dA‐dT’ base pair. Modification at the 5‐position of the pyrimidine base or at the 7‐position of the 7‐deazapurine residue gave steric freedom to the spin label in the major groove of duplex DNA. By applying cw and pulse EPR spectroscopy, very accurate distances between spin labels, within the range of 1–2 nm, were measured. The spin–spin distance was 1.8±0.2 nm for DNA duplex 17 ( dA*^7,10 ) ?11 containing two spin labels that are separated by two nucleotides within one individual strand. A distance of 1.4±0.2 nm was found for the spin‐labeled ‘dA‐dT’ base pair 15 ( dA*⁷ ) ?16 ( dT*⁶ ). The ‘click’ approach has the potential to be applied to all four constituents of DNA, which indicates the universal applicability of the method. New insights into the structural changes of canonical or modified DNA are expected to provide additional information on novel DNA structures, protein interaction, DNA architecture, and synthetic biology.     

Enzymatic Synthesis of a DNA Triblock Copolymer that is Composed of Natural and Unnatural Nucleotides

DNA molecules have come under the spotlight as potential templates for the fabrication of nanoscale products, such as molecular‐scale electronic or photonic devices. Herein, we report an enhanced approach for the synthesis of oligoblock copolymer‐type DNA by using the Klenow fragment exonuclease minus of E. coli DNA polymerase I (KF^?) in a multi‐step reaction with natural and unnatural nucleotides. First, we confirmed the applicability of unnatural nucleotides with 7‐deaza‐nucleosides—which was expected because they were non‐metalized nucleotides—on the unique polymerization process known as the “strand‐slippage model”. Because the length of the DNA sequence could be controlled by tuning the reaction time, analogous to a living polymerization reaction on this process, stepwise polymerization provided DNA block copolymers with natural and unnatural bases. AFM images showed that this DNA block copolymer could be metalized sequence‐selectively. This approach could expand the utility of DNA as a template.     

Low-energy electron-induced single strand breaks in 2'-deoxycytidine-3'-monophosphate using the local complex potential based time-dependent wave packet approach

Recent experimental and theoretical investigations on resonant electron scattering off DNA and DNA fragments using low-energy electrons (LEEs), to propose the mechanism for single strand breaks (SSBs) and double strand breaks (DSBs), have received considerable attention. It is our purpose here to understand theoretically the comprehensive route to SSB in a selected DNA fragment, namely, 2'-deoxycytidine-3'-monophosphate (3'-dCMPH), induced by LEE (0-3 eV) scattering using the local complex potential based time-dependent wave packet (LCP-TDWP) approach. To the best of our knowledge, there is no time-dependent quantum mechanical study that has been reported in the literature for this DNA fragment to date. Initial results obtained from our calculation in the gas phase provide a good agreement with experimental observation and show the plausibility of SSB at 0.75 eV, which is very close to the highest SSB yield reported from the experimental measurement (0.8 eV) on plasmid DNA in the condensed phase.     

Covalently linked DNA/protein multilayered film for controlled DNA release

A stable, biocompatible single strand DNA (ssDNA)/bovine serum albumin (BSA) multilayered film for control release of DNA was fabricated on PEI-coated quartz slides, gold-evaporated plates and silicon wafers, respectively through a formaldehyde-induced, covalently linked layer-by-layer (LBL) assembly technique. The constructed film structure was well characterized by using UV-vis spectrometry, surface plasmon resonance (SPR) and atomic force microscopy (AFM). The results showed that the DNA incorporated LBL film was fabricated successfully and the amount of ssDNA and BSA in the film could be tailored simply by controlling the number of the bilayers. The control release of DNA from the film was also monitored in this study. UV-vis spectrometry, SPR and AFM measurements indicated that the release of ssDNA and amino acid was adjustable by changing the proteinase K incubation time. This biocompatible covalently assembled film demonstrates an innovative approach to engineer a DNA/protein based nanostructure for controlled DNA release, which could provide stability, controllability and flexibility superior to that of LBL film assembled by electrostatic attraction. Since the film in this work can be assembled on different substrates, it is very feasible to fabricate nanoparticle-based gene therapy systems with this new approach and to have great potential in biomedical applications.     

Quantitative Assessment of Tip Effects in Single‐Molecule High‐Speed Atomic Force Microscopy Using DNA Origami Substrates

High‐speed atomic force microscopy (HS‐AFM) is widely employed in the investigation of dynamic biomolecular processes at a single‐molecule level. However, it remains an open and somewhat controversial question, how these processes are affected by the rapidly scanned AFM tip. While tip effects are commonly believed to be of minor importance in strongly binding systems, weaker interactions may significantly be disturbed. Herein, we quantitatively assess the role of tip effects in a strongly binding system using a DNA origami‐based single‐molecule assay. Despite its femtomolar dissociation constant, we find that HS‐AFM imaging can disrupt monodentate binding of streptavidin (SAv) to biotin (Bt) even under gentle scanning conditions. To a lesser extent, this is also observed for the much stronger bidentate SAv–Bt complex. The presented DNA origami‐based assay can be universally employed to quantify tip effects in strongly and weakly binding systems and to optimize the experimental settings for their reliable HS‐AFM imaging.