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Escherichia coli β-galactosidase was labelled with 1 mmol/L fluorescein 5-carbamoylmethylthiopropanoic N-hydroxysuccinimidyl ester for 1 and 3 min. The samples were separated by capillary electrophoresis and peak areas compared to that of labelled BSA for the purpose of quantification of the concentration of attached label. Enzyme concentration in the samples was determined by single molecule counting. The average number of labels attached to each molecule of enzyme was found to be 3.1 and 4.5 when labelled for 1 and 3 min, respectively. The distribution of single enzyme molecule electrophoretic mobilities for the unlabelled enzyme and that labelled for 1 and 3 min were measured using capillary electrophoresis. The average mobilities were found determined to be −(1.99 ± 0.13) × 10–8 m2 V−1 s−1 (N = 39), −(2.16 ± 0.19) × 10–8 m2 V−1 s−1 (N = 46), and –(2.18 ± 0.21) × 10–8 m2 V−1 s−1 (N = 39), respectively. A protein electrophoresis model was applied and predicted that the differences in average mobilities could be explained through relatively minor changes in overall charge, Stokes radius, and shape. This difference was similar to the range in mobilities observed in the unlabelled protein. This is consistent with the electrophoretic heterogeneity of the unmodified enzyme being caused by relatively small differences in charge, size, and shape of the individual molecules in the population. [ABSTRACT FROM AUTHOR]

DEAD-box helicases, crucial for many aspects of RNA metabolism, often contain intrinsically disordered regions (IDRs) whose functions remain unclear. Using multiparameter confocal microscopy, we reveal that sex chromosome-encoded homologous RNA helicases, DDX3X and DDX3Y, form nanometer-scale RNA-protein clusters (RPCs) that foster their catalytic activities in vitro and in cells. The IDRs are critical for the formation of these RPCs. A thorough analysis of the catalytic cycle of DDX3X and DDX3Y by ensemble biochemistry and single-molecule photon bursts in the confocal microscope showed that RNA release is a major step that differentiates the unwinding activities of DDX3X and DDX3Y. The N-terminal IDRs of DDX3X and DDX3Y are both the drivers of RPC formation and the major differentiators of their enzymatic activities. Our findings provide new insights that the nanoscale helicase RPCs may be the normal state of these helicases under non-stressed conditions that promote their RNA unwinding and might act as nucleation points for stress granule formation. This mechanism may apply broadly among other members of the DEAD-box helicase family. [Display omitted] • DDX3X and DDX3Y form nanometer-scale protein-RNA clusters in vitro and in cells • Sequence differences in IDRs drive differences in cluster formation and catalysis • Single-strand RNA release rates underlie catalytic differences between DDX3X/DDX3Y • DDX3X mutants show a relationship between cluster size and RNA unwinding activity Yanas et al. report that RNA helicases DDX3X and DDX3X form nanometer-scale RNA-protein clusters (RPCs) both in vitro and in cells. Differences in RPC size and catalytic activity between DDX3X and DDX3Y are determined by sequence differences in the two homologs' IDRs. Using DDX3X mutants, the authors find that RPC size correlates with helicase activity. [ABSTRACT FROM AUTHOR]

Chemical studies usually consist of measurements made on large ensembles of molecules with data representing average values for the population. It has been shown that individual molecules of a given enzyme have different properties. Large-scale averaging has in the past masked these differences. Alkaline phosphatase has been used as a model to study this enzyme heterogeneity. The catalytic rates of the individual molecules have been found to differ by over 10-fold, and the activation energy of catalysis by more than two-fold. Differences in properties indicate that differences in structure must exist between the molecules. For alkaline phosphatase, the structural differences have been suggested to be differences in glycosylation, differences due to partial proteolysis, and due to some molecules containing mixtures of active and inactive subunits. The determination of the distribution of activities of populations of this enzyme within a sample has also been shown to be a useful tool in diagnostics. This review discusses the advent of single-molecule enzymology and summarizes its use in the study of alkaline phosphatase using capillary electrophoresis, microscopic well assays, and single-molecule tracking. [ABSTRACT FROM AUTHOR]

Nanopipettes, as a class of solid-state nanopores, have evolved into universal tools in biomedicine for the detection of biomarkers and different biological analytes. Nanopipette-based methods combine high sensitivity, selectivity, single-molecule resolution, and multifunctionality. The features have significantly expanded interest in their applications for the biomolecular detection, imaging, and molecular diagnostics of real samples. Moreover, the ease of manufacturing nanopipettes, coupled with their compatibility with fluorescence and electrochemical methods, makes them ideal for portable point-of-care diagnostic devices. This review summarized the latest progress in nanopipette-based nanopore technology for the detection of biomarkers, DNA, RNA, proteins, and peptides, in particular β-amyloid or α-synuclein, emphasizing the impact of technology on molecular diagnostics. By addressing key challenges in single-molecule detection and expanding applications in diverse biological areas, nanopipettes are poised to play a transformative role in the future of personalized medicine. [ABSTRACT FROM AUTHOR]

Experiments to measure a single molecule/particle, i.e., an individual molecule/particle, at room temperature or under physiological conditions without immobilization—for example, on a surface or without significant hydrodynamic flow—have so far failed. This failure has given impetus to the underlying theory of Brownian molecular motion towards its stochastics due to diffusion. Quantifying the thermodynamic jitter of molecules/particles inspires many and forms the theoretical basis of single-molecule/single-particle biophysics and biochemistry. For the first time, our simulation results for a live cell (cytoplasm) show that the tracks of individual single molecules are localized in Brownian motion, while there is fanning out in fractal diffusion (anomalous diffusion).

A new type of material, organic salts in the crystal and crystalline powder state, with both excitation wavelength dependent (Ex‐De) fluorescence and Ex‐De phosphorescence under ambient conditions have been reported. The single component triphenylsulfonium chloride displays tunable fluorescent colors ranging from light purple to sky blue and tunable afterglow colors varying from green to yellowish green, to yellow (lifetimes: 57, 141, 66 ms, afterglow lasting for 2.1, 2.0, 2.3 s). The relationship between the structure and luminescence performance of 17 sulfonium salt derivatives confirms the pivotal roles of both the anions and the electronic and steric effect of substituent factors for luminescence. Single‐crystal analysis reveals that unique ionic bonding and intermolecular interaction can promote an ordered arrangement of organic salts in a crystal state, which then can facilitate molecular aggregation for phosphorescence generation. Theoretical calculations have also confirmed this viewpoint. More importantly, these sulfonium salt derivatives can be used for advanced multimodal anti‐counterfeiting and mitochondrial imaging, respectively. This study has not only expanded the scope of Ex‐De materials but also extended their applications. [ABSTRACT FROM AUTHOR]

Understanding the mechanisms underlying amyloid‐β (Aβ) aggregation is pivotal in the context of Alzheimer's disease. This study aims to elucidate the secondary nucleation process of Aβ42 peptides by combining experimental and computational methods. Using a newly developed nanopipette‐based amyloid seeding and translocation assay, confocal fluorescence spectroscopy, and molecular dynamics simulations, the influence of the seed properties on Aβ aggregation is investigated. Both fragmented and unfragmented seeds played distinct roles in the formation of oligomers, with fragmented seeds facilitating the formation of larger aggregates early in the incubation phase. The results show that secondary nucleation leads to the formation of oligomers of various sizes and structures as well as larger fibrils structured in β‐sheets. From these findings a mechanism of secondary nucleation involving two types of aggregate populations, one released and one growing on the mother fiber is proposed. [ABSTRACT FROM AUTHOR]

Experiments to measure a single molecule/particle, i.e., an individual molecule/particle, at room temperature or under physiological conditions without immobilization—for example, on a surface or without significant hydrodynamic flow—have so far failed. This failure has given impetus to the underlying theory of Brownian molecular motion towards its stochastics due to diffusion. Quantifying the thermodynamic jitter of molecules/particles inspires many and forms the theoretical basis of single-molecule/single-particle biophysics and biochemistry. For the first time, our simulation results for a live cell (cytoplasm) show that the tracks of individual single molecules are localized in Brownian motion, while there is fanning out in fractal diffusion (anomalous diffusion). [ABSTRACT FROM AUTHOR]

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Water is ubiquitous and indispensable on the Earth. Its importance has long been recognized on a macroscopic scale. However, it took a long time to comprehend the impact of water molecules on the microscopic level. According to the hydrophilicity of matter, the impact of water can be divided into two categories: 1) intermolecular hydrogen bonds (H-bonds) and 2) hydrophobic interactions. In recent years, atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) has been used to investigate the effect of water on the single-chain properties of macromolecules. Herein, we summarize recent advances in the AFM-SMFS study on the impact of water on some kinds of synthetic polymers, biomacromolecules, and molecules containing supramolecular interactions from the two aspects of H-bonds and hydrophobic interactions. It is expected that a deeper understanding of the interactions between water molecules and macromolecules will enable the design of polymer materials with specific functionalities and properties in a bottom-up way.

The concept that dimeric protein complexes in synapses can sequentially replace their subunits has been a cornerstone of Francis Crick’s 1984 hypothesis, explaining how long-term memories could be maintained in the face of short protein lifetimes. However, it is unknown whether the subunits of protein complexes that mediate memory are sequentially replaced in the brain and if this process is linked to protein lifetime. We address these issues by focusing on supercomplexes assembled by the abundant postsynaptic scaffolding protein PSD95, which plays a crucial role in memory. We used single-molecule detection, super-resolution microscopy and MINFLUX to probe the molecular composition of PSD95 supercomplexes in mice carrying genetically encoded HaloTags, eGFP, and mEoS2. We found a population of PSD95-containing supercomplexes comprised of two copies of PSD95, with a dominant 12.7 nm separation. Time-stamping of PSD95 subunits in vivo revealed that each PSD95 subunit was sequentially replaced over days and weeks. Comparison of brain regions showed subunit replacement was slowest in the cortex, where PSD95 protein lifetime is longest. Our findings reveal that protein supercomplexes within the postsynaptic density can be maintained by gradual replacement of individual subunits providing a mechanism for stable maintenance of their organization. Moreover, we extend Crick’s model by suggesting that synapses with slow subunit replacement of protein supercomplexes and long-protein lifetimes are specialized for long-term memory storage and that these synapses are highly enriched in superficial layers of the cortex where long-term memories are stored.

Electrochemiluminescence (ECL) is rapidly evolving from an analytical method into an optical microscopy. The orthogonality of the electrochemical trigger and the optical readout distinguishes it from classic microscopy and electrochemical techniques, owing to its near‐zero background, remarkable sensitivity, and absence of photobleaching and phototoxicity. In this minireview, we summarize the recent advances in ECL imaging technology, emphasizing original configurations which enable the imaging of biological entities and the improvement of the analytical properties by increasing the complexity and multiplexing of bioassays. Additionally, mapping the (electro)chemical reactivity in space provides valuable information on nanomaterials and facilitates deciphering ECL mechanisms for improving their performances in diagnostics and (electro)catalysis. Finally, we highlight the recent achievements in imaging at the ultimate limits of single molecules, single photons or single chemical reactions, and the current challenges to translate the ECL imaging advances to other fields such as material science, catalysis and biology. [ABSTRACT FROM AUTHOR]

SUMMARY: Plasma membrane (PM)‐associated abscisic acid (ABA) signal transduction is an important component of ABA signaling. The C2‐domain ABA‐related (CAR) proteins have been reported to play a crucial role in recruiting ABA receptor PYR1/PYL/RCAR (PYLs) to the PM. However, the molecular details of the involvement of CAR proteins in membrane‐delimited ABA signal transduction remain unclear. For instance, where this response process takes place and whether any additional members besides PYL are taking part in this signaling process. Here, the GUS‐tagged materials for all Arabidopsis CAR members were used to comprehensively visualize the extensive expression patterns of the CAR family genes. Based on the representativeness of CAR1 in response to ABA, we determined to use it as a target to study the function of CAR proteins in PM‐associated ABA signaling. Single‐particle tracking showed that ABA affected the spatiotemporal dynamics of CAR1. The presence of ABA prolonged the dwell time of CAR1 on the membrane and showed faster lateral mobility. Surprisingly, we verified that CAR1 could directly recruit hypersensitive to ABA1 (HAB1) and SNF1‐related protein kinase 2.2 (SnRK2.2) to the PM at both the bulk and single‐molecule levels. Furthermore, PM localization of CAR1 was demonstrated to be related to membrane microdomains. Collectively, our study revealed that CARs recruited the three main components of ABA signaling to the PM to respond positively to ABA. This study deepens our understanding of ABA signal transduction. [ABSTRACT FROM AUTHOR]

Abstract Understanding the mechanisms underlying amyloid‐β (Aβ) aggregation is pivotal in the context of Alzheimer's disease. This study aims to elucidate the secondary nucleation process of Aβ42 peptides by combining experimental and computational methods. Using a newly developed nanopipette‐based amyloid seeding and translocation assay, confocal fluorescence spectroscopy, and molecular dynamics simulations, the influence of the seed properties on Aβ aggregation is investigated. Both fragmented and unfragmented seeds played distinct roles in the formation of oligomers, with fragmented seeds facilitating the formation of larger aggregates early in the incubation phase. The results show that secondary nucleation leads to the formation of oligomers of various sizes and structures as well as larger fibrils structured in β‐sheets. From these findings a mechanism of secondary nucleation involving two types of aggregate populations, one released and one growing on the mother fiber is proposed.

Optical tweezers are a means to manipulate objects with light. Optical tweezers can obtain a nanometer space, piconewton force, and a millisecond resolution; thus, they are excellently suited for studying biological processes from the single-cell to the single-molecule level. Optical tweezers can screen and manipulate tumor cells, study single molecule, and monitor cancer treatments. Thus, optical tweezers will promote the progress of cancer research and treatments.

Although eicosapentaenoic acid (EPA) as a functional fatty acid has shown significant benefits for human health, its susceptibility to oxidation significantly limits its application. In this study, we developed a nanoemulsion of the lactoferrin (LTF)–EPA complex and conducted a thorough investigation of its macro- and molecular properties. By characterizing the emulsion with different LTF concentrations, we found that 1.0% LTF formed the most stable complex with EPA, which benefited the formation and stability of the emulsion against storage and freezing/thawing treatment. As the foundation block of the emulsion structure, the binding mechanism and the entire dynamic reaction process of the complex have been fully revealed through various molecular simulations and theoretical calculations. This study establishes a comprehensive picture of the LTF–EPA complex across multiple length scales, providing new insights for further applications and productions of its emulsion.

Nanopipettes, as a class of solid-state nanopores, have evolved into universal tools in biomedicine for the detection of biomarkers and different biological analytes. Nanopipette-based methods combine high sensitivity, selectivity, single-molecule resolution, and multifunctionality. The features have significantly expanded interest in their applications for the biomolecular detection, imaging, and molecular diagnostics of real samples. Moreover, the ease of manufacturing nanopipettes, coupled with their compatibility with fluorescence and electrochemical methods, makes them ideal for portable point-of-care diagnostic devices. This review summarized the latest progress in nanopipette-based nanopore technology for the detection of biomarkers, DNA, RNA, proteins, and peptides, in particular β-amyloid or α-synuclein, emphasizing the impact of technology on molecular diagnostics. By addressing key challenges in single-molecule detection and expanding applications in diverse biological areas, nanopipettes are poised to play a transformative role in the future of personalized medicine.

Optical tweezers are a means to manipulate objects with light. Optical tweezers can obtain a nanometer space, piconewton force, and a millisecond resolution; thus, they are excellently suited for studying biological processes from the single-cell to the single-molecule level. Optical tweezers can screen and manipulate tumor cells, study single molecule, and monitor cancer treatments. Thus, optical tweezers will promote the progress of cancer research and treatments. [ABSTRACT FROM AUTHOR]

Due to the ability to perform the parallel measurement of multiple single chains and exert precise control over stretching force in the sub‐nanonewton regime, magnetic tweezers (MT) are a suitable tool to study the individual chain conformations and inherent behaviors of polymers. Herein, we examined the applications of MT in studying single synthetic polymers, distinct from previous reviews focusing on biological polymers such as DNAs. We first presented an overview of the technical aspects of MT, including the imaging setup, the algorithm of three‐dimensional single particle tracking, the configuration of magnets, the calibration and control of magnetic forces, the assembly of flow cells, and the polymer tethering methods. Then, we discussed selected examples highlighting the utilization of MT in studying the chain conformation, mechanical properties, ion and ligands effect, regime transition mechanism, and polymerization dynamics of single synthetic polymers. We envision that MT can serve as a powerful toolbox for delving into the structure–property correlations at the single chain level, which provides quantitative validations for building the theoretical models of synthetic polymers. In the end, we contemplated potential avenues and opportunities for future research in this domain. [ABSTRACT FROM AUTHOR]

G‐quadruplex (G4) is a four‐stranded noncanonical DNA structure that has long been recognized as a potential hindrance to DNA replication. However, how replisomes effectively deal with G4s to avoid replication failure is still obscure. Here, using single‐molecule and ensemble approaches, the consequence of the collision between bacteriophage T7 replisome and an intramolecular G4 located on either the leading or lagging strand is examined. It is found that the adjacent fork junctions induced by G4 formation incur the binding of T7 DNA polymerase (DNAP). In addition to G4, these inactive DNAPs present insuperable obstacles, impeding the progression of DNA synthesis. Nevertheless, T7 helicase can dismantle them and resolve lagging‐strand G4s, paving the way for the advancement of the replication fork. Moreover, with the assistance of the single‐stranded DNA binding protein (SSB) gp2.5, T7 helicase is also capable of maintaining a leading‐strand G4 structure in an unfolded state, allowing for a fraction of T7 DNAPs to synthesize through without collapse. These findings broaden the functional repertoire of a replicative helicase and underscore the inherent G4 tolerance of a replisome. [ABSTRACT FROM AUTHOR]

The cooperative action of the subunits in oligomeric receptors enables fine-tuning of receptor activation, as demonstrated for the regulation of voltage-activated HCN pacemaker ion channels by relating cAMP binding to channel activation in ensemble signals. HCN channels generate electric rhythmicity in specialized brain neurons and cardiomyocytes. There is conflicting evidence on whether binding cooperativity does exist independent of channel activation or not, as recently reported for detergent-solubilized receptors positioned in zero-mode waveguides. Here, we show positive cooperativity in ligand binding to closed HCN2 channels in native cell membranes by following the binding of individual fluorescence-labeled cAMP molecules. Kinetic modeling reveals that the affinity of the still empty binding sites rises with increased degree of occupation and that the transition of the channel to a flip state is promoted accordingly. We conclude that ligand binding to the subunits in closed HCN2 channels not pre-activated by voltage is already cooperative. Hence, cooperativity is not causally linked to channel activation by voltage. Our analysis also shows that single-molecule binding measurements at equilibrium can quantify cooperativity in ligand binding to receptors in native membranes. [ABSTRACT FROM AUTHOR]

Chloroquine has been used as a potent antimalarial, anticancer drug, and prophylactic. While chloroquine is known to interact with DNA, the details of DNA–ligand interactions have remained unclear. Here we characterize chloroquine–double-stranded DNA binding with four complementary approaches, including optical tweezers, atomic force microscopy, duplex DNA melting measurements, and isothermal titration calorimetry. We show that chloroquine intercalates into double stranded DNA (dsDNA) with a KD ~ 200 µM, and this binding is entropically driven. We propose that chloroquine-induced dsDNA intercalation, which happens in the same concentration range as its observed toxic effects on cells, is responsible for the drug's cytotoxicity. [ABSTRACT FROM AUTHOR]

Abstract G‐quadruplex (G4) is a four‐stranded noncanonical DNA structure that has long been recognized as a potential hindrance to DNA replication. However, how replisomes effectively deal with G4s to avoid replication failure is still obscure. Here, using single‐molecule and ensemble approaches, the consequence of the collision between bacteriophage T7 replisome and an intramolecular G4 located on either the leading or lagging strand is examined. It is found that the adjacent fork junctions induced by G4 formation incur the binding of T7 DNA polymerase (DNAP). In addition to G4, these inactive DNAPs present insuperable obstacles, impeding the progression of DNA synthesis. Nevertheless, T7 helicase can dismantle them and resolve lagging‐strand G4s, paving the way for the advancement of the replication fork. Moreover, with the assistance of the single‐stranded DNA binding protein (SSB) gp2.5, T7 helicase is also capable of maintaining a leading‐strand G4 structure in an unfolded state, allowing for a fraction of T7 DNAPs to synthesize through without collapse. These findings broaden the functional repertoire of a replicative helicase and underscore the inherent G4 tolerance of a replisome.

Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement, and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and two-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding, respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/s on extended linear DNA under tension. Processivity and opposing push–pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.

Biological macromolecules, the fundamental building blocks of life, exhibit dynamic structures in their natural environment. Traditional structure determination techniques often oversimplify these multifarious conformational spectra by capturing only ensemble- and time-averaged molecular structures. Addressing this gap, in this work, we extend the application of the single-object scattering sampling (SOSS) method to diverse biological molecules, including RNAs and proteins. Our approach, referred to as "Bio-SOSS", leverages ultrashort X-ray pulses to capture instantaneous structures. In Bio-SOSS, we employ two gold nanoparticles (AuNPs) as labels, which provide strong contrast in the X-ray scattering signal, to ensure precise distance determinations between labeled sites. We generated hypothetical Bio-SOSS images for RNAs, proteins, and an RNA–protein complex, each labeled with two AuNPs at specified positions. Subsequently, to validate the accuracy of Bio-SOSS, we extracted distances between these nanoparticle labels from the images and compared them with the actual values used to generate the Bio-SOSS images. Specifically, for a representative RNA (1KXK), the standard deviation in distance discrepancies between molecular dynamics snapshots and Bio-SOSS retrievals was found to be optimally around 0.2 Å, typically within 1 Å under practical experimental conditions at state-of-the-art X-ray free-electron laser facilities. Furthermore, we conducted an in-depth analysis of how various experimental factors, such as AuNP size, X-ray properties, and detector geometry, influence the accuracy of Bio-SOSS. This comprehensive investigation highlights the practicality and potential of Bio-SOSS in accurately capturing the diverse conformation spectrum of biological macromolecules, paving the way for deeper insights into their dynamic natures. [ABSTRACT FROM AUTHOR]

Previously limited to highly symmetrical homoleptic triple‐helical complexes [Er(Lk)3]3+, where Lk are polyaromatic tridentate ligands, single‐center molecular‐based upconversion using linear optics and exploiting the excited‐state absorption mechanism (ESA) greatly benefits from the design of stable and low‐symmetrical [LkEr(hfa)3] heteroleptic adducts (hfa−=hexafluoroacetylacetonate anion). Depending on (i) the extended π‐electron delocalization, (ii) the flexibility and (iii) the heavy atom effect brought by the bound ligand Lk, the near‐infrared (801 nm) to visible green (542 nm) upconversion quantum yield measured for [LkEr(hfa)3] in solution at room temperature can be boosted by up to three orders of magnitude. [ABSTRACT FROM AUTHOR]

Single-cell multiomics techniques have been widely applied to detect the key signature of cells. These methods have achieved a single-molecule resolution and can even reveal spatial localization. These emerging methods provide insights elucidating the features of genomic, epigenomic and transcriptomic heterogeneity in individual cells. However, they have given rise to new computational challenges in data processing. Here, we describe S ingle- c ell S ingle- m olecule m ultiple O mics P ipeline (ScSmOP), a universal pipeline for barcode-indexed single-cell single-molecule multiomics data analysis. Essentially, the C language is utilized in ScSmOP to set up spaced-seed hash table-based algorithms for barcode identification according to ligation-based barcoding data and synthesis-based barcoding data, followed by data mapping and deconvolution. We demonstrate high reproducibility of data processing between ScSmOP and published pipelines in comprehensive analyses of single-cell omics data (scRNA-seq, scATAC-seq, scARC-seq), single-molecule chromatin interaction data (ChIA-Drop, SPRITE, RD-SPRITE), single-cell single-molecule chromatin interaction data (scSPRITE) and spatial transcriptomic data from various cell types and species. Additionally, ScSmOP shows more rapid performance and is a versatile, efficient, easy-to-use and robust pipeline for single-cell single-molecule multiomics data analysis. [ABSTRACT FROM AUTHOR]

Inhomogeneity in single molecule electron transfer at the surface of lipid in a single vesicle has been explored by single molecule spectroscopic technique. In our study we took Di-methyl aniline (DMA), as the electron donor (D) and three different organic dyes as acceptor. These dyes are C153, C480 and C152 and they reside in different regions in the vesicle depending upon their preference of residence. For each probe, we found fluctuations in the single-molecule fluorescence decay, which are attributed to the variation in the reactivity of interfacial electron transfer. We found a non-exponential auto-correlation fluctuation of the intensity of the probe, which is ascribed to the kinetic disorder in the rate of electron transfer. We have also shown the power law distribution of the dark state (off time), which obeys the levy's statistics. We found a shift in lifetime distribution for the probe (C153) from 3.9 ns to 3.5 ns. This observed quenching is due to the dynamic electron transfer. We observed the kinetic disorderness in the electron transfer reaction for each dye. This source of fluctuation in electron transfer rate may be ascribed to the inherent fluctuation, occurring on the time scale of ~ 1.1 ms (for C153) of the vesicle, containing lipids. [ABSTRACT FROM AUTHOR]

Molecular motion provides a way for biomolecules to mix and interact in living systems. Quantifying their motion is critical to the understanding of how biomolecules perform its function. However, it has been a challenged task to spatially map the fast diffusion of unbound proteins in the heterogenous intracellular environment. Here we reported a new imaging technique named cumulative area based on single-molecule diffusivity mapping (CA-SMdM). The strategy is based on the comparison of single-molecule images between a shorter and longer exposure time. With longer exposure time, molecules will travel further, thus giving more blurred single-molecule images, hence implying its local diffusion rates. We validated our technique through measuring the fast diffusion rates (10–40 µm2/s) of fluorescent dye in glycerol-water mixture, and found the values fit well with Stokes-Einstein equation. We further showed that the spatially mapping of diffusivity in live cells is plausible through CA-SMdM, and it faithfully reported the local diffusivity heterogeneity in cytosol and nucleus. CA-SMdM provides an efficient way to mapping the local molecular motion, and therefore will have profound applications in probing the biomolecular interactions for living systems. [ABSTRACT FROM AUTHOR]

α-synuclein (α-Syn) is a presynaptic protein that is involved in Parkinson's and other neurodegenerative diseases and binds to negatively charged phospholipids. Previously, we reported that α-Syn clusters synthetic proteoliposomes that mimic synaptic vesicles. This vesicle-clustering activity depends on a specific interaction of α-Syn with anionic phospholipids. Here, we report that α-Syn surprisingly also interacts with the neutral phospholipid lysophosphatidylcholine (lysoPC). Even in the absence of anionic lipids, lysoPC facilitates α-Syn-induced vesicle clustering but has no effect on Ca2+-triggered fusion in a single vesicle-vesicle fusion assay. The A30P mutant of α-Syn that causes familial Parkinson disease has a reduced affinity to lysoPC and does not induce vesicle clustering. Taken together, the α-Syn-lysoPC interaction may play a role in α-Syn function. [ABSTRACT FROM AUTHOR]

• A simple method for fluorescently labeling yeast histones and how to re-fold them into H2A-H2B dimers and H3/H4 tetramers. • A labeling strategy for histone sub-complexes. • A method for real-time visualization of nucleosomes on dsDNA. Recent advances in single molecule imaging have allowed the evolution of biochemical techniques that directly visualize protein-DNA interactions in real-time. These techniques rely on diffraction limited total internal reflection microscopy (TIRFM), and have significantly improved our understanding of RNA transcription, DNA replication, homologous recombination, and general DNA repair in the context of chromatin. Here we described a general single molecule TIRFM technique called DNA curtains to directly visualize how enzymes function on chromatinized DNA. The goal of this manuscript is to introduce the reader to methods to express and reconstitute nucleosomes on long stretches of DNA, and to directly visualize this process using DNA curtains with TIRFM. [ABSTRACT FROM AUTHOR]

In this article, we provide an overview of our recent study on light-induced electron emission from single fullerene molecules and subnanometric optical control of their electron emission sites. After depositing molecules on a sharp metallic needle and applying strong electric fields at the apex of the needle, single-molecule protrusions appear on the apex. The electric fields are further enhanced at the protrusions and the enhanced fields drive electron emissions from the single molecules. Single-molecule electron sources can thereby be created. By irradiating such electron sources with light, we observed large modulations in the electron emission patterns. Our simulations revealed that the emission patterns represent molecular orbitals in a single molecule, a mystery scientists have been trying to get to the bottom of for the past 70 years. Our simulations also explain that light-induced modulation is driven by changes in the molecular orbitals that the emitted electrons pass through. In effect, we realize that there are subnanometric modulations in electron emission sites [ABSTRACT FROM AUTHOR]

Mechanical forces play a vital role in biological processes at molecular and cellular levels, significantly impacting various diseases such as cancer, cardiovascular disease, and COVID-19. Recent advancements in dynamic force spectroscopy (DFS) techniques have enabled the application and measurement of forces and displacements with high resolutions, providing crucial insights into the mechanical pathways underlying these diseases. Among DFS techniques, the biomembrane force probe (BFP) stands out for its ability to measure bond kinetics and cellular mechanosensing with pico-newton and nano-meter resolutions. Here, a comprehensive overview of the classical BFP-DFS setup is presented and key advancements are emphasized, including the development of dual biomembrane force probe (dBFP) and fluorescence biomembrane force probe (fBFP). BFP-DFS allows us to investigate dynamic bond behaviors on living cells and significantly enhances the understanding of specific ligand-receptor axes mediated cell mechanosensing. The contributions of BFP-DFS to the fields of cancer biology, thrombosis, and inflammation are delved into, exploring its potential to elucidate novel therapeutic discoveries. Furthermore, future BFP upgrades aimed at improving output and feasibility are anticipated, emphasizing its growing importance in the field of cell mechanobiology. Although BFP-DFS remains a niche research modality, its impact on the expanding field of cell mechanobiology is immense. [ABSTRACT FROM AUTHOR]

Summary: The epidermal growth factor receptor (EGFR) is a poster child for the understanding of receptor behaviour, and of paramount importance to cell function and human health. Cloned almost forty years ago, the interest in EGFR's structure/function relationships remains unabated, not least because changes in oncogenic EGFR mutants are key drivers of the formation of lung and brain tumours. The structure of the assemblies formed by EGFR have been comprehensibly investigated by techniques such as high‐resolution X‐ray crystallography, NMR and all‐atom molecular dynamics (MD) simulations. However, the complexity embedded in the portfolio of EGFR states that are only possible in the physiological environment of cells has often proved refractory to cell‐free structural methods. Conversely, some key inroads made by quantitative fluorescence microscopy and super‐resolution have depended on exploiting the wealth of structures available. Here, a brief personal perspective is provided on how quantitative fluorescence microscopy and super‐resolution methods have cross‐fertilised with cell‐free‐derived EGFR structural information. I primarily discuss areas in which my research group has made a contribution to fill gaps in EGFR's cellular structural biology and towards developing new tools to investigate macromolecular assemblies in cells. [ABSTRACT FROM AUTHOR]

Base excision repair (BER) is a cellular process that removes damaged bases arising from exogenous and endogenous sources including reactive oxygen species, alkylation agents, and ionizing radiation. BER is mediated by the actions of multiple proteins which work in a highly concerted manner to resolve DNA damage efficiently to prevent toxic repair intermediates. During the initiation of BER, the damaged base is removed by one of 11 mammalian DNA glycosylases, resulting in abasic sites. Many DNA glycosylases are product-inhibited by binding to the abasic site more avidly than the damaged base. Traditionally, apurinic/apyrimidinic endonuclease 1, APE1, was believed to help turn over the glycosylases to undergo multiple rounds of damaged base removal. However, in a series of papers from our laboratory, we have demonstrated that UV-damaged DNA binding protein (UV-DDB) stimulates the glycosylase activities of human 8-oxoguanine glycosylase (OGG1), MUTY DNA glycosylase (MUTYH), alkyladenine glycosylase/N-methylpurine DNA glycosylase (AAG/MPG), and single-strand selective monofunctional glycosylase (SMUG1), between three- and five-fold. Moreover, we have shown that UV-DDB can assist chromatin decompaction, facilitating access of OGG1 to 8-oxoguanine damage in telomeres. This review summarizes the biochemistry, single-molecule, and cell biology approaches that our group used to directly demonstrate the essential role of UV-DDB in BER. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Clinical-grade preparations of adeno-associated virus (AAV) vectors used for gene therapy typically undergo a series of diagnostics to determine titer, purity, homogeneity, and the presence of DNA contaminants. One type of contaminant that remains poorly investigated is replication-competent (rc)AAVs. rcAAVs form through recombination of DNA originating from production materials, yielding intact, replicative, and potentially infectious virus-like virions. They can be detected through the serial passaging of lysates from cells transduced by AAV vectors in the presence of wildtype adenovirus. Cellular lysates from the last passage are subjected to qPCR to detect the presence of the rep gene. Unfortunately, the method cannot be used to query the diversity of recombination events, nor can qPCR provide insights into how rcAAVs arise. Thus, the formation of rcAAVs through errant recombination events between ITR-flanked gene of interest (GOI) constructs and expression constructs carrying the rep-cap genes is poorly described. We have used single molecule, real-time sequencing (SMRT) to analyze virus-like genomes expanded from rcAAV-positive vector preparations. We present evidence that sequence-independent and non-homologous recombination between the ITR-bearing transgene and the rep/cap plasmid occurs under several events and rcAAVs spawn from diverse clones. [ABSTRACT FROM AUTHOR]

The charge transport through single‐molecule electronic devices can be controlled mechanically by changing the molecular geometrical configuration in situ, but the tunable conductance range is typically less than two orders of magnitude. Herein, we proposed a new mechanical tuning strategy to control the charge transport through the single‐molecule junctions via switching quantum interference patterns. By designing molecules with multiple anchoring groups, we switched the electron transport between the constructive quantum interference (CQI) pathway and the destructive quantum interference (DQI) pathway, and more than four orders of magnitude conductance variation can be achieved by shifting the electrodes in a range of about 0.6 nm, which is the highest conductance range ever achieved using mechanical tuning. [ABSTRACT FROM AUTHOR]

Abstract Mechanical forces play a vital role in biological processes at molecular and cellular levels, significantly impacting various diseases such as cancer, cardiovascular disease, and COVID‐19. Recent advancements in dynamic force spectroscopy (DFS) techniques have enabled the application and measurement of forces and displacements with high resolutions, providing crucial insights into the mechanical pathways underlying these diseases. Among DFS techniques, the biomembrane force probe (BFP) stands out for its ability to measure bond kinetics and cellular mechanosensing with pico‐newton and nano‐meter resolutions. Here, a comprehensive overview of the classical BFP‐DFS setup is presented and key advancements are emphasized, including the development of dual biomembrane force probe (dBFP) and fluorescence biomembrane force probe (fBFP). BFP‐DFS allows us to investigate dynamic bond behaviors on living cells and significantly enhances the understanding of specific ligand‐receptor axes mediated cell mechanosensing. The contributions of BFP‐DFS to the fields of cancer biology, thrombosis, and inflammation are delved into, exploring its potential to elucidate novel therapeutic discoveries. Furthermore, future BFP upgrades aimed at improving output and feasibility are anticipated, emphasizing its growing importance in the field of cell mechanobiology. Although BFP‐DFS remains a niche research modality, its impact on the expanding field of cell mechanobiology is immense.