Single-molecule calorimeter and free energy landscape

Single molecule-driven nanomotors reveal the dynamic-disordered chemomechanical transduction of active enzymes

Enzymes facilitate the conversion of chemical energy into mechanical work during biochemical reactions, thereby regulating the dynamic metabolic activity of living systems. However, directly observing the energy release facilitated by fluctuating individual enzymes remains a challenge, leading to a contentious debate regarding the underlying reasons for this phenomenon. Here, we aim to overcome this challenge by developing an oscillating nanomotor powered by a single-molecule enzyme, which allows real-time tracking of energy transduction in enzymatic reactions. Through analysis of the shifts in free energy profiles within the nanomotors, our results unveil not only the heterogeneous energy release patterns of individual enzyme molecules but also the dynamic disorder of a particular enzyme in energy release over extended monitoring periods. By exploring six distinct types of single-molecule enzymatic reactions, we provide the direct evidence supporting the argument that the reaction enthalpy governs the enzymatic energy release. This approach has implications for understanding the mechanism of enzymatic catalysis and developing highly efficient nanomotors.

Dielectric Surface-Based Biosensors for Enhanced Detection of Biomolecular Interactions: Advances and Applications

Surface plasmon resonance (SPR) biosensors are extensively utilized for analyzing molecular interactions due to their high sensitivity and label-free detection capabilities. Recent innovations in surface-sensitive biosensors with dielectric surfaces address the inherent limitations associated with traditional gold surfaces, such as thermal effects and biocompatibility issues, which can impede broader applications. This review examines state-of-the-art biosensor configurations, including total internal reflection, optical waveguide, photonic crystal resonators, Bloch surface wave biosensors, and surface electrochemical biosensors, which can enhance analyte signals and augment the molecular detection efficiency at the sensor interface. These technological advancements not only improve the resolution of binding kinetics analysis and single-molecule detection but also extend the analytical capabilities of these systems. Additionally, this review explores prospective advancements in augmenting field enhancement and incorporating multimodal sensing functionalities, emphasizing the significant potential of these sophisticated biosensing technologies to profoundly enhance our understanding of molecular interactions.

Visualizing Single-Molecule Protein Conformational Transitions and Free Energy Landscape

Monitoring the conformational dynamics of individual proteins is essential to understand the relationship between structure and function in molecular regulatory mechanisms. However, the fast dynamics of single proteins remain poorly understood. Here, we construct a single-molecule sensing platform by introducing plasmonic imaging of single nanoparticles to sense and report the protein conformational changes at the single-molecule level. Tracking the fluctuations of individual nanoparticles with high resolution, we detect and characterize distinct conformational states of molecular chaperone heat shock protein 90 (Hsp90). We also explore the conformational changes of Hsp90 in situ under different nucleotide conditions. Analysis of the conformational fluctuations between the open and closed states of single Hsp90 provides important information on free energy profiles, effective spring constants, and multiphase behaviors. This method offers a strategy to visualize the conformational changes of single proteins in real-time and provides insights into the underlying molecular mechanisms.

Label-Free Optical Imaging of Nanoscale Single Entities

The advancement of optical microscopy technologies has achieved imaging of nanoscale objects, including nanomaterials, virions, organelles, and biological molecules, at the single entity level. Recently developed plasmonic and scattering based optical microscopy technologies have enabled label-free imaging of single entities with high spatial and temporal resolutions. These label-free methods eliminate the complexity of sample labeling and minimize the perturbation of the analyte native state. Additionally, these imaging-based methods can noninvasively probe the dynamics and functions of single entities with sufficient throughput for heterogeneity analysis. This perspective will review label-free single entity imaging technologies and discuss their principles, applications, and key challenges.

Surface Plasmon Resonance Biosensors: A Review of Molecular Imaging with High Spatial Resolution

Surface plasmon resonance (SPR) is a powerful tool for determining molecular interactions quantitatively. SPR imaging (SPRi) further improves the throughput of SPR technology and provides the spatially resolved capability for observing the molecular interaction dynamics in detail. SPRi is becoming more and more popular in biological and chemical sensing and imaging. However, SPRi suffers from low spatial resolution due to the imperfect optical components and delocalized features of propagating surface plasmonic waves along the surface. Diverse kinds of approaches have been developed to improve the spatial resolution of SPRi, which have enormously impelled the development of the methodology and further extended its possible applications. In this minireview, we introduce the mechanisms for building a high-spatial-resolution SPRi system and present its experimental schemes from prism-coupled SPRi and SPR microscopy (SPRM) to surface plasmonic scattering microscopy (SPSM); summarize its exciting applications, including molecular interaction analysis, molecular imaging and profiling, tracking of single entities, and analysis of single cells; and discuss its challenges in recent decade as well as the promising future.

Plasmonic Scattering Microscopy for Label-Free Imaging of Molecular Binding Kinetics: From Single Molecules to Single Cells

Measuring molecular binding kinetics represents one of the most important tasks in molecular interaction analysis. Surface plasmon resonance (SPR) is a popular tool for analyzing molecular binding. Plasmonic scattering microscopy (PSM) is a newly developed SPR imaging technology, which detects the out-of-plane scattering of surface plasmons by analytes and has pushed the detection limit of label-free SPR imaging down to a single-protein level. In addition, PSM also allows SPR imaging with high spatiotemporal resolution, making it possible to analyze cellular response to the molecular bindings. In this Mini Review, we present PSM as a method of choice for chemical and biological imaging, introduce its theoretical mechanism, present its experimental schemes, summarize its exciting applications, and discuss its challenges as well as the promising future.

Quasi-Free Electron States Responsible for Single-Molecule Conductance Enhancement in Stable Radical

Stable organic radicals, which possess half-filled orbitals in the vicinity of the Fermi energy, are promising candidates for electronic devices. In this Letter, using a combination of scanning-tunneling-microscopy-based break junction (STM-BJ) experiments and quantum transport theory, a stable fluorene-based radical is investigated. We demonstrate that the transport properties of a series of fluorene derivatives can be tuned by controlling the degree of localization of certain orbitals. More specifically, radical 36-FR has a delocalized half-filled orbital resulting in Breit-Wigner resonances, leading to an unprecedented conductance enhancement of 2 orders of magnitude larger than the neutral nonradical counterpart (36-FOH). In other words, conversion from a closed-shell fluorene derivative to the free radical in 36-FR opens an electron transport path which massively enhances the conductance. This new understanding of the role of radicals in single-molecule junctions opens up a novel design strategy for single-molecule-based spintronic devices.

Rapid Regulation of Local Temperature and Transient Receptor Potential Vanilloid 1 Ion Channels with Wide-Field Plasmonic Thermal Microscopy

Plasmonic absorption of light can create significant local heat and has become a promising tool for rapid temperature regulation in diverse fields, from biomedical technology to optoelectronics. Current plasmonic heating usually relies on specially designed nanomaterials randomly distributed in the space and barely provides uniform temperature regulation in a wide field. Herein, we report a rapid temperature regulation strategy on a plain gold-coated glass slip using a plasmonic scattering microscopy, which can be referred to as wide-field plasmonic thermal microscopy (W-PTM). We calibrated the W-PTM by monitoring the phase transition of the temperature-sensitive polymer solutions, showing that it can provide a temperature regulation range of 33-80 °C. Moreover, the W-PTM provides imaging capability, thus allowing the statistical analysis of the phase-transitioned polymeric nanoparticles. Finally, we demonstrated that W-PTM can be used for noninvasive and local regulation of the transient receptor potential vanilloid 1 (TRPV1) ion channels in the living cells, which can be monitored by simultaneous fluorescence imaging of the calcium influx. With the nondestructive local temperature-regulating and concurrent fluorescence imaging capability, we anticipate that W-PTM can be a powerful tool to study cellular activities associated with cellular membrane temperature changes.

In Situ Analysis of Membrane-Protein Binding Kinetics and Cell-Surface Adhesion Using Plasmonic Scattering Microscopy

Surface plasmon resonance microscopy (SPRM) is an excellent platform for in situ studying cell-substrate interactions. However, SPRM suffers from poor spatial resolution and small field of view. Herein, we demonstrate plasmonic scattering microscopy (PSM) by adding a dry objective on a popular prism-coupled surface plasmon resonance (SPR) system. PSM not only retains SPRM's high sensitivity and real-time analysis capability, but also provides ≈7 times higher spatial resolution and ≈70 times larger field of view than the typical SPRM, thus providing more details about membrane protein response to ligand binding on over 100 cells simultaneously. In addition, PSM allows quantifying the target movements in the axial direction with a high spatial resolution, thus allowing mapping adhesion spring constants for quantitatively describing the mechanical properties of the cell-substrate contacts. This work may offer a powerful and cost-effective strategy for upgrading current SPR products.

Complete Inhibition of the Rotation in a Barrierless TICT Probe for Fluorescence-On Qualitative Analysis

Inhibition of twisting intramolecular charge transfer (TICT) is one of the most attractive methods for fluorescence-on analysis, whereas it remains enigmatic whether the fluorescence in a TICT-based probe could be thoroughly lightened. Here, for maximizing the fluorescence-on signal of the TICT-based probe, we develop a model by employing chemical reaction to directly cleave the linkage between the rotational electron donor and acceptor with a predisposed fluorescent signal close to zero. To validate this assumption, a nonfluorescent probe with barrierless rotation is successfully achieved by grafting acryloyl with -C═C- recognition sites onto coumarin, and 7-hydroxycoumarin with bright blue fluorescence could be released within 3 s upon probing KMnO₄ with an amount as low as 0.95 nM and 6.6 pg. We believe that the present strategy could not only deepen the insights of photochemistry but also facilitate the development of a theranostic drug delivery system, energy conversion, pollution control, and health risk reduction.

Evanescent scattering imaging of single protein binding kinetics and DNA conformation changes

Evanescent illumination has been widely used to detect single biological macromolecules because it can notably enhance light-analyte interaction. However, the current evanescent single-molecule detection system usually requires specially designed microspheres or nanomaterials. Here we show that single protein detection and imaging can be realized on a plain glass surface by imaging the interference between the evanescent lights scattered by the single proteins and by the natural roughness of the cover glass. This allows us to quantify the sizes of single proteins, characterize the protein-antibody interactions at the single-molecule level, and analyze the heterogeneity of single protein binding behaviors. In addition, owing to the exponential distribution of evanescent field intensity, the evanescent imaging system can track the analyte axial movement with high resolution, which can be used to analyze the DNA conformation changes, providing one solution for detecting small molecules, such as microRNA. This work demonstrates a label-free single protein imaging method with ordinary consumables and may pave a road for detecting small biological molecules.

Label-Free Imaging of Nanoscale Displacements and Free-Energy Profiles of Focal Adhesions with Plasmonic Scattering Microscopy

Cell adhesion plays a critical role in cell communication, cell migration, cell proliferation, and integration of medical implants with tissues. Focal adhesions physically link the cell cytoskeleton to the extracellular matrix, but it remains challenging to image single focal adhesions directly. Here, we show that plasmonic scattering microscopy (PSM) can directly image the single focal adhesions in a label-free, real-time, and non-invasive manner with sub-micrometer spatial resolution. PSM is developed based on surface plasmon resonance (SPR) microscopy, and the evanescent illumination makes it immune to the interference of intracellular structures. Unlike the conventional SPR microscopy, PSM can provide a high signal-to-noise ratio and sub-micrometer spatial resolution for imaging the analytes with size down to a single-molecule level, thus allowing both the super-resolution lateral localization for measuring the nanoscale displacement and precise tracking of vertical distances between the analyte centroid and the sensor surface for analysis of free-energy profiles. PSM imaging of the RBL-2H3 cell with temporal resolution down to microseconds shows that the focal adhesions have random diffusion behaviors in addition to their directional movements during the antibody-mediated activation process. The free-energy mapping also shows a similar movement tendency, indicating that the cell may change its morphology upon varying the binding conditions of adhesive structures. PSM provides insights into the individual focal adhesion activities and can also serve as a promising tool for investigating the cell/surface interactions, such as cell capture and detection and tissue adhesive materials screening.