Recent Advances in Biological Single-Molecule Applications of Optical Tweezers and Fluorescence Microscopy

Effect of photoconversion conditions on the spectral and cytotoxic properties of photoconvertible fluorescent polymer markers

Fluorescence labeling of cells is a versatile tool used to study cell behavior, which is of significant importance in biomedical sciences. Fluorescent photoconvertible markers based on polymer microcapsules have been recently considered as efficient and perspective ones for long-term tracking of individual cells. However, the dependence of photoconversion conditions on the polymeric capsule structure is still not sufficiently clear. Here, we have studied the structural and spectral properties of fluorescent photoconvertible polymeric microcapsules doped with Rhodamine B and irradiated using a pulsed laser in various regimes, and shown the dependence between the photoconversion degree and laser irradiation intensity. The effect of microcapsule composition on the photoconversion process was studied by monitoring structural changes in the initial and photoconverted microcapsules using X-ray diffraction analysis with synchrotron radiation source, and Fourier transform infrared, Raman and fluorescence spectroscopy. We demonstrated good biocompatibility of free-administered initial and photoconverted microcapsules through long-term monitoring of the RAW 264.7 monocyte/macrophage cells with unchanged viability. These data open new perspectives for using the developed markers as safe and precise cell labels with switchable fluorescent properties.

Elucidating the novel mechanisms of molecular chaperones by single-molecule technologies

Molecular chaperones play central roles in sustaining protein homeostasis and preventing protein aggregation. Most studies of these systems have been performed in bulk, providing averaged measurements, though recent single-molecule approaches have provided an in-depth understanding of the molecular mechanisms of their activities and structural rearrangements during substrate recognition. Chaperone activities have been observed to be substrate specific, with some associated with ATP-dependent structural dynamics and others via interactions with co-chaperones. This Review aims to describe the novel mechanisms of molecular chaperones as revealed by single-molecule approaches, and to provide insights into their functioning and its implications for protein homeostasis and human diseases.

The Histone Chaperones SET/TAF-1β and NPM1 Exhibit Conserved Functionality in Nucleosome Remodeling and Histone Eviction in a Cytochrome c-Dependent Manner

Chromatin homeostasis mediates essential processes in eukaryotes, where histone chaperones have emerged as major regulatory factors during DNA replication, repair, and transcription. The dynamic nature of these processes, however, has severely impeded their characterization at the molecular level. Here, fluorescence optical tweezers are applied to follow histone chaperone dynamics in real time. The molecular action of SET/template-activating factor-Iβ and nucleophosmin 1-representing the two most common histone chaperone folds-are examined using both nucleosomes and isolated histones. It is shown that these chaperones present binding specificity for fully dismantled nucleosomes and are able to recognize and disrupt non-native histone-DNA interactions. Furthermore, the histone eviction process and its modulation by cytochrome c are scrutinized. This approach shows that despite the different structures of these chaperones, they present conserved modes of action mediating nucleosome remodeling.

A Review of Single-Cell Microrobots: Classification, Driving Methods and Applications

Single-cell microrobots are new microartificial devices that use a combination of single cells and artificial devices, with the advantages of small size, easy degradation and ease of manufacture. With externally driven strategies such as light fields, sound fields and magnetic fields, microrobots are able to carry out precise micromanipulations and movements in complex microenvironments. Therefore, single-cell microrobots have received more and more attention and have been greatly developed in recent years. In this paper, we review the main classifications, control methods and recent advances in the field of single-cell microrobot applications. First, different types of robots, such as cell-based microrobots, bacteria-based microrobots, algae-based microrobots, etc., and their design strategies and fabrication processes are discussed separately. Next, three types of external field-driven technologies, optical, acoustic and magnetic, are presented and operations realized in vivo and in vitro by applying these three technologies are described. Subsequently, the results achieved by these robots in the fields of precise delivery, minimally invasive therapy are analyzed. Finally, a short summary is given and current challenges and future work on microbial-based robotics are discussed.

Velocity and Out-Step Frequencies for a Micro-Swimmer Based on Spiral Carbon Nanotubes

The existing producing processes of micro spiral swimmers are complex. Here, a microswimmer with a magnetic layer on the surface of the spiral carbon nanotubes is proposed, which has a simple producing process. For the microswimmer, its equations of the velocities and out-step frequency are deduced. Using these equations, the velocities and out-step frequency of the microswimmer and their changes with related parameters are investigated. Results show that its velocities are proportional to the radius and helix angle of the spiral carbon nanotubes, and its out-step frequencies are proportional to magnetic field strength, the helix angle and magnetic layer thicknesses of the spiral carbon nanotubes, and inversely proportional to the fluid viscosity. The out-step frequency of the microswimmer is measured, which is in good agreement with the calculative ones.

Differential dynamics specify MeCP2 function at methylated DNA and nucleosomes

Methyl-CpG-binding protein 2 (MeCP2) is an essential chromatin-binding protein whose mutations cause Rett syndrome (RTT), a leading cause of monogenic intellectual disabilities in females. Despite its significant biomedical relevance, the mechanism by which MeCP2 navigates the chromatin epigenetic landscape to regulate chromatin structure and gene expression remains unclear. Here, we used correlative single-molecule fluorescence and force microscopy to directly visualize the distribution and dynamics of MeCP2 on a variety of DNA and chromatin substrates. We found that MeCP2 exhibits differential diffusion dynamics when bound to unmethylated and methylated bare DNA. Moreover, we discovered that MeCP2 preferentially binds nucleosomes within the context of chromatinized DNA and stabilizes them from mechanical perturbation. The distinct behaviors of MeCP2 at bare DNA and nucleosomes also specify its ability to recruit TBLR1, a core component of the NCoR1/2 co-repressor complex. We further examined several RTT mutations and found that they disrupt different aspects of the MeCP2-chromatin interaction, rationalizing the heterogeneous nature of the disease. Our work reveals the biophysical basis for MeCP2's methylation-dependent activities and suggests a nucleosome-centric model for its genomic distribution and gene repressive functions. These insights provide a framework for delineating the multifaceted functions of MeCP2 and aid in our understanding of the molecular mechanisms of RTT.

Fluorescent polymer markers photoconvertible with a 532 nm laser for individual cell labeling

Fluorescent photoconvertible materials and molecules have been successfully exploited as bioimaging markers and cell trackers. Recently, the novel fluorescent photoconvertible polymer markers have been developed that allow the long-term tracking of individual labeled cells. However, it is still necessary to study the functionality of this type of fluorescent labels for various operating conditions, in particular for commonly used discrete wavelength lasers. In this article, the photoconversion of fluorescent polymer labels with both pulsed and continuous-wave lasers with 532 nm-irradiation wavelength, and under different laser power densities were studied. The photoconversion process was described and its possible mechanism was proposed. The peculiarities of fluorescent polymer capsules performance as an aqueous suspension and as a single capsule were described. We performed the successful nondestructivity marker photoconversion inside RAW 264.7 monocyte/macrophage cells under continuous-wave laser with 532 nm-irradiation wavelength, showing prospects of these fluorescent markers for long-term live cell labeling.

Theoretical Analysis and Experimental Verification of the Influence of Polarization on Counter-Propagating Optical Tweezers

Counter-propagating optical tweezers are experimental platforms for the frontier exploration of science and precision measurement. The polarization of the trapping beams significantly affects the trapping status. Using the T-matrix method, we numerically analyzed the optical force distribution and the resonant frequency of counter-propagating optical tweezers in different polarizations. We also verified the theoretical result by comparing it with the experimentally observed resonant frequency. Our analysis shows that polarization has little influence on the radial axis motion, while the axial axis force distribution and the resonant frequency are sensitive to polarization change. Our work can be used in designing harmonic oscillators which can change their stiffness conveniently, and monitoring polarization in counter-propagating optical tweezers.

Unravelling 3D Dynamics and Hydrodynamics during Incorporation of Dielectric Particles to an Optical Trapping Site

Mapping of the spatial and temporal motion of particles inside an optical field is critical for understanding and further improvement of the 3D spatio-temporal control over their optical trapping dynamics. However, it is not trivial to capture the 3D motion, and most imaging systems only capture a 2D projection of the 3D motion, in which the information about the axial movement is not directly available. In this work, we resolve the 3D incorporation trajectories of 200 nm fluorescent polystyrene particles in an optical trapping site under different optical experimental conditions using a recently developed widefield multiplane microscope (imaging volume of 50 × 50 × 4 μm3). The particles are gathered at the focus following some preferential 3D channels that show a shallow cone distribution. We demonstrate that the radial and the axial flow speed components depend on the axial distance from the focus, which is directly related to the scattering/gradient optical forces. While particle velocities and trajectories are mainly determined by the trapping laser profile, they cannot be completely explained without considering collective effects resulting from hydrodynamic forces.

Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers

Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.

Optical trapping and fluorescence control with vectorial structured light

Here we functionalized micro-scaled polymer beads with nano-scaled quantum dots and demonstrate optical trapping and tweezing, with in-situ fluorescence measurement, in an all-digital all-optical configuration. We outline the chemistry required to facilitate this, from deactivating the optical trapping environment to size, adhesion and agglomeration control. We introduce a novel holographic optical trapping set-up that leverages on vectorially structured light, allowing for the delivery of tuneable forms of light from purely scalar to purely vector, including propagation invariant flat-top beams for uniform illumination and tailored intensity gradient landscapes. Finally, we show how this has the potential to quench bleaching in a single wavelength trap by linear (spatial mode) rather than non-linear effects, advancing the nascent field of optics for chemistry.

Stochastically multimerized ParB orchestrates DNA assembly as unveiled by single-molecule analysis

The tripartite ParABS system mediates chromosome segregation in a wide range of bacteria. Dimeric ParB was proposed to nucleate on parS sites and spread to neighboring DNA. However, how properly distributed ParB dimers further compact chromosomal DNA into a higher-order nucleoprotein complex for partitioning remains poorly understood. Here, using a single-molecule approach, we show that tens of Bacillus subtilis ParB (Spo0J) proteins can stochastically multimerize on and stably bind to nonspecific DNA. The introduction of CTP promotes the formation and diffusion of the multimeric ParB along DNA, offering an opportunity for ParB proteins to further forgather and cluster. Intriguingly, ParB multimers can recognize parS motifs and are more inclined to remain immobile on them. Importantly, the ParB multimer features distinct capabilities of not only bridging two independent DNA molecules but also mediating their transportation, both of which are enhanced by the presence of either CTP or parS in the DNA. These findings shed new light on ParB dynamics in self-multimerization and DNA organization and help to better comprehend the assembly of the ParB-DNA partition complex.

Localized Nanopore Fabrication via Controlled Breakdown

Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.

POTATO: Automated pipeline for batch analysis of optical tweezers data

Optical tweezers are a single-molecule technique that allows probing of intra- and intermolecular interactions that govern complex biological processes involving molecular motors, protein-nucleic acid interactions, and protein/RNA folding. Recent developments in instrumentation eased and accelerated optical tweezers data acquisition, but analysis of the data remains challenging. Here, to enable high-throughput data analysis, we developed an automated python-based analysis pipeline called POTATO (practical optical tweezers analysis tool). POTATO automatically processes the high-frequency raw data generated by force-ramp experiments and identifies (un)folding events using predefined parameters. After segmentation of the force-distance trajectories at the identified (un)folding events, sections of the curve can be fitted independently to a worm-like chain and freely jointed chain models, and the work applied on the molecule can be calculated by numerical integration. Furthermore, the tool allows plotting of constant force data and fitting of the Gaussian distance distribution over time. All these features are wrapped in a user-friendly graphical interface, which allows researchers without programming knowledge to perform sophisticated data analysis.

Implementation of 3D Multi-Color Fluorescence Microscopy in a Quadruple Trap Optical Tweezers System

Recent advances in the design and measurement capabilities of optical tweezers instruments, and especially the combination with multi-color fluorescence detection, have accommodated a dramatic increase in the versatility of optical trapping. Quadruple (Q)-trap optical tweezers are an excellent example of such an advance, by providing three-dimensional control over two constructs and thereby enabling for example DNA-DNA braiding. However, the implementation of fluorescence detection in such a Q-trapping system poses several challenges: (1) since typical samples span a distance in the order of tens of micrometers, it requires imaging of a large field of view, (2) in order to capture fast molecular dynamics, fast imaging with single-molecule sensitivity is desired, (3) in order to study three-dimensional objects, it could be needed to detect emission light at different axial heights while keeping the objective lens and thus the optically trapped microspheres in a fixed position. In this chapter, we describe design guidelines for a fluorescence imaging module on a Q-trap system that overcomes these challenges and provide a step-by-step description for construction and alignment of such a system. Finally, we present detailed instructions for proof-of-concept experiments that can be used to validate and highlight the capabilities of the instruments.

Virus self-assembly proceeds through contact-rich energy minima

Self-assembly of supramolecular complexes such as viral capsids occurs prominently in nature. Nonetheless, the mechanisms underlying these processes remain poorly understood. Here, we uncover the assembly pathway of hepatitis B virus (HBV), applying fluorescence optical tweezers and high-speed atomic force microscopy. This allows tracking the assembly process in real time with single-molecule resolution. Our results identify a specific, contact-rich pentameric arrangement of HBV capsid proteins as a key on-path assembly intermediate and reveal the energy balance of the self-assembly process. Real-time nucleic acid packaging experiments show that a free energy change of ~1.4 k_BT per condensed nucleotide is used to drive protein oligomerization. The finding that HBV assembly occurs via contact-rich energy minima has implications for our understanding of the assembly of HBV and other viruses and also for the development of new antiviral strategies and the rational design of self-assembling nanomaterials.

In vitro single-molecule manipulation studies of viral DNA replication

Faithfull replication of genomic information relies on the coordinated activity of the multi-protein machinery known as the replisome. Several constituents of the replisome operate as molecular motors that couple thermal and chemical energy to a mechanical task. Over the last few decades, in vitro single-molecule manipulation techniques have been used to monitor and manipulate mechanically the activities of individual molecular motors involved in DNA replication with nanometer, millisecond, and picoNewton resolutions. These studies have uncovered the real-time kinetics of operation of these biological systems, the nature of their transient intermediates, and the processes by which they convert energy to work (mechano-chemistry), ultimately providing new insights into their inner workings of operation not accessible by ensemble assays. In this chapter, we describe two of the most widely used single-molecule manipulation techniques for the study of DNA replication, optical and magnetic tweezers, and their application in the study of the activities of proteins involved in viral DNA replication.

Elucidating Protein Translocon Dynamics with Single-Molecule Precision

Translocons are protein assemblies that facilitate the targeting and transport of proteins into and across biological membranes. Our understanding of these systems has been advanced using genetics, biochemistry, and structural biology. Despite these classic advances, until recently we have still largely lacked a detailed understanding of how translocons recognize and facilitate protein translocation. With the advent and improvements of cryogenic electron microscopy (cryo-EM) single-particle analysis and single-molecule fluorescence microscopy, the details of how translocons function are finally emerging. Here, we introduce these methods and evaluate their importance in understanding translocon structure, function, and dynamics.

DNA replication machinery: Insights from in vitro single-molecule approaches

The replisome is the multiprotein molecular machinery that replicates DNA. The replisome components work in precise coordination to unwind the double helix of the DNA and replicate the two strands simultaneously. The study of DNA replication using in vitro single-molecule approaches provides a novel quantitative understanding of the dynamics and mechanical principles that govern the operation of the replisome and its components. ‘Classical’ ensemble-averaging methods cannot obtain this information. Here we describe the main findings obtained with in vitro single-molecule methods on the performance of individual replisome components and reconstituted prokaryotic and eukaryotic replisomes. The emerging picture from these studies is that of stochastic, versatile and highly dynamic replisome machinery in which transient protein-protein and protein-DNA associations are responsible for robust DNA replication.

From folding to function: complex macromolecular reactions unraveled one-by-one with optical tweezers

Single-molecule manipulation with optical tweezers has uncovered macromolecular behaviour hidden to other experimental techniques. Recent instrumental improvements have made it possible to expand the range of systems accessible to optical tweezers. Beyond focusing on the folding and structural changes of isolated single molecules, optical tweezers studies have evolved into unraveling the basic principles of complex molecular processes such as co-translational folding on the ribosome, kinase activation dynamics, ligand-receptor binding, chaperone-assisted protein folding, and even dynamics of intrinsically disordered proteins (IDPs). In this mini-review, we illustrate the methodological principles of optical tweezers before highlighting recent advances in studying complex protein conformational dynamics - from protein synthesis to physiological function - as well as emerging future issues that are beginning to be addressed with novel approaches.

Optical Biosensors for Virus Detection: Prospects for SARS-CoV-2/COVID-19

The recent pandemic of the novel coronavirus disease 2019 (COVID-19) has caused huge worldwide disruption due to the lack of available testing locations and equipment. The use of optical techniques for viral detection has flourished in the past 15 years, providing more reliable, inexpensive, and accurate detection methods. In the current minireview, optical phenomena including fluorescence, surface plasmons, surface-enhanced Raman scattering (SERS), and colorimetry are discussed in the context of detecting virus pathogens. The sensitivity of a viral detection method can be dramatically improved by using materials that exhibit surface plasmons or SERS, but often this requires advanced instrumentation for detection. Although fluorescence and colorimetry lack high sensitivity, they show promise as point-of-care diagnostics because of their relatively less complicated instrumentation, ease of use, lower costs, and the fact that they do not require nucleic acid amplification. The advantages and disadvantages of each optical detection method are presented, and prospects for applying optical biosensors in COVID-19 detection are discussed.

Single Cell Reactomics: Real-Time Single-Cell Activation Kinetics of Optically Trapped Macrophages

Macrophages are well known for their role in immune responses and tissue homeostasis. They can polarize towards various phenotypes in response to biophysical and biochemical stimuli. However, little is known about the early kinetics of macrophage polarization in response to single biophysical or biochemical stimuli. Our approach, combining optical tweezers, confocal fluorescence microscopy, and microfluidics, allows us to isolate single macrophages and follow their immediate responses to a biochemical stimulus in real-time. This strategy enables live-cell imaging at high spatiotemporal resolution and omits surface adhesion and cell-cell contact as biophysical stimuli. The approach is validated by successfully following the early phase of an oxidative stress response of macrophages upon phorbol 12-myristate 13-acetate (PMA) stimulation, allowing detailed analysis of the initial macrophage response upon a single biochemical stimulus within seconds after its application, thereby eliminating delay times introduced by other techniques during the stimulation procedure. Hence, an unprecedented view of the early kinetics of macrophage polarization is provided.

Determining Trap Compliances, Microsphere Size Variations, and Response Linearities in Single DNA Molecule Elasticity Measurements with Optical Tweezers

We previously introduced the use of DNA molecules for calibration of biophysical force and displacement measurements with optical tweezers. Force and length scale factors can be determined from measurements of DNA stretching. Trap compliance can be determined by fitting the data to a nonlinear DNA elasticity model, however, noise/drift/offsets in the measurement can affect the reliability of this determination. Here we demonstrate a more robust method that uses a linear approximation for DNA elasticity applied to high force range (25-45 pN) data. We show that this method can be used to assess how small variations in microsphere sizes affect DNA length measurements and demonstrate methods for correcting for these errors. We further show that these measurements can be used to check assumed linearities of system responses. Finally, we demonstrate methods combining microsphere imaging and DNA stretching to check the compliance and positioning of individual traps.

Electro-opening of a microtubule lattice in silico

Modulation of the structure and function of biomaterials is essential for advancing bio-nanotechnology and biomedicine. Microtubules (MTs) are self-assembled protein polymers that are essential for fundamental cellular processes and key model compounds for the design of active bio-nanomaterials. In this in silico study, a 0.5 μs-long all-atom molecular dynamics simulation of a complete MT with approximately 1.2 million atoms in the system indicated that a nanosecond-scale intense electric field can induce the longitudinal opening of the cylindrical shell of the MT lattice, modifying the structure of the MT. This effect is field-strength- and temperature-dependent and occurs on the cathode side. A model was formulated to explain the opening on the cathode side, which resulted from an electric-field-induced imbalance between electric torque on tubulin dipoles and cohesive forces between tubulin heterodimers. Our results open new avenues for electromagnetic modulation of biological and artificial materials through action on noncovalent molecular interactions.

Cutting-Edge Single-Molecule Technologies Unveil New Mechanics in Cellular Biochemistry

Single-molecule technologies have expanded our ability to detect biological events individually, in contrast to ensemble biophysical technologies, where the result provides averaged information. Recent developments in atomic force microscopy have not only enabled us to distinguish the heterogeneous phenomena of individual molecules, but also allowed us to view up to the resolution of a single covalent bond. Similarly, optical tweezers, due to their versatility and precision, have emerged as a potent technique to dissect a diverse range of complex biological processes, from the nanomechanics of ClpXP protease-dependent degradation to force-dependent processivity of motor proteins. Despite the advantages of optical tweezers, the time scales used in this technology were inconsistent with physiological scenarios, which led to the development of magnetic tweezers, where proteins are covalently linked with the glass surface, which in turn increases the observation window of a single biomolecule from minutes to weeks. Unlike optical tweezers, magnetic tweezers use magnetic fields to impose torque, which makes them convenient for studying DNA topology and topoisomerase functioning. Using modified magnetic tweezers, researchers were able to discover the mechanical role of chaperones, which support their substrate proteinsby pulling them during translocation and assist their native folding as a mechanical foldase. In this article, we provide a focused review of many of these new roles of single-molecule technologies, ranging from single bond breaking to complex chaperone machinery, along with the potential to design mechanomedicine, which would be a breakthrough in pharmacological interventions against many diseases.

Genome-in-a-Box: Building a Chromosome from the Bottom Up

Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics, which we briefly review. While these technologies have yielded a wealth of data, such studies still leave a significant gap between top-down experiments on live cells and bottom-up in vitro single-molecule studies of DNA-protein interactions. Here, we introduce "genome-in-a-box" (GenBox) as an alternative in vitro approach to build and study chromosomes, which bridges this gap. The concept is to assemble a chromosome from the bottom up by taking deproteinated genome-sized DNA isolated from live cells and subsequently add purified DNA-organizing elements, followed by encapsulation in cell-sized containers using microfluidics. Grounded in the rationale of synthetic cell research, the approach would enable to experimentally study emergent effects at the global genome level that arise from the collective action of local DNA-structuring elements. We review the various DNA-structuring elements present in nature, from nucleoid-associated proteins and SMC complexes to phase separation and macromolecular crowders. Finally, we discuss how GenBox can contribute to several open questions on chromosome structure and dynamics.

Physics of viral dynamics

Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.

Aminophenyl chalcones potentiating antibiotic activity and inhibiting bacterial efflux pump

Chalcones and their derivatives are substances of great interest for medicinal chemistry due to their antibacterial activities. As the bacterial resistance to clinically available antibiotics has become a worldwide public health problem, it is essential to search for compounds capable of reverting the bacterial resistance. As a possibility, the chalcone class could be an interesting answer to this problem. The chalcones (2E)-1-(4'-aminophenyl)-3-(phenyl)‑prop-2-en-1-one (APCHAL), and (2E)-1-(4'-aminophenyl)-3-(4-chlorophenyl)‑prop-2-en-1-one (ACLOPHENYL) were synthesized by the Claisen-Schmidt condensation and characterized by ¹H and ¹³C nuclear magnetic resonance (NMR), Fourier-transform infrared (FT-IR), and mass spectrometry (MS), In addition, microbiological tests were performed to investigate the antibacterial activity, modulatory potential, and efflux pump inhibition against Staphylococcus aureus (S. aureus) multi-resistant strains. Regarding the S. aureus Gram-positive model, the APCHAL presented synergism with gentamicin and antagonism with penicillin. APCHAL reduced the Minimum inhibitory concentration (MIC) of gentamicin by almost 70%. When comparing the effects of the antibiotic modifying activity of ACLOPHENYL and APCHAL, a loss of synergism is noted with gentamicin due to the addition of a chlorine to the substance structure. For Escherichia coli (E. coli) a total lack of effect, synergistic or antagonistic, was observed between ACLOPHENYL and the antibiotics. In the evaluation of inhibition of the efflux pump, both chalcones presented a synergistic effect with norfloxacin and ciprofloxacin against S. aureus, although the effect is much less pronounced with ACLOPHENYL. The effect of APCHAL is particularly notable against the K2068 (MepA overexpresser) strain, with synergistic effects with both ciprofloxacin and ethidium bromide. The docking results also show that both compounds bind to roughly the same region of the binding site of 1199B (NorA overexpresser), and that this region overlaps with the preferred binding region of norfloxacin. The APCHAL chalcone may contribute to the prevention or treatment of infectious diseases caused by multidrug-resistant S. aureus.

Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin

Polycomb repressive complex 2 (PRC2) installs and spreads repressive histone methylation marks on eukaryotic chromosomes. Because of the key roles that PRC2 plays in development and disease, how this epigenetic machinery interacts with DNA and nucleosomes is of major interest. Nonetheless, the mechanism by which PRC2 engages with native-like chromatin remains incompletely understood. In this work, we employ single-molecule force spectroscopy and molecular dynamics simulations to dissect the behavior of PRC2 on polynucleosome arrays. Our results reveal an unexpectedly diverse repertoire of PRC2 binding configurations on chromatin. Besides reproducing known binding modes in which PRC2 interacts with bare DNA, mononucleosomes, and adjacent nucleosome pairs, our data also provide direct evidence that PRC2 can bridge pairs of distal nucleosomes. In particular, the "1-3" bridging mode, in which PRC2 engages two nucleosomes separated by one spacer nucleosome, is a preferred low-energy configuration. Moreover, we show that the distribution and stability of different PRC2-chromatin interaction modes are modulated by accessory subunits, oncogenic histone mutations, and the methylation state of chromatin. Overall, these findings have implications for the mechanism by which PRC2 spreads histone modifications and compacts chromatin. The experimental and computational platforms developed here provide a framework for understanding the molecular basis of epigenetic maintenance mediated by Polycomb-group proteins.

Molecular mechanism for direct actin force-sensing by α-catenin

The actin cytoskeleton mediates mechanical coupling between cells and their tissue microenvironments. The architecture and composition of actin networks are modulated by force; however, it is unclear how interactions between actin filaments (F-actin) and associated proteins are mechanically regulated. Here we employ both optical trapping and biochemical reconstitution with myosin motor proteins to show single piconewton forces applied solely to F-actin enhance binding by the human version of the essential cell-cell adhesion protein αE-catenin but not its homolog vinculin. Cryo-electron microscopy structures of both proteins bound to F-actin reveal unique rearrangements that facilitate their flexible C-termini refolding to engage distinct interfaces. Truncating α-catenin’s C-terminus eliminates force-activated F-actin binding, and addition of this motif to vinculin confers force-activated binding, demonstrating that α-catenin’s C-terminus is a modular detector of F-actin tension. Our studies establish that piconewton force on F-actin can enhance partner binding, which we propose mechanically regulates cellular adhesion through α-catenin.

All of the cells in our bodies rely on cues from their surrounding environment to alter their behavior. As well sending each other chemical signals, such as hormones, cells can also detect pressure and physical forces applied by the cells around them. These physical interactions are coordinated by a network of proteins called the cytoskeleton, which provide the internal scaffold that maintains a cell’s shape. However, it is not well understood how forces transmitted through the cytoskeleton are converted into mechanical signals that control cell behavior.

The cytoskeleton is primarily made up protein filaments called actin, which are frequently under tension from external and internal forces that push and pull on the cell. Many proteins bind directly to actin, including adhesion proteins that allow the cell to ‘stick’ to its surroundings. One possibility is that when actin filaments feel tension, they convert this into a mechanical signal by altering how they bind to other proteins.

To test this theory, Mei et al. isolated and studied an adhesion protein called α-catenin which is known to interact with actin. This revealed that when tiny forces – similar to the amount cells experience in the body – were applied to actin filaments, this caused α-catenin and actin to bind together more strongly. However, applying the same level of physical force did not alter how well actin bound to a similar adhesion protein called vinculin. Further experiments showed that this was due to differences in a small, flexible region found on both proteins. Manipulating this region revealed that it helps α-catenin attach to actin when a force is present, and was thus named a ‘force detector’.

Proteins that bind to actin are essential in all animals, making it likely that force detectors are a common mechanism. Scientists can now use this discovery to identify and manipulate force detectors in other proteins across different cells and animals. This may help to develop drugs that target the mechanical signaling process, although this will require further understanding of how force detectors work at the molecular level.

Recent Advances on the Model, Measurement Technique, and Application of Single Cell Mechanics

Since the cell was discovered by humans, it has been an important research subject for researchers. The mechanical response of cells to external stimuli and the biomechanical response inside cells are of great significance for maintaining the life activities of cells. These biomechanical behaviors have wide applications in the fields of disease research and micromanipulation. In order to study the mechanical behavior of single cells, various cell mechanics models have been proposed. In addition, the measurement technologies of single cells have been greatly developed. These models, combined with experimental techniques, can effectively explain the biomechanical behavior and reaction mechanism of cells. In this review, we first introduce the basic concept and biomechanical background of cells, then summarize the research progress of internal force models and experimental techniques in the field of cell mechanics and discuss the latest mechanical models and experimental methods. We summarize the application directions of cell mechanics and put forward the future perspectives of a cell mechanics model.

Replication Fork Activation Is Enabled by a Single-Stranded DNA Gate in CMG Helicase

The eukaryotic replicative helicase CMG is a closed ring around double-stranded (ds)DNA at origins yet must transition to single-stranded (ss)DNA for helicase action. CMG must also handle repair intermediates, such as reversed forks that lack ssDNA. Here, using correlative single-molecule fluorescence and force microscopy, we show that CMG harbors a ssDNA gate that enables transitions between ss and dsDNA. When coupled to DNA polymerase, CMG remains on ssDNA, but when uncoupled, CMG employs this gate to traverse forked junctions onto dsDNA. Surprisingly, CMG undergoes rapid diffusion on dsDNA and can transition back onto ssDNA to nucleate a functional replisome. The gate-distinct from that between Mcm2/5 used for origin loading-is intrinsic to CMG; however, Mcm10 promotes strand passage by enhancing the affinity of CMG to DNA. This gating process may explain the dsDNA-to-ssDNA transition of CMG at origins and help preserve CMG on dsDNA during fork repair.

Revealing in real-time a multistep assembly mechanism for SV40 virus-like particles

Many viruses use their genome as template for self-assembly into an infectious particle. However, this reaction remains elusive because of the transient nature of intermediate structures. To elucidate this process, optical tweezers and acoustic force spectroscopy are used to follow viral assembly in real time. Using Simian virus 40 (SV40) virus-like particles as model system, we reveal a multistep assembly mechanism. Initially, binding of VP1 pentamers to DNA leads to a significantly decreased persistence length. Moreover, the pentamers seem able to stabilize DNA loops. Next, formation of interpentamer interactions results in intermediate structures with reduced contour length. These structures stabilize into objects that permanently decrease the contour length to a degree consistent with DNA compaction in wild-type SV40. These data indicate that a multistep mechanism leads to fully assembled cross-linked SV40 particles. SV40 is studied as drug delivery system. Our insights can help optimize packaging of therapeutic agents in these particles.

Active probing of the mechanical properties of biological and synthetic vesicles

BACKGROUND

The interest in mechanics of synthetic and biological vesicles has been continuously growing during the last decades. Liposomes serve as model systems for investigating fundamental membrane processes and properties. More recently, extracellular vesicles (EVs) have been investigated mechanically as well. EVs are widely studied in fundamental and applied sciences, but their material properties remained elusive until recently. Elucidating the mechanical properties of vesicles is essential to unveil the mechanisms behind a variety of biological processes, e.g. budding, vesiculation and cellular uptake mechanisms.

SCOPE OF REVIEW

The importance of mechanobiology for studies of vesicles and membranes is discussed, as well as the different available techniques to probe their mechanical properties. In particular, the mechanics of vesicles and membranes as obtained by nanoindentation, micropipette aspiration, optical tweezers, electrodeformation and electroporation experiments is addressed.

MAJOR CONCLUSIONS

EVs and liposomes possess an astonishing rich, diverse behavior. To better understand their properties, and for optimization of their applications in nanotechnology, an improved understanding of their mechanical properties is needed. Depending on the size of the vesicles and the specific scientific question, different techniques can be chosen for their mechanical characterization.

GENERAL SIGNIFICANCE

Understanding the mechanical properties of vesicles is necessary to gain deeper insight in the fundamental biological mechanisms involved in vesicle generation and cellular uptake. This furthermore facilitates technological applications such as using vesicles as targeted drug delivery vehicles. Liposome studies provide insight into fundamental membrane processes and properties, whereas the role and functioning of EVs in biology and medicine are increasingly elucidated.

Multi-parameter measurements of conformational dynamics in nucleic acids and nucleoprotein complexes

Biological macromolecules undergo dynamic conformational changes. Single-molecule methods can track such structural rearrangements in real time. However, while the structure of large macromolecules may change along many degrees of freedom, single-molecule techniques only monitor a limited number of these axes of motion. Advanced single-molecule methods are being developed to track multiple degrees of freedom in nucleic acids and nucleoprotein complexes at high resolution, to enable better manipulation and control of the system under investigation, and to collect measurements in massively parallel fashion. Combining complementary single-molecule methods within the same assay also provides unique measurement opportunities. Implementations of magnetic and optical tweezers combined with fluorescence and FRET have demonstrated results unattainable by either technique alone. Augmenting other advanced single-molecule methods with fluorescence detection will allow us to better capture the multidimensional dynamics of nucleic acids and nucleoprotein complexes central to biology.

Real-Time Assembly of Viruslike Nucleocapsids Elucidated at the Single-Particle Level

While the structure of a multitude of viral particles has been resolved to atomistic detail, their assembly pathways remain largely elusive. Key unresolved issues are particle nucleation, particle growth, and the mode of genome compaction. These issues are difficult to address in bulk approaches and are effectively only accessible by the real-time tracking of assembly dynamics of individual particles. This we do here by studying the assembly into rod-shaped viruslike particles (VLPs) of artificial capsid polypeptides. Using fluorescence optical tweezers, we establish that small oligomers perform one-dimensional diffusion along the DNA. Larger oligomers are immobile and nucleate VLP growth. A multiplexed acoustic force spectroscopy approach reveals that DNA is compacted in regular steps, suggesting packaging via helical wrapping into a nucleocapsid. By reporting how real-time assembly tracking elucidates viral nucleation and growth principles, our work opens the door to a fundamental understanding of the complex assembly pathways of both VLPs and naturally evolved viruses.

Expanding single-molecule fluorescence spectroscopy to capture complexity in biology

Fundamental biological processes are driven by diverse molecular machineries. In recent years, single-molecule fluorescence spectroscopy has matured as a unique tool in biology to study how structural dynamics of molecular complexes drive various biochemical reactions. In this review, we highlight underlying developments in single-molecule fluorescence methods that enable deep biological investigations. Recent progress in these methods points toward increasing complexity of measurements to capture biological processes in a living cell, where multiple processes often occur simultaneously and are mechanistically coupled.

Single-Molecule Techniques and Cell-Free Protein Synthesis: A Perfect Marriage

Single-molecule techniques are currently an essential tool to study conformational changes as well as the synthesis and folding of proteins. However, the preparation of suitable protein samples is often time-consuming and demanding. The rapid development of cell-free protein synthesis over the last few years opened new perspectives for fast and easy sample preparation, but this was not fully exploited until now. Here, we take a look at the advancements in sample preparation as well as in the development of technical approaches and analytical tools, which unavoidably lead to the combination of single-molecule techniques and cell-free protein synthesis. It is an ideal combination that can unlock the full potential of studying complex biological processes in the near future.

Influence of permittivity on gradient force exerted on Mie spheres

In optical trapping, whether a particle could be stably trapped into the focus region greatly depends on the strength of the gradient force. Individual theoretical study on gradient force exerted on a Mie particle is rare because the mathematical separation of the gradient force and the scattering force in the Mie regime is difficult. Based on the recent forces separation work by Du et al. [Sci. Rep.7, 18042 (2017)SRCEC32045-232210.1038/s41598-017-17874-1], we investigate the influence of permittivity (an important macroscopic physical quantity) on the gradient force exerted on a Mie particle by cooperating numerical calculation using fast Fourier transform and analytical analysis using multipole expansion. It is revealed that gradient forces exerted on small spheres are mainly determined by the electric dipole moment except for certain permittivity with which the real part of polarizability of the electric dipole approaches zero, and gradient forces exerted on larger spheres are complex because of the superposition of the multipole moments. The classification of permittivity corresponding to different varying tendencies of gradient forces exerted on small spheres or larger Mie particles are illustrated. Absorption of particles favors the trapping of small spheres by gradient force, while it is bad for the trapping of larger particles. Moreover, the absolute values of the maximal gradient forces exerted on larger Mie particles decline greatly versus the varied imaginary part of permittivity. This work provides elaborate investigation on the different varying tendencies of gradient forces versus permittivity, which favors more accurate and free optical trapping.

Excitonic Coupling Modulated by Mechanical Stimuli

Understanding energy transfer is of vital importance in a diverse range of applications from biological systems to photovoltaics. The ability to tune excitonic coupling in any of these systems, however, is generally limited. In this work, we have simulated a new class of single-molecule spectroscopy in which force microscopy is used to control the excitonic coupling between chromophores. Here we demonstrate that the excitonic coupling can be controlled by mechanical manipulation of the molecule (perylenediimide dimers and terrylenediimide-perylenediimide heterodimers) and can be tuned over a broad range of values (0.02-0.15 eV) that correspond to different regimes of exciton dynamics going from the folded to the elongated structure of the dimer. In all of the systems considered here, the switching from high to low coupling takes place simultaneously with the mechanical deformation detected by a strong increase and subsequent decay of the force. These simulations suggest that single-molecule force spectroscopy can be used to understand and eventually aid the design of excitonic devices.

Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level

Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS), and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented.