Advances in Optical Single‐Molecule Detection: En Route to Supersensitive Bioaffinity Assays

The ability to detect low concentrations of analytes and in particular low‐abundance biomarkers is of fundamental importance, e.g., for early‐stage disease diagnosis. The prospect of reaching the ultimate limit of detection has driven the development of single‐molecule bioaffinity assays. While many review articles have highlighted the potentials of single‐molecule technologies for analytical and diagnostic applications, these technologies are not as widespread in real‐world applications as one should expect. This Review provides a theoretical background on single‐molecule—or better digital—assays to critically assess their potential compared to traditional analog assays. Selected examples from the literature include bioaffinity assays for the detection of biomolecules such as proteins, nucleic acids, and viruses. The structure of the Review highlights the versatility of optical single‐molecule labeling techniques, including enzymatic amplification, molecular labels, and innovative nanomaterials.     

Nanopore‐Based Confined Spaces for Single‐Molecular Analysis

The field of nanopore sensing at the single‐molecular level is in a “boom” period. Such nanopores, which are either composed of biological materials or are fabricated from solid‐state substrates, offer a unique confined space that is compatible with the single‐molecular scale. Under the influence of an electrical field, such single‐biomolecular interfaces can read single‐molecular information and, if appropriately fine‐tuned, each molecule plays its individual ionic rhythm to compose a “molecular symphony”. Over the past few decades, many research groups have worked on nanopore‐based single‐molecular sensors for a range of thrilling chemical and clinical applications. Furthermore, for the past decade, we have also focused on nanopore‐based sensors. In this Minireview, we summarize the recent developments in fundamental research and applications in this area, along with data algorithms and advances in hardware, which act as infrastructure for the electrochemical analysis.     

Covalent Assembly and Characterization of Nonsymmetrical Single‐Molecule Nodes

The covalent linking of molecular building blocks on surfaces enables the construction of specific molecular nanostructures of well‐defined shape. Molecular nodes linked to various entities play a key role in such networks, but represent a particular challenge because they require a well‐defined arrangement of different building blocks. Herein, we describe the construction of a chemically and geometrically well defined covalent architecture made of one central node and three molecular wires arranged in a nonsymmetrical way and thus encoding different conjugation pathways. Very different architectures of either very limited or rather extended size were obtained depending on the building blocks used for the covalent linking process on the Au(111) surface. Electrical measurements were carried out by pulling individual molecular nodes with the tip of a scanning tunneling microscope. The results of this challenging procedure indicate subtle differences if the nodes are contacted at inequivalent termini.     

Direct Measurement of Single‐Molecule DNA Hybridization Dynamics with Single‐Base Resolution

Herein, we report label‐free detection of single‐molecule DNA hybridization dynamics with single‐base resolution. By using an electronic circuit based on point‐decorated silicon nanowires as electrical probes, we directly record the folding/unfolding process of individual hairpin DNAs with sufficiently high signal‐to‐noise ratio and bandwidth. These measurements reveal two‐level current oscillations with strong temperature dependence, enabling us to determine the thermodynamic and kinetic properties of hairpin DNA hybridization. More importantly, successive, stepwise increases and decreases in device conductance at low temperature on a microsecond timescale are successfully observed, indicating a base‐by‐base unfolding/folding process. The process demonstrates a kinetic zipper model for DNA hybridization/dehybridization at the single base‐pair level. This measurement capability promises a label‐free single‐molecule approach to probe biomolecular interactions with fast dynamics.     

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.     

Addressing the Requirements of High‐Sensitivity Single‐Molecule Imaging of Low‐Copy‐Number Proteins in Bacteria

Single‐molecule fluorescence super‐resolution imaging and tracking provide nanometer‐scale information about subcellular protein positions and dynamics. These single‐molecule imaging experiments can be very powerful, but they are best suited to high‐copy number proteins where many measurements can be made sequentially in each cell. We describe artifacts associated with the challenge of imaging a protein expressed in only a few copies per cell. We image live Bacillus subtilis in a fluorescence microscope, and demonstrate that under standard single‐molecule imaging conditions, unlabeled B. subtilis cells display punctate red fluorescent spots indistinguishable from the few PAmCherry fluorescent protein single molecules under investigation. All Bacillus species investigated were strongly affected by this artifact, whereas we did not find a significant number of these background sources in two other species we investigated, Enterococcus faecalis and Escherichia coli. With single‐molecule resolution, we characterize the number, spatial distribution, and intensities of these impurity spots.     

A General Mechanism of Photoconversion of Green‐to‐Red Fluorescent Proteins Based on Blue and Infrared Light Reduces Phototoxicity in Live‐Cell Single‐Molecule Imaging

Photoconversion of fluorescent proteins by blue and complementary near‐infrared light, termed primed conversion (PC), is a mechanism recently discovered for Dendra2. We demonstrate that controlling the conformation of arginine at residue 66 by threonine at residue 69 of fluorescent proteins from Anthozoan families (Dendra2, mMaple, Eos, mKikGR, pcDronpa protein families) represents a general route to facilitate PC. Mutations of alanine 159 or serine 173, which are known to influence chromophore flexibility and allow for reversible photoswitching, prevent PC. In addition, we report enhanced photoconversion for pcDronpa variants with asparagine 116. We demonstrate live‐cell single‐molecule imaging with reduced phototoxicity using PC and record trajectories of RNA polymerase in Escherichia coli cells.     

Selective and Wash‐Resistant Fluorescent Dihydrocodeinone Derivatives Allow Single‐Molecule Imaging of μ‐Opioid Receptor Dimerization

μ‐Opioid receptors (μ‐ORs) play a critical role in the modulation of pain and mediate the effects of the most powerful analgesic drugs. Despite extensive efforts, it remains insufficiently understood how μ‐ORs produce specific effects in living cells. We developed new fluorescent ligands based on the μ‐OR antagonist E‐p‐nitrocinnamoylamino‐dihydrocodeinone (CACO), that display high affinity, long residence time and pronounced selectivity. Using these ligands, we achieved single‐molecule imaging of μ‐ORs on the surface of living cells at physiological expression levels. Our results reveal a high heterogeneity in the diffusion of μ‐ORs, with a relevant immobile fraction. Using a pair of fluorescent ligands of different color, we provide evidence that μ‐ORs interact with each other to form short‐lived homodimers on the plasma membrane. This approach provides a new strategy to investigate μ‐OR pharmacology at single‐molecule level.     

Peering into Biological Nanopore: A Practical Technology to Single‐Molecule Analysis

As a unique technique at the singe‐molecule level to explore the distribution and temporal order of events, nanopore technology has attracted increasing attention. In comparison to the previous applications in DNA sequencing, this Focus Review highlights the technical details of biological nanopores, especially α‐hemolysin, in the analysis of peptides and proteins. The instrument configurations, experimental interferences, and data analysis including the conformation of peptides and proteins and their interactions for single‐molecule detection are discussed.     

DCDHF Fluorophores for Single‐Molecule Imaging in Cells

There is a persistent need for small‐molecule fluorescent labels optimized for single‐molecule imaging in the cellular environment. Application of these labels comes with a set of strict requirements: strong absorption, efficient and stable emission, water solubility and membrane permeability, low background emission, and red‐shifted absorption to avoid cell autofluorescence. We have designed and characterized several fluorophores, termed “DCDHF” fluorophores, for use in live‐cell imaging based on the push–pull design: an amine donor group and a 2‐dicyanomethylene‐3‐cyano‐2,5‐dihydrofuran (DCDHF) acceptor group, separated by a π‐rich conjugated network. In general, the DCDHF fluorophores are comparatively photostable, sensitive to local environment, and their chemistries and photophysics are tunable to optimize absorption wavelength, membrane affinity, and solubility. Especially valuable are fluorophores with sophisticated photophysics for applications requiring additional facets of control, such as photoactivation. For example, we have reengineered a red‐emitting DCDHF fluorophore so that it is dark until photoactivated with a short burst of low‐intensity violet light. This molecule and its relatives provide a new class of bright photoactivatable small‐molecule fluorophores, which are needed for super‐resolution imaging schemes that require active control (here turning‐on) of single‐molecule emission.     

Recent Developments in Lanthanide Single‐Molecule Magnets

Single‐molecule magnets (SMMs) exhibiting slow relaxation of magnetization of purely molecular origin are highly attractive owing to their potential applications in spintronic devices, high‐density information storage, and quantum computing. In particular, lanthanide SMMs have been playing a major role in the advancement of this field because of the large intrinsic magnetic anisotropy of lanthanide metal ions. Herein, some recent breakthroughs that are changing the perspective of the field are highlighted, with special emphasis on synthetic strategies towards the design of high‐performance SMMs.     

Substrate‐Independent Magnetic Bistability in Monolayers of the Single‐Molecule Magnet Dy2ScN@C80 on Metals and Insulators

Magnetic hysteresis is demonstrated for monolayers of the single‐molecule magnet (SMM) Dy₂ScN@C₈₀ deposited on Au(111), Ag(100), and MgO|Ag(100) surfaces by vacuum sublimation. The topography and electronic structure of Dy₂ScN@C₈₀ adsorbed on Au(111) were studied by STM. X‐ray magnetic CD studies show that the Dy₂ScN@C₈₀ monolayers exhibit similarly broad magnetic hysteresis independent on the substrate used, but the orientation of the Dy₂ScN cluster depends strongly on the surface. DFT calculations show that the extent of the electronic interaction of the fullerene molecules with the surface is increasing dramatically from MgO to Au(111) and Ag(100). However, the charge redistribution at the fullerene‐surface interface is fully absorbed by the carbon cage, leaving the state of the endohedral cluster intact. This Faraday cage effect of the fullerene preserves the magnetic bistability of fullerene‐SMMs on conducting substrates and facilitates their application in molecular spintronics.     

Achieving Efficient Multichannel Conductance in Through‐Space Conjugated Single‐Molecule Parallel Circuits

Constructing single‐molecule parallel circuits with multiple conduction channels is an effective strategy to improve the conductance of a single molecular junction, but rarely reported. We present a novel through‐space conjugated single‐molecule parallel circuit (f‐4Ph‐4SMe) comprised of a pair of closely parallelly aligned p‐quaterphenyl chains tethered by a vinyl bridge and end‐capped with four SMe anchoring groups. Scanning‐tunneling‐microscopy‐based break junction (STM‐BJ) and transmission calculations demonstrate that f‐4Ph‐4SMe holds multiple conductance states owing to different contact configurations. When four SMe groups are in contact with two electrodes at the same time, the through‐bond and through‐space conduction channels work synergistically, resulting in a conductance much larger than those of analogous molecules with two SMe groups or the sum of two p‐quaterphenyl chains. The system is an ideal model for understanding electron transport through parallel π‐stacked molecular systems and may serve as a key component for integrated molecular circuits with controllable conductance.     

Direct Identification of Protein–Protein Interactions by Single‐Molecule Force Spectroscopy

Single‐molecule force spectroscopy based on atomic force microscopy (AFM‐SMFS) has allowed the measurement of the intermolecular forces involved in protein‐protein interactions at the molecular level. While intramolecular interactions are routinely identified directly by the use of polyprotein fingerprinting, there is a lack of a general method to directly identify single‐molecule intermolecular unbinding events. Here, we have developed an internally controlled strategy to measure protein–protein interactions by AFM‐SMFS that allows the direct identification of dissociation force peaks while ensuring single‐molecule conditions. Single‐molecule identification is assured by polyprotein fingerprinting while the intermolecular interaction is reported by a characteristic increase in contour length released after bond rupture. The latter is due to the exposure to force of a third protein that covalently connects the interacting pair. We demonstrate this strategy with a cohesin–dockerin interaction.     

Integrated Transmission Electron and Single‐Molecule Fluorescence Microscopy Correlates Reactivity with Ultrastructure in a Single Catalyst Particle

Establishing structure–activity relationships in complex, hierarchically structured nanomaterials, such as fluid catalytic cracking (FCC) catalysts, requires characterization with complementary, correlated analysis techniques. An integrated setup has been developed to perform transmission electron microscopy (TEM) and single‐molecule fluorescence (SMF) microscopy on such nanostructured samples. Correlated structure–reactivity information was obtained for 100 nm thin, microtomed sections of a single FCC catalyst particle using this novel SMF‐TEM high‐resolution combination. High reactivity in a thiophene oligomerization probe reaction correlated well with TEM‐derived zeolite locations, while matrix components, such as clay and amorphous binder material, were found not to display activity. Differences in fluorescence intensity were also observed within and between distinct zeolite aggregate domains, indicating that not all zeolite domains are equally active.     

Cryogenic Correlative Single‐Particle Photoluminescence Spectroscopy and Electron Tomography for Investigation of Nanomaterials

Cryogenic single‐particle photoluminescence (PL) spectroscopy has been used with great success to directly observe the heterogeneous photophysical states present in a population of luminescent particles. Cryogenic electron tomography provides complementary nanometer scale structural information to PL spectroscopy, but the two techniques have not been correlated due to technical challenges. Here, we present a method for correlating single‐particle information from these two powerful microscopy modalities. We simultaneously observe PL brightness, emission spectrum, and in‐plane excitation dipole orientation of CdSSe/ZnS quantum dots suspended in vitreous ice. Stable and fluctuating emitters were observed, as well as a surprising splitting of the PL spectrum into two bands with an average energy separation of 80 meV. In some cases, the onset of the splitting corresponded to changes in the in‐plane excitation dipole orientation. These dynamics were assigned to structures of individual quantum dots and the excitation dipoles were visualized in the context of structural features.     

Surface Plasmon Resonance Microscopy: From Single‐Molecule Sensing to Single‐Cell Imaging

Surface plasmon resonance microscopy (SPRM) is a versatile platform for chemical and biological sensing and imaging. Great progress in exploring its applications, ranging from single‐molecule sensing to single‐cell imaging, has been made. In this Minireview, we introduce the principles and instrumentation of SPRM. We also summarize the broad and exciting applications of SPRM to the analysis of single entities. Finally, we discuss the challenges and limitations associated with SPRM and potential solutions.