An Engineered OmpG Nanopore with Displayed Peptide Motifs for Single-Molecule Multiplex Protein Detection

Molecular detection via nanopore, achieved by monitoring changes in ionic current arising from analyte interaction with the sensor pore, is a promising technology for multiplex sensing development. Outer Membrane Protein G (OmpG), a monomeric porin possessing seven functionalizable loops, has been reported as an effective sensing platform for selective protein detection. Using flow cytometry to screen unfavorable constructs, we identified two OmpG nanopores with unique peptide motifs displayed in either loop 3 or 6, which also exhibited distinct analyte signals in single-channel current recordings. We exploited these motif-displaying loops concurrently to facilitate single-molecule multiplex protein detection in a mixture. We additionally report a strategy to increase sensor sensitivity via avidity motif display. These sensing schemes may be expanded to more sophisticated designs utilizing additional loops to increase multiplicity and sensitivity.     

Quantitative Single-Molecule Electrochemiluminescence Bioassay

A single-molecule electrochemiluminescence bioassay is developed here which allows imaging and direct quantification of single biomolecules. Imaging single biomolecules is realized by localizing the electrochemiluminescence events of the labeled molecules. Such an imaging system allows mapping the spatial distribution of biomolecules with electrochemiluminescence and contains quantitative single-molecule insights. We further quantify biomolecules by spatiotemporally merging the repeated reactions at one molecule site and then counting the clustered molecules. The proposed single-molecule electrochemiluminescence bioassay is used to detect carcinoembryonic antigen, showing a limit of detection of 67 attomole concentration which is 10 000 times better than conventional electrochemiluminescence bioassays. This spatial resolution and sensitivity enable single-molecule electrochemiluminescence bioassay a new toolbox for both specific bioimaging and ultrasensitive quantitative analysis.     

Spontaneously Blinking Rhodamine Dyes for Single-Molecule Localization Microscopy

Single-molecule localization microscopy (SMLM) has found extensive applications in various fields of biology and chemistry. As a vital component of SMLM, fluorophores play an essential role in obtaining super-resolution fluorescence images. Recent research on spontaneously blinking fluorophores has greatly simplified the experimental setups and extended the imaging duration of SMLM. To support this crucial development, this review provides a comprehensive overview of the development of spontaneously blinking rhodamines from 2014 to 2023, as well as the key mechanistic aspects of intramolecular spirocyclization reactions. We hope that by offering insightful design guidelines, this review will contribute to accelerating the advancement of super-resolution imaging technologies.     

Direct Comparison of Lysine versus Site-Specific Protein Surface Immobilization in Single-Molecule Mechanical Assays**

Single-molecule force spectroscopy (SMFS) is powerful for studying folding states and mechanical properties of proteins, however, it requires protein immobilization onto force-transducing probes such as cantilevers or microbeads. A common immobilization method relies on coupling lysine residues to carboxylated surfaces using 1-ethyl-3-(3-dimethyl-aminopropyl) carbodiimide and N-hydroxysuccinimide (EDC/NHS). Because proteins typically contain many lysine groups, this strategy results in a heterogeneous distribution of tether positions. Genetically encoded peptide tags (e.g., ybbR) provide alternative chemistries for achieving site-specific immobilization, but thus far a direct comparison of site-specific vs. lysine-based immobilization strategies to assess effects on the observed mechanical properties was lacking. Here, we compared lysine- vs. ybbR-based protein immobilization in SMFS assays using several model polyprotein systems. Our results show that lysine-based immobilization results in significant signal deterioration for monomeric streptavidin-biotin interactions, and loss of the ability to correctly classify unfolding pathways in a multipathway Cohesin-Dockerin system. We developed a mixed immobilization approach where a site-specifically tethered ligand was used to probe surface-bound proteins immobilized through lysine groups, and found partial recovery of specific signals. The mixed immobilization approach represents a viable alternative for mechanical assays on in vivo-derived samples or other proteins of interest where genetically encoded tags are not feasible.     

Self-quenched Fluorophore Dimers for DNA-PAINT and STED Microscopy

Super-resolution techniques like single-molecule localisation microscopy (SMLM) and stimulated emission depletion (STED) microscopy have been extended by the use of non-covalent, weak affinity-based transient labelling systems. DNA-based hybrid systems are a prominent example among these transient labelling systems, offering excellent opportunities for multi-target fluorescence imaging. However, these techniques suffer from higher background relative to covalently bound fluorophores, originating from unbound fluorophore-labelled single-stranded oligonucleotides. Here, we introduce short-distance self-quenching in fluorophore dimers as an efficient mechanism to reduce background fluorescence signal, while at the same time increasing the photon budget in the bound state by almost 2-fold. We characterise the optical and thermodynamic properties of fluorophore-dimer single-stranded DNA, and show super-resolution imaging applications with STED and SMLM with increased spatial resolution and reduced background.     

Photoactivatable Carbo- and Silicon-Rhodamines and Their Application in MINFLUX Nanoscopy

New photoactivatable fluorescent dyes (rhodamine, carbo- and silicon-rhodamines [SiR]) with emission ranging from green to far red have been prepared, and their photophysical properties studied. The photocleavable 2-nitrobenzyloxycarbonyl unit with an alpha-carboxyl group as a branching point and additional functionality was attached to a polycyclic and lipophilic fluorescent dye. The photoactivatable probes having the HaloTagTM amine (O2) ligand bound with a dye core were obtained and applied for live-cell staining in stable cell lines incorporating Vimentin (VIM) or Nuclear Pore Complex Protein NUP96 fused with the HaloTag. The probes were applied in 2D (VIM, NUP96) and 3D (VIM) MINFLUX nanoscopy, as well as in superresolution fluorescence microscopy with single fluorophore activation (VIM, live-cell labeling). Images of VIM and NUPs labeled with different dyes were acquired and their apparent dimensions and shapes assessed on a lower single-digit nanometer scale. Applicability and performance of the photoactivatable dye derivatives were evaluated in terms of photoactivation rate, labeling and detection efficiency, number of detected photons per molecule and other parameters related to MINFLUX nanoscopy.     

Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging

The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.     

Desolvation-Induced Highly Symmetrical Terbium(III) Single-Molecule Magnet Exhibiting Luminescent Self-Monitoring of Temperature

A conjunction of Single-Molecule Magnet (SMM) behavior and luminescence thermometry is an emerging research line aiming at contactless read-out of temperature in future SMM-based devices. The shared working range between slow magnetic relaxation and the thermometric response is typically narrow or absent. We report Tb^III-based emissive SMMs formed in a cyanido-bridged framework whose properties are governed by the reversible structural transformation from [Tb^III(H₂O)₂][Co^III(CN)₆] ⋅ 2.7H₂O ( 1 ) to its dehydrated phase, Tb^III[Co^III(CN)₆] ( 2 ). The 8-coordinated complexes in 1 show the moderate SMM effect but it is enhanced for trigonal-prismatic Tb^III complexes in 2 , showing the SMM features up to 42 K. They are governed by the combination of QTM, Raman, and Orbach relaxation with the energy barrier of 594(18) cm⁻¹ (854(26) K), one of the highest among the Tb^III-based molecular nanomagnets. Both systems exhibit emission related to the f–f electronic transitions, with the temperature variations resulting in the optical thermometry below 100 K. The dehydration leads to a wide temperature overlap between the SMM behavior and thermometry, from 6 K to 42 K. These functionalities are further enriched after the magnetic dilution. The role of post-synthetic formation of high-symmetry Tb^III complexes in achieving the SMM effect and hot-bands-based optical thermometry is discussed.     

Expanded Conformations of Monomeric Tau Initiate Its Amyloidogenesis**

Understanding early amyloidogenesis is key to rationally develop therapeutic strategies. Tau protein forms well-characterized pathological deposits but its aggregation mechanism is still poorly understood. Using single-molecule force spectroscopy based on a mechanical protection strategy, we studied the conformational landscape of the monomeric tau repeat domain (tau-RD_244-368). We found two sets of conformational states, whose frequency is influenced by mutations and the chemical context. While pathological mutations Δ280K and P301L and a pro-amyloidogenic milieu favored expanded conformations and destabilized local structures, an anti-amyloidogenic environment promoted a compact ensemble, including a conformer whose topology might mask two amyloidogenic segments. Our results reveal that to initiate aggregation, monomeric tau-RD_244-368 decreases its polymorphism adopting expanded conformations. This could account for the distinct structures found in vitro and across tauopathies.     

生物分子的单分子检测研究

本文评述了生物单分子检测的方法及其在生物大分子结构与功能之间的关系、酶的活性、反应动力学、分子构象、DNA和RNA的转录、蛋白质折叠等生物学重要问题研究上的应用。对生物单分子检测技术这一研究领域的发展趋势作了展望。     

Single-Molecule FRET Study of DNA G-Quadruplex

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Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy

Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.     

Control of Intrachain Morphology in the Formation of Polyfluorene Aggregates on the Single-Molecule Level

Controlling the morphology of π-conjugated polymers for organic optoelectronic devices has long been a goal in the field of materials science. Since the morphology of a polymer chain is closely intertwined with its photophysical properties, it is desirable to be able to change the arrangement of the polymers at will. We investigate the π-conjugated polymer poly(9,9-dioctylfluorene) (PFO), which can exist in three distinctly different structural phases: the α-, β-, and γ-phase. Every phase has a different chain structure and a unique photoluminescence (PL) spectrum. Due to its unique properties and the pronounced spectral structure-property relations, PFO can be used as a model system to study the morphology of π-conjugated polymers. To avoid ensemble averaging, we examine the PL spectrum of single PFO chains embedded in a non-fluorescent matrix. With single-molecule spectroscopy the structural phase of every single chain can be determined, and changes can be monitored very easily. To manipulate the morphology, solvent vapor annealing (SVA) was applied, which leads to a diffusion of the polymer chains in the matrix. The β- and γ-phases appear during the self-assembly of single α-phase PFO chains into mesoscopic aggregates. The extent of β- and γ-phase formation is directed by the solvent-swelling protocol used for aggregation. Aggregation unequivocally promotes formation of the more planar β- and γ-phases. Once these lower-energy more ordered structural phases are formed, SVA cannot return the polymer chain to the less ordered phase by aggregate swelling.     

在单个分子水平上研究罗丹明标记的磷脂分子的扩散

利用共焦荧光显微镜在单个分子水平上检测了罗丹明标记的磷脂分子(T1 391 )在溶液中和玻璃表面的扩散行为 ,并获得了单个分子分辨的荧光成像 .用穿越时间分布函数拟合分子通过焦点时发射荧光信号的宽度分布 ,得到　T1 391分子在水溶液中的扩散常数为 2 .3× 1 0 - 6 cm2 ·s- 1,　在亲水玻璃表面上的扩散常数为 3.4× 1 0 - 8cm2 ·s- 1.部分磷脂分子与玻璃表面发生强吸附作用 ,其停留在焦点内的时间较长 ,特征穿越时间为 85ms     

Organic fluorescence reagents in the study of enzymes and proteins.

Studies designed to elucidate life processes require close cooperation between various scientific disciplines. A pertinent example is seen in the application of fluorescence spectroscopy to biological studies, where biological sciences, physical and organic chemistry, and technical innovations complement one another. This report reviews the application of fluorescence probes which bind covalently to certain sites of proteins. The major organic fluorescence reagents used in this field are tabulated.     

重力场和电解质浓度对胶体凝聚体分形结构的影响

运用李航等提出的新方法, 克服了DLVO理论中无法理论计算不同电解质浓度下颗粒的表面电位这一困难, 从而可以直接计算出不同电解质浓度下胶体颗粒间的位能. 同时, 还运用胶体颗粒动能的玻耳兹曼分布原理和蒙特卡罗方法来模拟胶体的运动, 并采用非弹性碰撞理论解决了碰撞后凝聚的有效概率问题. 在改进DDA模型的基础上, 成功地建立了以往的模拟中未能建立的重力场中电解质浓度与碰撞凝聚概率间的联系, 结果发现, (1)重力场作用下的凝聚体分形维数随电解质浓度变化的曲线完全不同于无重力条件下的曲线. 无重力作用下, 凝聚结构体分形维数随电解质浓度的变化比较缓慢, 曲线呈“L”形；而重力作用下的分形维数则呈明显的“S”形曲线. (2) 在重力条件下, 慢凝聚包括两个区域, 对电解质浓度不敏感区域和敏感区域. 在敏感区域存在一个电解质浓度的拐点. (3)无重力条件下,不同大小的胶体颗粒在快凝聚时的分形维数都是在1.86±0.01.当电解质浓度降低,凝聚速率变慢,分形维数增加,最大达到2.01±0.02,但不会形成重力条件下的分形维数接近3的结构体.     

头孢唑酮与Triton X-100缔合体系的相互作用

抗生素头孢唑酮的加入使得非离子表面活性剂Triton X-100的表面活性降低. ¹H-NMR的结果表明，头孢唑酮增溶于胶束极性基团附近.头孢唑酮与Triton X-100胶束的结合常数随Triton X-100含量的增加而下降，但头孢唑酮在Triton X-100胶束相和水连续相之间的分配系数不随Triton X-100含量变化而变化.     

Increased Surface Density of States at the Fermi Level for Electron Transport Across Single-Molecule Junctions

Fermi's golden rule, a remarkable concept for the transition probability involving continuous states, is applicable to the interfacial electron-transporting efficiency via correlation with the surface density of states (SDOS). Yet, this concept has not been reported to tailor single-molecule junctions where gold is an overwhelmingly popular electrode material due to its superior amenability in regenerating molecular junctions. At the Fermi level, however, the SDOS of gold is small due to its fully filled d-shell. To increase the electron-transport efficiency, herein, gold electrodes are modified by a monolayer of platinum or palladium that bears partially filled d-shells and exhibits significant SDOS at the Fermi energy. An increase by 2–30 fold is found for single-molecule conductance of α,ω-hexanes bridged via common headgroups. The improved junction conductance is attributed to the electrode self-energy which involves a stronger coupling with the molecule and a larger SDOS participated by d-electrons at the electrode-molecule interfaces.     

Formation of Neutral Peptide Aggregates as Studied by Mass‐Selective IR Action Spectroscopy

The spontaneous aggregation of proteins and peptides is widely studied owing to its relation to neurodegenerative diseases. To understand the underlying principles of peptide aggregation, elucidation of structure and structural changes upon their formation is key. This level of detail can be obtained by studying the peptide self‐assembly in the gas phase. Structural characterization of aggregates is mainly done on charged species, as adding charges is an intrinsic part of the technique to bring molecules into the gas phase. Studying neutral peptide aggregates will complement the existing picture. These studies are restricted to dimers due to experimental limitations. Herein, we present advances in laser desorption molecular beam spectroscopy to form neutral peptide aggregates consisting of up to 14 monomeric peptides in the gas phase. The combination of this technique with IR–UV spectroscopy allowed us to select each aggregate by size and subsequently characterize its structure.