Recent Advances in Optical Tweezers

Symmetry breakdown in the sol-gel transition of a Guar gum transient physical network

The gelation of the mixture of guar gum and borax in an aqueous solution was studied by diffusing-wave spectroscopy microrheology. The Winter and Chambon power-law domain was evidenced at high-frequency range. The time-cure superposition was applied to the mean square displacement of the probe particles and the critical power-law behavior of the shifting factors was revealed close to the percolation threshold. Morphological characterization revealed the emergence of ribbon-like structures at high borax concentrations. The Rubinstein and Semenov plateau was demonstrated. The correlations between the critical exponents that govern the gelation of the transient networks were reviewed with regard to the scaling laws of both permanent and transient networks. Unlike permanent networks, the relation n₊= n_- was assumed as the unique condition to establish the hyperscaling laws in transient networks. Whereas, the symmetry breakdown of the longest relaxation time was found to be a common feature of the flowable gels.

Optical tweezers study of membrane fluidity in small cell lung cancer cells

The fluidity of the cell membrane is closely related to cancer metastasis/invasion. To test the relationship of membrane fluidity and invasiveness, we first demonstrated that transfection of small RNA miR-92b-3p can significantly increase invasiveness of the small cell lung cancer cell line SHP77. Then optical tweezers were used to measure membrane fluidity. This study employed continuous and step-like stretching methods to examine fluidity changes in SHP77 cell membranes before and after miR-92b-3p transfection. A newly developed physical model was used to derive the effective viscosity and static tension of the cell membrane from relaxation curves obtained via step-like stretching. Experiments showed that invasiveness and fluidity increased significantly after miR-92b-3p transfection. This study paved the way toward a better understanding of cancer cell invasion and membrane mechanical characteristics.

Direct axial plane imaging of particle manipulation with nondiffracting Bessel beams

Optical manipulation with nondiffracting beams has been attracting great interest and finding widespread applications in many fields such as chemistry, physics, and biomedicine. Generally, optical manipulation is conducted in an optical microscopy system, which, in general, only allows for imaging motions of particles in the transverse plane, rendering the observation of dynamics processes occurring in the axial plane impractical. We propose and demonstrate an optical manipulation system that incorporates an axial plane imaging module. With this system, the trapping behavior in the transverse plane and the transportation process in the axial plane of a particle immersed in a Bessel beam were acquired simultaneously in real time.

Elucidating Recombination Mediator Function Using Biophysical Tools

Simple Summary

This review recapitulates the initial knowledge acquired with genetics and biochemical experiments on Recombination mediator proteins in different domains of life. We further address how recent in vivo and in vitro biophysical tools were critical to deepen the understanding of RMPs molecular mechanisms in DNA and replication repair, and unveiled unexpected features. For instance, in bacteria, genetic and biochemical studies suggest a close proximity and coordination of action of the RecF, RecR and RecO proteins in order to ensure their RMP function, which is to overcome the single-strand binding protein (SSB) and facilitate the loading of the recombinase RecA onto ssDNA. In contrary to this expectation, using single-molecule fluorescent imaging in living cells, we showed recently that RecO and RecF do not colocalize and moreover harbor different spatiotemporal behavior relative to the replication machinery, suggesting distinct functions. Finally, we address how new biophysics tools could be used to answer outstanding questions about RMP function.

Abstract

The recombination mediator proteins (RMPs) are ubiquitous and play a crucial role in genome stability. RMPs facilitate the loading of recombinases like RecA onto single-stranded (ss) DNA coated by single-strand binding proteins like SSB. Despite sharing a common function, RMPs are the products of a convergent evolution and differ in (1) structure, (2) interaction partners and (3) molecular mechanisms. The RMP function is usually realized by a single protein in bacteriophages and eukaryotes, respectively UvsY or Orf, and RAD52 or BRCA2, while in bacteria three proteins RecF, RecO and RecR act cooperatively to displace SSB and load RecA onto a ssDNA region. Proteins working alongside to the RMPs in homologous recombination and DNA repair notably belongs to the RAD52 epistasis group in eukaryote and the RecF epistasis group in bacteria. Although RMPs have been studied for several decades, molecular mechanisms at the single-cell level are still not fully understood. Here, we summarize the current knowledge acquired on RMPs and review the crucial role of biophysical tools to investigate molecular mechanisms at the single-cell level in the physiological context.

Optical tweezers in single-molecule biophysics

Optical tweezers have become the method of choice in single-molecule manipulation studies. In this Primer, we first review the physical principles of optical tweezers and the characteristics that make them a powerful tool to investigate single molecules. We then introduce the modifications of the method to extend the measurement of forces and displacements to torques and angles, and to develop optical tweezers with single-molecule fluorescence detection capabilities. We discuss force and torque calibration of these instruments, their various modes of operation and most common experimental geometries. We describe the type of data obtained in each experimental design and their analyses. This description is followed by a survey of applications of these methods to the studies of protein-nucleic acid interactions, protein/RNA folding and molecular motors. We also discuss data reproducibility, the factors that lead to the data variability among different laboratories and the need to develop field standards. We cover the current limitations of the methods and possible ways to optimize instrument operation, data extraction and analysis, before suggesting likely areas of future growth.

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.

Nanoparticle Assembling Dynamics Induced by Pulsed Optical Force

Femtosecond (fs) laser trapping dynamics is summarized for silica, hydrophobically modified silica, and polystyrene nanoparticles (NPs) in aqueous solution, highlighting their distinct optical trapping dynamics under CW laser. Mutually repulsive silica nanoparticles are tightly confined under fs laser compared to CW laser trapping and, upon increasing laser power, they are ejected from the focus as an assembly. Hydrophobically modified silica and polystyrene (PS) NPs are sequentially ejected just like a stream or ablated, giving bubbles. The ejection and bubbling take place with the direction perpendicular to laser polarization and its direction is randomly switched from one to the other. These characteristic features are interpreted from the viewpoint of single assembly formation of NPs at an asymmetric position in the optical potential. Temporal change in optical forces map is prepared for a single PS NP by calculating scattering, gradient, and temporal forces. The relative contribution of the forces changes with the volume increase of the assembly and, when the pushing force along the trapping pulse propagation overcome the gradient in the focal plane, the assembly undergoes the ejection. Further fs multiphoton absorption is induced for the larger assembly leading to bubble generation. The assembling, ejection, and bubbling dynamics of NPs are characteristic features of pulsed optical force and are considered as a new platform for developing new material fabrication method.

From Nanosecond Photochemistry to Optical Force Chemistry: My Journey

Laser was invented in 1960 and soon introduced to chemistry research. We started time-resolved spectroscopy and photochemistry and initial trial was focused to nanosecond and then picosecond electronic absorption spectroscopy for studying molecular electronic excited states, charge separation in molecular complexes, and intermolecular electron transfer in solution. We considered that not only time-resolved but also space-resolved chemistry would be important for future laser-based chemistry and combined pulsed lasers with optical microscopes. Spectroscopy, photochemistry, ablation, and spatial arrangement of single microparticles and microdroplets in solution were carried out. Further we shifted from micro to nano and opened a new field covering spectroscopy, ablation, phase transition, crystallization, patterning, and fabrication. The progress is summarized and discussed as time-resolved nano spectroscopy, ablation nano dynamics, and optical force chemistry.

Efficient Brownian oscillators and nanoheaters based on gallium-doped ε-Fe2O3

Wireless actuation at the nanoscale is vital in many contexts, and magnetic fields acting on nanoparticles (NPs) are among the most effective tools when actuation concerns linear forces. However, effective tools to apply torques at the nanoscale are still missing, because NPs where the magnetic moment is strongly coupled to the lattice agglomerate due to their high magnetic moment. Here, we show that gallium-doped ε-iron oxide NPs have small interparticle magnetic interactions and huge lattice-coupling for efficiently applying torques at the nanoscale. In this view, they are expected to be useful tools to efficiently apply mechanical forces to induce cellular apoptosis and to discern between mechanical and thermal contributions to cellular apoptosis currently under debate.

Germanium nanospheres for ultraresolution picotensiometry of kinesin motors

Kinesin motors are essential for the transport of cellular cargo along microtubules. How the motors step, detach, and cooperate with each other is still unclear. To dissect the molecular motion of kinesin-1, we developed germanium nanospheres as ultraresolution optical trapping probes. We found that single motors took 4-nanometer center-of-mass steps. Furthermore, kinesin-1 never detached from microtubules under hindering load conditions. Instead, it slipped on microtubules in microsecond-long, 8-nanometer steps and remained in this slip state before detaching or reengaging in directed motion. Unexpectedly, reengagement and thus rescue of directed motion was more frequent. Our observations broaden our knowledge on the mechanochemical cycle and slip state of kinesin. This state and rescue need to be accounted for to understand long-range transport by teams of motors.

Exploring the effects of approach velocity on depletion force and coalescence in oil-in-water emulsions

An emulsion is a thermodynamically unstable system consisting of at least two immiscible liquid phases, one of which is dispersed in the other in the form of droplets of varying size. Most studies on emulsions have focused on the behaviour of emulsion droplets with diameter from ∼50 μm and upwards. However, the properties of smaller droplets may be highly relevant in order to understand the behaviour of emulsions, including their performance in numerous applications within the fields of food, industry, and medical science. The relatively long life-time and small size of these droplets compared to other emulsion droplets, make them suited for optical trapping and micromanipulation technologies. Optical tweezers have previously shown potential in the study of stabilized emulsions. Here we employ optical tweezers to examine unstable oil-in-water emulsions to determine the effects of system parameters on depletion force and coalescence times.

DNA Manipulation and Single-Molecule Imaging

DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.

Single-molecule stretching experiments of flexible (wormlike) chain molecules in different ensembles: Theory and a potential application of finite chain length effects to nick-counting in DNA

We propose a formalism for deriving force-elongation and elongation-force relations for flexible chain molecules from analytical expressions for their radial distribution function, which provides insight into the factors controlling the asymptotic behavior and finite chain length corrections. In particular, we apply this formalism to our previously developed interpolation formula for the wormlike chain end-to-end distance distribution. The resulting expression for the asymptotic limit of infinite chain length is of similar quality to the numerical evaluation of Marko and Siggia's variational theory and considerably more precise than their interpolation formula. A comparison to numerical data suggests that our analytical finite chain length corrections achieve a comparable accuracy. As an application of our results, we discuss the possibility of inferring the time-dependent number of nicks in single-molecule stretching experiments on double-stranded DNA from the accompanying changes in the effective chain length.

Elasticity of connected semiflexible quadrilaterals

Using the positional-orientational propagator of a semiflexible filament in the weakly bending regime, we analytically calculate the probability densities associated with the fluctuating tip and the corners of a grafted system of connected quadrilaterals. We calculate closed analytic expressions for the probability densities within the framework of the worm-like chain model, which are valid in the weakly bending regime. The probability densities give the physical quantities related to the elasticity of the system such as the force-extension relation in the fixed extension ensemble, the Poisson's ratio and the average of the force exerted to a confining stiff planar wall by the fluctuating tip of the system. Our analysis reveals that the force-extension relations depend on the contour length of the system (material content), the bending stiffness (chemical nature), the geometrical angle and the number of the quadrilaterals, while the Poisson's ratio depends only on the geometrical angle and the number of the quadrilaterals, and is thus a purely geometric property of the system.

Microfluidic Devices for Magnetic Separation of Biological Particles: A Review

Separation of microparticles and cells serves a critical step in many applications such as in biological analyses, food production, chemical processing, and medical diagnostics. Sorting on the microscale exhibits certain advantages in comparison with that on the macroscale as it requires minuscule sample or reagents volume and thus reduced analysis cycle time, smaller size of devices, and lower fabrication costs. Progresses have been made over time to improve the efficiency of these microscale particle manipulation techniques. Many different techniques have been used to attain accurate particle sorting and separation in a continuous manner on the microscale level, which can be categorized as either passive or active methods. Passive techniques achieve accurate manipulation of particles through their interaction with surrounding flow by carefully designed channel structures, without using external fields. As an alternative, active techniques utilize external fields (e.g., acoustic, electronic, optical, and magnetic field, etc.) to realize desired pattern of motion for particles with specific properties. Among numerous active methods for microfluidic particle sorting, the magnetic field has been widely used in biomedical and chemical applications to achieve mixing, focusing, and separating of reagents and bioparticles. This paper aims to provide a thorough review on the classic and most up-to-date magnetic sorting and separation techniques to manipulate microparticles including the discussions on the basic concept, working principle, experimental details, and device performance.

Aerosol Optical Tweezers Elucidate the Chemistry, Acidity, Phase Separations, and Morphology of Atmospheric Microdroplets

ConspectusAerosol particles represent unique chemical environments because of their high surface area-to-volume ratio that promotes the effects of interfacial chemistry in confined environments. Properties such as viscosity, diffusivity, water content, pH, and morphology-following liquid-liquid phase separation-can strongly alter how a particle interacts with condensable vapors and reactive trace gases, thus modifying its continual evolution and environmental effects. Our understanding of this chemical evolution of atmospheric particulate matter and its environmental impacts is largely limited by our ability to directly observe how these critical particle properties respond to the addition or reactive uptake of new chemical components. Aerosol optical tweezers (AOT) stably trap particles in focused laser beams, providing positional control and the retrieval of many of these critical properties required to understand and predict the chemistry of aerosolized microdroplets. The analytical power of the AOT stems from the retrieval of the cavity-enhanced Raman spectrum induced by the trapping laser. Analysis of the whispering gallery modes (WGMs) that resonate as a standing wave around the droplet's interface, provide high accuracy measurements of the droplet's size, refractive index (and thus a measurement of composition), and can distinguish between core-shell, partially engulfed, and homogeneous morphologies. We have advanced the ability to determine the properties of the core and shell phases in biphasic droplets, including obtaining high-accuracy pH measurements. These capabilities were applied to perform AOT physical chemistry experiments on authentic secondary organic aerosol (SOA) produced directly in the AOT chamber by ozonolysis of terpene vapors. The propensity of the SOA to phase separate as a shell from a wide range of nonpolar to polar core phases was observed, along with the discovery of a stable emulsified state of SOA particles in an aqueous salt droplet. Micron-thick SOA shells did not impede the gain or loss of water or squalane from the core to the surrounding air, indicating no significant diffusional limitations to condensational growth or partitioning even under dry conditions. These experiments formed the foundation of a new framework that predicts how the phase-separated morphology of complex aerosols containing organic carbon evolves during continual atmospheric oxidation processes. Increases in oxidation state will quickly drive conversion from a partially engulfed to core-shell morphology that has dramatically different chemical reactivity since the core phase is completely concealed by the shell. The recent advances in the experimental capabilities of the AOT technique such as presented here enable novel experimental methodologies that provide insights into the chemistry and multidimensional properties of aerosol microdroplets, and how these coevolve and respond to continual chemical reactions.

A review on nonlinear DNA physics

The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard-Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of 'self-trapping' of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo, possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.

An Approach to Ring Resonator Biosensing Assisted by Dielectrophoresis: Design, Simulation and Fabrication

The combination of extreme miniaturization with a high sensitivity and the potential to be integrated in an array form on a chip has made silicon-based photonic microring resonators a very attractive research topic. As biosensors are approaching the nanoscale, analyte mass transfer and bonding kinetics have been ascribed as crucial factors that limit their performance. One solution may be a system that applies dielectrophoretic forces, in addition to microfluidics, to overcome the diffusion limits of conventional biosensors. Dielectrophoresis, which involves the migration of polarized dielectric particles in a non-uniform alternating electric field, has previously been successfully applied to achieve a 1000-fold improved detection efficiency in nanopore sensing and may significantly increase the sensitivity in microring resonator biosensing. In the current work, we designed microring resonators with integrated electrodes next to the sensor surface that may be used to explore the effect of dielectrophoresis. The chip design, including two different electrode configurations, electric field gradient simulations, and the fabrication process flow of a dielectrohoresis-enhanced microring resonator-based sensor, is presented in this paper. Finite element method (FEM) simulations calculated for both electrode configurations revealed ∇E² values above 10¹⁷ V²m⁻³ around the sensing areas. This is comparable to electric field gradients previously reported for successful interactions with larger molecules, such as proteins and antibodies.

Multipole interplay controls optical forces and ultra-directional scattering

We analyze the superposition of Cartesian multipoles to reveal the mechanisms underlying the origin of optical forces. We show that a multipolar decomposition approach significantly simplifies the analysis of this problem and leads to a very intuitive explanation of optical forces based on the interference between multipoles. We provide an in-depth analysis of the radiation coming from the object, starting from low-order multipole interactions up to quadrupolar terms. Interestingly, by varying the phase difference between multipoles, the optical force as well as the total radiation directivity can be well controlled. The theory developed in this paper may also serve as a reference for ultra-directional light steering applications.

Void-free 3D Bioprinting for In-situ Endothelialization and Microfluidic Perfusion

Two major challenges of 3D bioprinting are the retention of structural fidelity and efficient endothelialization for tissue vascularization. We address both of these issues by introducing a versatile 3D bioprinting strategy, in which a templating bioink is deposited layer-by-layer alongside a matrix bioink to establish void-free multimaterial structures. After crosslinking the matrix phase, the templating phase is sacrificed to create a well-defined 3D network of interconnected tubular channels. This void-free 3D printing (VF-3DP) approach circumvents the traditional concerns of structural collapse, deformation and oxygen inhibition, moreover, it can be readily used to print materials that are widely considered "unprintable". By pre-loading endothelial cells into the templating bioink, the inner surface of the channels can be efficiently cellularized with a confluent endothelial layer. This in-situ endothelialization method can be used to produce endothelium with a far greater uniformity than can be achieved using the conventional post-seeding approach. This VF-3DP approach can also be extended beyond tissue fabrication and towards customized hydrogel-based microfluidics and self-supported perfusable hydrogel constructs.

Acousto-holographic optical tweezers

Acousto-optic deflectors (AODs) allow the creation of multiple optical traps by time-sharing, that is, by rapidly cycling the laser focus between designated spatial locations. The traps thus formed are not permanent. In this Letter, we successfully demonstrate the creation of multiple and permanent traps by means of AODs driven by specially encoded radio frequency signals. The generation of complex acoustic signals allows us to treat such devices as super-fast spatial light modulators. Using this technique, it is possible to generate several static optical trap arrays and switch them at kilohertz (kHz) rates, allowing independent control of each trap group. Additionally, we discuss the compatibility of this method with precise force and position measurements, and the improvement in their frequency bandwidth compared to time-sharing optical tweezers, especially when many objects are trapped.

In-flow measurement of cell-cell adhesion using oscillatory inertial microfluidics

Multicellular clusters in circulation can exhibit a substantially different function and biomarker significance compared to individual cells. Notably, clusters of circulating tumor cells (CTCs) are much more effective initiators of metastasis than single CTCs, and correlate with worse patient prognoses. Measuring the cell-cell adhesion strength of CTC clusters is a critical step towards understanding their subsistence in the circulation and mechanism of elevated tumorigenicity. However, measuring cell-cell adhesion forces in flow is elusive using existing methods. Here, we report an oscillatory inertial microfluidics system which exerts a repeating fluidic force profile on suspended cell doublets to determine their cell-cell adhesion strength (Fs), without any biophysical modifications to the cell surface and physiological morphology. Using our system, we analyzed a large number (N > 500) of doublets from a patient-derived breast cancer CTC line. We discovered that the cell-cell adhesion strength of CTC doublets varied almost 20-fold between the weakly adhered (Fs < 28 nN) and strongly bound subpopulations (Fs > 542 nN). Our system can be used with other cancer or noncancer cells without restrictions, and may be used for rapid screening of drugs aiming to disrupt the highly-metastatic CTC clusters in circulation.

Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids

The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression, but tracing their molecular origin has been difficult due to the structural and chemical complexity. We posit that concepts from machine learning can help to tackle this long-standing challenge. Here, we demonstrate the feasibility and advantage of this strategy through developing a structure-mechanics statistical learning scheme to elucidate how local rigidity in double-stranded (ds)DNA and dsRNA may lead to their global flexibility in bend, stretch, and twist. Specifically, the mechanical parameters in a heavy-atom elastic network model are computed from the trajectory data of all-atom molecular dynamics simulation. The results show that the inter-atomic springs for backbone and ribose puckering in dsRNA are stronger than those in dsDNA, but are similar in strengths for base-stacking and base-pairing. Our analysis shows that the experimental observation of dsDNA being easier to bend but harder to stretch than dsRNA comes mostly from the respective B- and A-form topologies. The computationally resolved composition of local rigidity indicates that the flexibility of both nucleic acids is mostly due to base-stacking. But for properties like twist-stretch coupling, backbone springs are shown to play a major role instead. The quantitative connection between local rigidity and global flexibility sets foundation for understanding how local binding and chemical modification of genetic materials effectuate longer-ranged regulatory signals.

The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression. We devise structural mechanics statistical learning method to reveal their molecular origin in terms of chemical interactions.

Biofabrication Strategies and Engineered In Vitro Systems for Vascular Mechanobiology

The vascular system is integral for maintaining organ-specific functions and homeostasis. Dysregulation in vascular architecture and function can lead to various chronic or acute disorders. Investigation of the role of the vascular system in health and disease has been accelerated through the development of tissue-engineered constructs and microphysiological on-chip platforms. These in vitro systems permit studies of biochemical regulation of vascular networks and parenchymal tissue and provide mechanistic insights into the biophysical and hemodynamic forces acting in organ-specific niches. Detailed understanding of these forces and the mechanotransductory pathways involved is necessary to develop preventative and therapeutic strategies targeting the vascular system. This review describes vascular structure and function, the role of hemodynamic forces in maintaining vascular homeostasis, and measurement approaches for cell and tissue level mechanical properties influencing vascular phenomena. State-of-the-art techniques for fabricating in vitro microvascular systems, with varying degrees of biological and engineering complexity, are summarized. Finally, the role of vascular mechanobiology in organ-specific niches and pathophysiological states, and efforts to recapitulate these events using in vitro microphysiological systems, are explored. It is hoped that this review will help readers appreciate the important, but understudied, role of vascular-parenchymal mechanotransduction in health and disease toward developing mechanotherapeutics for treatment strategies.

Opto-thermoelectric speckle tweezers

Opto-thermoelectric tweezers present a new paradigm for optical trapping and manipulation of particles using low-power and simple optics. New real-life applications of opto-thermoelectric tweezers in areas such as biophysics, microfluidics, and nanomanufacturing will require them to have large-scale and high-throughput manipulation capabilities in complex environments. Here, we present opto-thermoelectric speckle tweezers, which use speckle field consisting of many randomly distributed thermal hotspots that arise from an optical speckle pattern to trap multiple particles over large areas. By further integrating the speckle tweezers with a microfluidic system, we experimentally demonstrate their application for size-based nanoparticle filtration. With their low-power operation, simplicity, and versatility, opto-thermoelectric speckle tweezers will broaden the applications of optical manipulation techniques.

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.

Environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by atomic force microscopy-based single-molecule force spectroscopy and the implications for advanced polymer materials

"The Tao begets the One. One begets all things of the world." This quote from Tao Te Ching is still inspiring for scientists in chemistry and materials science: The "One" can refer to a single molecule. A macroscopic material is composed of numerous molecules. Although the relationship between the properties of the single molecule and macroscopic material is not well understood yet, it is expected that a deeper understanding of the single-chain mechanics of macromolecules will certainly facilitate the development of materials science. Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) has been exploited extensively as a powerful tool to study the single-chain behaviors of macromolecules. In this review, we summarize the recent advances in the emerging field of environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by means of AFM-SMFS. First, the single-chain inherent elasticities of several typical linear macromolecules are introduced, which are also confirmed by one of three polymer models with theoretical elasticities of the corresponding macromolecules obtained from quantum mechanical (QM) calculations. Then, the effects of the external environments on the single-chain mechanics of synthetic polymers and biomacromolecules are reviewed. Finally, the impacts of single-chain mechanics of macromolecules on the development of polymer science especially polymer materials are illustrated.

Type IV pili: dynamics, biophysics and functional consequences

The surfaces of many bacteria are decorated with long, exquisitely thin appendages called type IV pili (T4P), dynamic filaments that are rapidly polymerized and depolymerized from a pool of pilin subunits. Cycles of pilus extension, binding and retraction enable T4P to perform a phenomenally diverse array of functions, including twitching motility, DNA uptake and microcolony formation. On the basis of recent developments, a comprehensive understanding is emerging of the molecular architecture of the T4P machinery and the filament it builds, providing mechanistic insights into the assembly and retraction processes. Combined microbiological and biophysical approaches have revealed how T4P dynamics influence self-organization of bacteria, how bacteria respond to external stimuli to regulate T4P activity for directed movement, and the role of T4P retraction in surface sensing. In this Review, we discuss the T4P machine architecture and filament structure and present current molecular models for T4P dynamics, with a particular focus on recent insights into T4P retraction. We also discuss the functional consequences of T4P dynamics, which have important implications for bacterial lifestyle and pathogenesis.

Simultaneous optical trapping and imaging in the axial plane: a review of current progress

Optical trapping has become a powerful tool in numerous fields such as biology, physics, chemistry, etc. In conventional optical trapping systems, trapping and imaging share the same objective lens, confining the region of observation to the focal plane. For the capture of optical trapping processes occurring in other planes, especially the axial plane (the one containing the z-axis), many methods have been proposed to achieve this goal. Here, we review the methods of acquiring the axial-plane information from which axial plane trapping is observed and discuss their advantages and limitations. To overcome the limitations existing in these methods, we developed an optical tweezers system that allows for simultaneous optical trapping and imaging in the axial plane. The versatility and usefulness of the system in axial-plane trapping and imaging are demonstrated by investigating its trapping performance with various optical fields, including Bessel, Airy, and snake-like beams. The potential applications of the reported technique are suggested to several research fields, including optical pulling, longitudinal optical binding, tomographic phase microscopy (TPM), and super-resolution microscopy.

Optical Tweezers in Studies of Red Blood Cells

Optical tweezers (OTs) are innovative instruments utilized for the manipulation of microscopic biological objects of interest. Rapid improvements in precision and degree of freedom of multichannel and multifunctional OTs have ushered in a new era of studies in basic physical and chemical properties of living tissues and unknown biomechanics in biological processes. Nowadays, OTs are used extensively for studying living cells and have initiated far-reaching influence in various fundamental studies in life sciences. There is also a high potential for using OTs in haemorheology, investigations of blood microcirculation and the mutual interplay of blood cells. In fact, in spite of their great promise in the application of OTs-based approaches for the study of blood, cell formation and maturation in erythropoiesis have not been fully explored. In this review, the background of OTs, their state-of-the-art applications in exploring single-cell level characteristics and bio-rheological properties of mature red blood cells (RBCs) as well as the OTs-assisted studies on erythropoiesis are summarized and presented. The advance developments and future perspectives of the OTs' application in haemorheology both for fundamental and practical in-depth studies of RBCs formation, functional diagnostics and therapeutic needs are highlighted.

Additive Manufacturing of Micromanipulator Mounted on a Glass Capillary for Biological Applications

In this study, a three-dimensional (3D) micromanipulator mounted on a glass capillary is developed for handling biological samples, such as multicellular spheroids and embryos. To fabricate the micromanipulator, we developed an additive manufacturing system based on high-resolution microstereolithography using a 405-nm blue laser. The fabrication system makes it possible to fabricate 3D microstructures on a glass capillary with 2.5 µm lateral resolution and 25 µm layer thickness. We also demonstrated the capture and release of a spheroid with the micromanipulator fabricated using our additive manufacturing system. We showed that spheroids can be easily handled by a simple operation with minimal damage using a cage-like multiple finger structure. Additive manufacturing of tailor-made micromanipulators mounted on a glass capillary will be useful in biological and tissue engineering research.

Focusing of sub-micrometer particles in microfluidic devices

Sub-micrometer particles (0.10-1.0 μm) are of great significance to study, e.g., microvesicles and protein aggregates are targets for therapeutic intervention, and sub-micrometer fluorescent polystyrene (PS) particles are used as probes for diagnostic imaging. Focusing of sub-micrometer particles - precisely control over the position of sub-micrometer particles in a tightly focused stream - has a wide range of applications in the field of biology, chemistry and environment, by acting as a prerequisite step for downstream detection, manipulation and quantification. Microfluidic devices have been attracting great attention as desirable tools for sub-micrometer particle focusing, due to their small size, low reagent consumption, fast analysis and low cost. Recent advancements in fundamental knowledge and fabrication technologies have enabled microfluidic focusing of particles at sub-micrometer scale in a continuous, label-free and high-throughput manner. Microfluidic methods for the focusing of sub-micrometer particles can be classified into two main groups depending on whether an external field is applied: 1) passive methods, which utilize intrinsic fluidic properties without the need of external actuation, such as inertial, deterministic lateral displacement (DLD), viscoelastic and hydrophoretic focusing; and 2) active methods, where external fields are used, such as dielectrophoretic, thermophoretic, acoustophoretic and optical focusing. This article mainly reviews the studies on the focusing of sub-micrometer particles in microfluidic devices over the past 10 years. It aims to bridge the gap between the focusing of micrometer and nanometer scale (1.0-100 nm) particles and to improve the understanding of development progress, current advances and future prospects in microfluidic focusing techniques.

Approaches for measuring the dynamics of RNA-protein interactions

RNA-protein interactions are pivotal for the regulation of gene expression from bacteria to human. RNA-protein interactions are dynamic; they change over biologically relevant timescales. Understanding the regulation of gene expression at the RNA level therefore requires knowledge of the dynamics of RNA-protein interactions. Here, we discuss the main experimental approaches to measure dynamic aspects of RNA-protein interactions. We cover techniques that assess dynamics of cellular RNA-protein interactions that accompany biological processes over timescales of hours or longer and techniques measuring the kinetic dynamics of RNA-protein interactions in vitro. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Evolution and Genomics > Ribonomics.

Molecular ring toss of circular BAC DNA using micropillar array for single-molecule studies

This paper reports a method for trapping circular DNA molecules and imaging the dynamics with high spatial resolution using a micropillar-array device. We successfully trapped circular bacterial artificial chromosome DNA molecules at a micropillar-based "ring toss" in the laminar flow of a microchannel under a fluorescence microscope and demonstrated the imaging of their extension by flow and condensation process induced by spermine solution. DNA molecules were visualized in an extended loop conformation, allowing high spatial resolution, and the results showed that the dynamics is induced by the microfluidic control of the surrounding chemical environment. The method is expected to lead to the elucidation of the physical characteristics and the dynamics of circular DNA molecules.

Optimization of metallic nanoapertures at short-wave infrared wavelengths for self-induced back-action trapping

This paper presents simulation results for double nanohole and inverted bowtie nanoapertures optimized to resonate in the short-wave infrared regime (1050 nm and 1550 nm). These geometries have shown great promise for trapping nanoparticles with applications in optical engineering, physics, and biology. Using a finite element analysis tool, we found that the outline length for inverted bowtie nanoapertures in a 100 nm thick gold film with a 20 nm gap dimension having an optimized transmission resonance for 1050 nm and 1550 nm optical wavelengths is 106.5 nm and 188.5 nm, respectively. With the same gap size, the radii of the circles for the double nanohole nanoapertures are 72 nm and 128 nm. The near-field enhancements of the two structures are almost the same, while the double nanohole geometries have a 20% larger full width at half-maximum than the inverted bowtie. Next, by studying the effect of changing the inner radii of the inverted bowtie corners, we found that the difference between 2 nm and 6 nm corner radii can blue-shift the optical resonance by up to 45 nm. As a result of not having any inner corners, the double nanohole structure requires less precise fabrication and therefore could potentially have a higher successful yield of nanoapertures during the manufacturing process. Lastly, we will show experimental results that confirm the optical resonance of the nanoapertures at 1550 nm. These results will enable better performance and signal-to-noise ratio in nanoaperture trapping for the short-wave infrared wavelength regime.

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.

Combined High-Resolution Optical Tweezers and Multicolor Single-Molecule Fluorescence with an Automated Single-Molecule Assembly Line

We present an instrument that combines high-resolution optical tweezers and multicolor confocal fluorescence spectroscopy along with automated single-molecule assembly. The multicolor allows the simultaneous observation of multiple molecules or multiple degrees of freedom, which allows, for example, the observation of multiple proteins simultaneously within a complex. The instrument incorporates three fluorescence excitation lasers, with a reliable alignment scheme, which will allow three independent fluorescent probe or FRET measurements and also increases flexibility in the choice of fluorescent molecules. We demonstrate the ability to simultaneously measure angstrom-scale changes in tether extension and fluorescence signals. Simultaneous tweezers and fluorescence measurement are particularly challenging because of fluorophore photobleaching, even more so if multiple fluorophores are to be measured. Therefore, (1) fluorescence excitation and detection is interlaced with time-shared dual optical traps. (2) We investigated the photostability of common fluorophores. The mean number of photons emitted before bleaching was unaffected by the trap laser and decreased only slightly with increasing excitation laser intensity. Surprisingly, we found that Cy5 outperforms other commonly used fluorophores by more than fivefold. (3) We devised computer-controlled automation, which conserves fluorophore lifetime by quickly detecting fluorophore-labeled molecule binding, turning off lasers, and moving to add the next fluorophore-labeled component. The single-molecule assembly line enables the precise assembly of multimolecule complexes while preserving fluorophores.

Probing force in living cells with optical tweezers: from single-molecule mechanics to cell mechanotransduction

The invention of optical tweezers more than three decades ago has opened new avenues in the study of the mechanical properties of biological molecules and cells. Quantitative force measurements still represent a challenging task in living cells due to the complexity of the cellular environment. Here, we review different methodologies to quantitatively measure the mechanical properties of living cells, the strength of adhesion/receptor bonds, and the active force produced during intracellular transport, cell adhesion, and migration. We discuss experimental strategies to attain proper calibration of optical tweezers and molecular resolution in living cells. Finally, we show recent studies on the transduction of mechanical stimuli into biomolecular and genetic signals that play a critical role in cell health and disease.

Mechanotransduction in neuronal cell development and functioning

Although many details remain still elusive, it became increasingly evident in recent years that mechanosensing of microenvironmental biophysical cues and subsequent mechanotransduction are strongly involved in the regulation of neuronal cell development and functioning. This review gives an overview about the current understanding of brain and neuronal cell mechanobiology and how it impacts on neurogenesis, neuronal migration, differentiation, and maturation. We will focus particularly on the events in the cell/microenvironment interface and the decisive extracellular matrix (ECM) parameters (i.e. rigidity and nanometric spatial organisation of adhesion sites) that modulate integrin adhesion complex-based mechanosensing and mechanotransductive signalling. It will also be outlined how biomaterial approaches mimicking essential ECM features help to understand these processes and how they can be used to control and guide neuronal cell behaviour by providing appropriate biophysical cues. In addition, principal biophysical methods will be highlighted that have been crucial for the study of neuronal mechanobiology.

Regulating, Measuring, and Modeling the Viscoelasticity of Bacterial Biofilms

Biofilms occur in a broad range of environments under heterogeneous physicochemical conditions, such as in bioremediation plants, on surfaces of biomedical implants, and in the lungs of cystic fibrosis patients. In these scenarios, biofilms are subjected to shear forces, but the mechanical integrity of these aggregates often prevents their disruption or dispersal. Biofilms' physical robustness is the result of the multiple biopolymers secreted by constituent microbial cells which are also responsible for numerous biological functions. A better understanding of the role of these biopolymers and their response to dynamic forces is therefore crucial for understanding the interplay between biofilm structure and function. In this paper, we review experimental techniques in rheology, which help quantify the viscoelasticity of biofilms, and modeling approaches from soft matter physics that can assist our understanding of the rheological properties. We describe how these methods could be combined with synthetic biology approaches to control and investigate the effects of secreted polymers on the physical properties of biofilms. We argue that without an integrated approach of the three disciplines, the links between genetics, composition, and interaction of matrix biopolymers and the viscoelastic properties of biofilms will be much harder to uncover.

Single-Molecule Analysis of Reverse Transcriptase Enzymes

The original discovery of enzymes that synthesize DNA using an RNA template appeared to contradict the central dogma of biology, in which information is transferred, in a unidirectional way, from DNA genes into RNA molecules. The paradigm-shifting discovery of RNA-dependent DNA polymerases, also called reverse transcriptases (RTs), reshaped existing views for how cells function; however, the scope of the impact RTs impose on biology had yet to be realized. In the decades of research since the early 1970s, the biomedical and biotechnological significance of retroviral RTs, as well as the evolutionarily related telomerase enzyme, has become exceedingly clear. One common theme that has emerged in the course of RT-related research is the central role of nucleic acid binding and dynamics during enzyme function. However, directly interrogating these dynamic properties is challenging because of the stochastic properties of biological macromolecules. In this review, we describe how the development of single-molecule biophysical techniques has opened new windows through which to observe the dynamic behavior of this remarkable class of enzymes. Specifically, we focus on how the powerful single-molecule Förster resonance energy transfer (FRET) method has been exploited to study the structure and function of the human immunodeficiency virus (HIV) RT and telomerase ribonucleoprotein (RNP) enzymes. These exciting studies have refined our understanding of RT catalysis, have revealed unforeseen structural rearrangements between RTs and their nucleic acid substrates, and have helped to characterize the mode of action of RT-inhibiting drugs. We conclude with a discussion of how the ongoing development of single-molecule technologies will continue to empower researchers to probe RT mechanisms in new and exciting ways.

Nanoscale integration of single cell biologics discovery processes using optofluidic manipulation and monitoring

The new and rapid advancement in the complexity of biologics drug discovery has been driven by a deeper understanding of biological systems combined with innovative new therapeutic modalities, paving the way to breakthrough therapies for previously intractable diseases. These exciting times in biomedical innovation require the development of novel technologies to facilitate the sophisticated, multifaceted, high-paced workflows necessary to support modern large molecule drug discovery. A high-level aspiration is a true integration of "lab-on-a-chip" methods that vastly miniaturize cellulmical experiments could transform the speed, cost, and success of multiple workstreams in biologics development. Several microscale bioprocess technologies have been established that incrementally address these needs, yet each is inflexibly designed for a very specific process thus limiting an integrated holistic application. A more fully integrated nanoscale approach that incorporates manipulation, culture, analytics, and traceable digital record keeping of thousands of single cells in a relevant nanoenvironment would be a transformative technology capable of keeping pace with today's rapid and complex drug discovery demands. The recent advent of optical manipulation of cells using light-induced electrokinetics with micro- and nanoscale cell culture is poised to revolutionize both fundamental and applied biological research. In this review, we summarize the current state of the art for optical manipulation techniques and discuss emerging biological applications of this technology. In particular, we focus on promising prospects for drug discovery workflows, including antibody discovery, bioassay development, antibody engineering, and cell line development, which are enabled by the automation and industrialization of an integrated optoelectronic single-cell manipulation and culture platform. Continued development of such platforms will be well positioned to overcome many of the challenges currently associated with fragmented, low-throughput bioprocess workflows in biopharma and life science research.

Co-temporal Force and Fluorescence Measurements Reveal a Ribosomal Gear Shift Mechanism of Translation Regulation by Structured mRNAs

The movement of ribosomes on mRNA is often interrupted by secondary structures that present mechanical barriers and play a central role in translation regulation. We investigate how ribosomes couple their internal conformational changes with the activity of translocation factor EF-G to unwind mRNA secondary structures using high-resolution optical tweezers with single-molecule fluorescence capability. We find that hairpin opening occurs during EF-G-catalyzed translocation and is driven by the forward rotation of the small subunit head. Modulating the magnitude of the hairpin barrier by force shows that ribosomes respond to strong barriers by shifting their operation to an alternative 7-fold-slower kinetic pathway prior to translocation. Shifting into a slow gear results from an allosteric switch in the ribosome that may allow it to exploit thermal fluctuations to overcome mechanical barriers. Finally, we observe that ribosomes occasionally open the hairpin in two successive sub-codon steps, revealing a previously unobserved translocation intermediate.