Recent Advances in Optical Tweezers

Digital Assembly of Colloidal Particles for Nanoscale Manufacturing

From unravelling the most fundamental phenomena to enabling applications that impact our everyday lives, the nanoscale world holds great promise for science, technology and medicine. However, the extent of its practical realization would rely on manufacturing at the nanoscale. Among the various nanomanufacturing approaches being investigated, the bottom-up approach involving assembly of colloidal nanoparticles as building blocks is promising. Compared to a top-down lithographic approach, particle assembly exhibits advantages such as smaller feature size, finer control of chemical composition, less defects, lower material wastage, and higher scalability. The capability to assemble colloidal particles one by one or "digitally" has been heavily sought as it mimics the natural way of making matter and enables construction of nanomaterials with sophisticated architectures. This progress report provides an insight into the tools and techniques for digital assembly of particles, including their working mechanisms and demonstrated particle assemblies. Examples of nanomaterials and nanodevices are presented to demonstrate the strength of digital assembly in nanomanufacturing.

Force-Dependent Binding Constants

Life is an emergent property of transient interactions between biomolecules and other organic and inorganic molecules that somehow leads to harmony and order. Measurement and quantitation of these biological interactions are of value to scientists and are major goals of biochemistry, as affinities provide insight into biological processes. In an organism, these interactions occur in the context of forces and the need for a consideration of binding affinities in the context of a changing mechanical landscape necessitates a new way to consider the biochemistry of protein–protein interactions. In the past few decades, the field of mechanobiology has exploded, as both the appreciation of, and the technical advances required to facilitate the study of, how forces impact biological processes have become evident. The aim of this review is to introduce the concept of force dependence of biomolecular interactions and the requirement to be able to measure force-dependent binding constants. The focus of this discussion will be on the mechanotransduction that occurs at the integrin-mediated adhesions with the extracellular matrix and the major mechanosensors talin and vinculin. However, the approaches that the cell uses to sense and respond to forces can be applied to other systems, and this therefore provides a general discussion of the force dependence of biomolecule interactions.

High Trap Stiffness Microcylinders for Nanophotonic Trapping

Nanophotonic waveguides have enabled on-chip optical trap arrays for high-throughput manipulation and measurements. However, the realization of the full potential of these devices requires trapping enhancement for applications that need large trapping force. Here, we demonstrate a solution via fabrication of high refractive index cylindrical trapping particles. Using two different fabrication processes, a cleaving method and a novel lift-off method, we produced cylindrical silicon nitride (Si₃N₄) particles and characterized their trapping properties using the recently developed nanophotonic standing-wave array trap (nSWAT) platform. Relative to conventionally used polystyrene microspheres, the fabricated Si₃N₄ microcylinders attain an approximately 3- to 6-fold trap stiffness enhancement. Furthermore, both fabrication processes permit tunable microcylinder geometry, and the lift-off method also results in ultrasmooth surface termination of the ends of the microcylinders. These combined features make the Si₃N₄ microcylinders uniquely suited for a broad range of high-throughput, high-force, nanophotonic waveguide-based optical trapping applications.

Re-evaluation of physical interaction between plant peroxisomes and other organelles using live-cell imaging techniques

The dynamic behavior of organelles is essential for plant survival under various environmental conditions. Plant organelles, with various functions, migrate along actin filaments and contact other types of organelles, leading to physical interactions at a specific site called the membrane contact site. Recent studies have revealed the importance of physical interactions in maintaining efficient metabolite flow between organelles. In this review, we first summarize peroxisome function under different environmental conditions and growth stages to understand organelle interactions. We then discuss current knowledge regarding the interactions between peroxisome and other organelles, i.e., the oil bodies, chloroplast, and mitochondria from the perspective of metabolic and physiological regulation, with reference to various organelle interactions and techniques for estimating organelle interactions occurring in plant cells.

Beaming light through a bow-tie nanoaperture at the tip of a single-mode optical fiber

We demonstrate coupling and directivity enhancement of electromagnetic fields emerging from a single metallic nanoaperture at the tip of a single-mode optical fiber. We achieve this by using circular grooves flanking the nanoaperture perforated in a 100 nm thick gold film. The film with nanostructure is transferred to the fiber tip by aligned stripping with optical epoxy. When incident from both sides of the nanoaperture, enhancement factors of 2.2 and 2.4 in power coupling into the fiber and in beaming into free-space were obtained. Numerical simulations show that the optimum grating period is nearly identical to the surface plasmon polariton wavelength that can be supported at the gold-epoxy interface. This integrated platform couples light between the single mode fiber and the nanoapeture without the need for cumbersome optics, with applications for optical trapping and single-photon detection.

Enhancement of optical force acting on vesicles via the binding of gold nanoparticles

Here we found that gold nanoparticles (AuNPs) enhance the optical force acting on vesicles prepared from phospholipids via hydrophobic and electrostatic interactions. A laser beam was introduced into a cuvette filled with a suspension of vesicles and it accelerated them in its propagation direction via a scattering force. The addition of the AuNPs exponentially increased the velocity of the vesicles as their concentration increased, but polystyrene particles had no significant impact on velocity in the presence of AuNPs. To elucidate the mechanism of the increased velocity, the surface charges in the vesicles and the AuNPs were controlled; the surface charges of the vesicles were varied via the use of anionic, cationic and neutral phospholipids, whereas AuNPs with positive and negative charges were synthesized by coating with citrate ion and 4-dimethylaminopyridine, respectively. All vesicles increased the velocity at different degrees depending on the surface charge. The vesicles were accelerated more efficiently when their charges were opposite those of the AuNPs. These results suggested that hydrophobic and electrostatic interactions between the vesicles and the AuNPs enhanced the optical force. By accounting for the binding constant between the vesicles and the AuNPs, we proposed a model for the relationship between the concentration of the AuNPs and the velocity of the vesicles. Consequently, the increased velocity of the vesicles was attributed to the light scattering that was enhanced when AuNPs were adsorbed onto the vesicles.

Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations

Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein-nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. In this review, we describe recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. We highlight the use of diverse computational methods to address specific problems of the fields and discuss unexplored possibilities that lie ahead for the computational approaches in these areas.

Energy landscape of colloidal dumbbells in a periodic distribution of light

Using a ray tracing calculation, the energy landscape of dumbbells, made of spherical colloidal particles, interacting with a periodic distribution of light is calculated. As shown previously [E. Sarmiento-Gomez, J. A. Rivera-Moran and J. L. Aruaz-Lara, Soft Matter, 2018, 14, 3684], planar aggregates of spherical particles adopt discrete configurations in such light distribution. Here we focus on the case of colloidal dumbbells both symmetric and asymmetric from an experimental and theoretical point of view. It has been shown that the direct calculation using the ray tracing approximation is in excellent agreement with the experiment in spite of the fact that the particles size and the wavelength of the trapping light are comparable. We also corroborate, at least for the more simple case of a single particle in a parabolic light distribution, that the simple method used here provides the same results as the more complex and general Lorenz-Mie approach giving a more simple yet reliable method for the calculation of the energy landscape of colloidal aggregates in periodic light distributions.

T-Cell Mechanobiology: Force Sensation, Potentiation, and Translation

A T cell is a sensitive self-referential mechanical sensor. Mechanical forces influence the recognition, activation, differentiation, and function throughout the lifetime of a T cell. T cells constantly perceive and respond to physical stimuli through their surface receptors, cytoskeleton, and subcellular structures. Surface receptors receive physical cues in the form of forces generated through receptor-ligand binding events, which are dynamically regulated by contact tension, shear stress, and substrate rigidity. The resulting mechanotransduction not only influences T-cell recognition and signaling but also possibly modulates cell metabolism and gene expression. Moreover, forces also dynamically regulate the deformation, organization, and translocation of cytoskeleton and subcellular structures, leading to changes in T-cell mobility, migration, and infiltration. However, the roles and mechanisms of how mechanical forces modulate T-cell recognition, signaling, metabolism, and gene expression, are largely unknown and underappreciated. Here, we review recent technological and scientific advances in T-cell mechanobiology, discuss possible roles and mechanisms of T-cell mechanotransduction, and propose new research directions of this emerging field in health and disease.

Measuring Unzipping and Rezipping of Single Long DNA Molecules with Optical Tweezers

The unwinding of double-stranded DNA is a frequently occurring event during the cellular processes of DNA replication, repair, and transcription. To help further investigate properties of this fundamental process as well as to study proteins acting on unzipped DNA at the single molecule level, we describe a novel method for efficient preparation of long DNA constructs (arbitrary sequences of many kilobasepairs (kbp) in length) that can be forcibly unzipped and manipulated with optical tweezers or other single-molecule manipulation techniques. This method utilizes PCR, a nicking endonuclease, and strand displacement synthesis by the Klenow fragment of DNA polymerase I to introduce labeled nucleotides at appropriate positions to facilitate unzipping of the DNA by application of force. We also describe various optical tweezers measurement modes for measuring DNA unzipping and rezipping. These methods have applications to studying helicases and DNA binding proteins.

Demonstration of Enhanced Optical Pressure on a Structured Surface

The interaction of electromagnetic waves with condensed matter and the resultant force is fundamental in the physical sciences. The maximum pressure on a planar surface is understood to be twice the incident wave power density normalized by the background velocity. We demonstrate for the first time that this pressure can be exceeded by a substantial factor by structuring a surface. Experimental results for direct optomechanical deflection of a nanostructured gold film on a silicon nitride membrane illuminated by a laser beam are shown to significantly exceed those for the planar surface. This enhanced pressure can be understood as being associated with an asymmetric optical cavity array realized in the membrane film. The possible enhancement depends on the material properties and the geometrical parameters of the structured material. Such control and increase of optical pressure with nanostructured material should impact applications across the physical sciences.

Rapid discrimination of colon cancer cells with single base mutation in KRAS gene segment using laser tweezers Raman spectroscopy

Laser tweezers Raman spectroscopy (LTRS) as a label-free and noninvasive technology has been proven to be an ideal tool for analysis of single living cells, which provides important fingerprint information without interference from surrounding environments. For the first time, LTRS system was successfully used to examine the colon cancer cells with single base mutation in KRAS gene segment, including DKS-8 (KRAS wild-type [WT]) and DLD-1 (KRAS mutant-type [MT]), HKE-3 (KRAS WT) and HCT-116 (KRAS MT). Spectra changes of some vital biomolecules due to the gene mutation state were sensitively recorded by our home-made LTRS system. As a result of the comparison between DKS-8 and DLD-1 cells, an index of 97.5% of correct classification was obtained by combining LTRS with principle component analysis coupled with linear discriminant analysis (PCA-LDA) statistical analysis, while an index of 97.0% of correct classification was achieved between HKE-3 and HCT-116 cells. Moreover, between WT cells (DKS-8 and HKE-3) vs MT cells (DLD-1 and HCT-116), the index of correct classification was 81.2%, which was quite encouraging. Our preliminary results showed that the LTRS system coupled with PCA-LDA analysis will have a great potential for further applications in the rapid and label-free detection of circulating tumor cells in liquid biopsy.

Optical tweezers as an effective tool for spermatozoa isolation from mixed forensic samples

A single focus optical tweezer is formed when a laser beam is launched through a high numerical aperture immersion objective. This objective focuses the beam down to a diffraction-limited spot, which creates an optical trap where cells suspended in aqueous solutions can be held fixed. Spermatozoa, an often probative cell type in forensic investigations, can be captured inside this optical trap and dragged one by one across millimeter-length distances in order to create a cluster of cells which can be subsequently drawn up into a capillary for collection. Sperm cells are then ejected onto a sterile cover slip, counted, and transferred to a tube for DNA analysis workflow. The objective of this research was to optimize sperm cell collection for maximum DNA yield, and to determine the number of trapped sperm cells necessary to produce a full STR profile. A varying number of sperm cells from both a single-source semen sample and a mock sexual assault sample were isolated utilizing optical tweezers and processed using conventional STR analysis methods. Results demonstrated that approximately 50 trapped spermatozoa were required to obtain a consistently full DNA profile. A complete, single-source DNA profile was also achieved by isolating sperm cells via optical trapping from a mixture of sperm and vaginal epithelial cells. Based on these results, optical tweezers are a viable option for forensic applications such as separation of mixed populations of cells in forensic evidence.

Dynamic Control of Light Direction Enabled by Stimuli-Responsive Liquid Crystal Gratings

The ability to control light direction with tailored precision via facile means is long-desired in science and industry. With the advances in optics, a periodic structure called diffraction grating gains prominence and renders a more flexible control over light propagation when compared to prisms. Today, diffraction gratings are common components in wavelength division multiplexing devices, monochromators, lasers, spectrometers, media storage, beam steering, and many other applications. Next-generation optical devices, however, demand nonmechanical, full and remote control, besides generating higher than 1D diffraction patterns with as few optical elements as possible. Liquid crystals (LCs) are great candidates for light control since they can form various patterns under different stimuli, including periodic structures capable of behaving as diffraction gratings. The characteristics of such gratings depend on several physical properties of the LCs such as film thickness, periodicity, and molecular orientation, all resulting from the internal constraints of the sample, and all of these are easily controllable. In this review, the authors summarize the research and development on stimuli-controllable diffraction gratings and beam steering using LCs as the active optical materials. Dynamic gratings fabricated by applying external field forces or surface treatments and made of chiral and nonchiral LCs with and without polymer networks are described. LC gratings capable of switching under external stimuli such as light, electric and magnetic fields, heat, and chemical composition are discussed. The focus is on the materials, designs, applications, and future prospects of diffraction gratings using LC materials as active layers.

Single-cell assay on microfluidic devices

Advances in microfluidic techniques have prompted researchers to study the inherent heterogeneity of single cells in cell populations.

B cell mechanosensing: A mechanistic overview

B cells are essential to the adaptive immune system for providing the humoral immunity against cohorts of pathogens. The presentation of antigen to the B cell receptor (BCR) leads to the initiation of B cell activation, which is a process sensitive to the stiffness features of the substrates presenting the antigens. Mechanosensing of the B cells, potentiated through BCR signaling and the adhesion molecules, efficiently regulates B cell activation, proliferation and subsequent antibody responses. Defects in sensing of the antigen-presenting substrates can lead to the activation of autoreactive B cells in autoimmune diseases. The use of high-resolution, high-speed live-cell imaging along with the sophisticated biophysical materials, has uncovered the mechanisms underlying the initiation of B cell activation within seconds of its engagement with the antigen presenting substrates. In this chapter, we reviewed studies that have contributed to uncover the molecular mechanisms of B cell mechanosensing during the initiation of B cell activation.

Joule heating-induced particle manipulation on a microfluidic chip

We develop an electrokinetic technique that continuously manipulates colloidal particles to concentrate into patterned particulate groups in an energy efficient way, by exclusive harnessing of the intrinsic Joule heating effects. Our technique exploits the alternating current electrothermal flow phenomenon which is generated due to the interaction between non-uniform electric and thermal fields. Highly non-uniform electric field generates sharp temperature gradients by generating spatially-varying Joule heat that varies along the radial direction from a concentrated point hotspot. Sharp temperature gradients induce a local variation in electric properties which, in turn, generate a strong electrothermal vortex. The imposed fluid flow brings the colloidal particles at the centre of the hotspot and enables particle aggregation. Furthermore, maneuvering structures of the Joule heating spots, different patterns of particle clustering may be formed in a low power budget, thus opening up a new realm of on-chip particle manipulation process without necessitating a highly focused laser beam which is much complicated and demands higher power budget. This technique can find its use in Lab-on-a-chip devices to manipulate particle groups, including biological cells.

High-Performance Image-Based Measurements of Biological Forces and Interactions in a Dual Optical Trap

Optical traps enable the nanoscale manipulation of individual biomolecules while measuring molecular forces and lengths. This ability relies on the sensitive detection of optically trapped particles, typically accomplished using laser-based interferometric methods. Recently, image-based particle tracking techniques have garnered increased interest as a potential alternative to laser-based detection; however, successful integration of image-based methods into optical trapping instruments for biophysical applications and force measurements has remained elusive. Here, we develop a camera-based detection platform that enables accurate and precise measurements of biological forces and interactions in a dual optical trap. In demonstration, we stretch and unzip DNA molecules while measuring the relative distances of trapped particles from their trapping centers with sub-nanometer accuracy and precision. We then use the DNA unzipping technique to localize bound proteins with sub-base-pair precision, revealing how thermal DNA "breathing" fluctuations allow an unzipping fork to detect and respond to the presence of a protein bound downstream. This work advances the capabilities of image tracking in optical traps, providing a state-of-the-art detection method that is accessible, highly flexible, and broadly compatible with diverse experimental substrates and other nanometric techniques.

Where No Hand Has Gone Before: Probing Mechanobiology at the Cellular Level

Physical forces and other mechanical stimuli are fundamental regulators of cell behavior and function. Cells are also biomechanically competent: they generate forces to migrate, contract, remodel, and sense their environment. As the knowledge of the mechanisms of mechanobiology increases, the need to resolve and probe increasingly small scales calls for novel technologies to mechanically manipulate cells, examine forces exerted by cells, and characterize cellular biomechanics. Here, we review novel methods to quantify cellular force generation, measure cell mechanical properties, and exert localized piconewton and nanonewton forces on cells, receptors, and proteins. The combination of these technologies will provide further insight on the effect of mechanical stimuli on cells and the mechanisms that convert these stimuli into biochemical and biomechanical activity.

The size dependant behaviour of particles driven by a travelling surface acoustic wave (TSAW)

The use of travelling surface acoustic waves (TSAW) in a microfluidic system provides a powerful tool for the manipulation of particles and cells. In a TSAW driven system, acoustophoretic effects can cause suspended micro-objects to display three distinct responses: (1) swirling, driven by acoustic streaming forces, (2) migration, driven by acoustic radiation forces and (3) patterning in a spatially periodic manner, resulting from diffraction effects. Whilst the first two phenomena have been widely discussed in the literature, the periodic patterning induced by TSAW has only recently been reported and is yet to be fully elucidated. In particular, more in-depth understanding of the size-dependant nature of this effect and the factors involved are required. Herein, we present an experimental and numerical study of the transition in acoustophoretic behaviour of particles influenced by relative dominance of these three mechanisms and characterise it based on particle diameter, channel height, frequency and intensity of the TSAW driven microfluidic system. This study will enable better understanding of the performance of TSAW sorters and allow the development of TSAW systems for particle collection and patterning.

Coaxial differential dynamic microscopy for measurement of Brownian motion in weak optical field

Weak optical fields cause less damage to active cells and are easier to realize than traditional and tightly focused optical fields. While these fields are promising for biomedical science and particle manipulation applications, they lack a method for precise particle diffusion measurement because the weak fields cause the small changes in particle motion caused by weak fields. In this paper, we present a coaxial differential dynamic microscopy (CDDM) technique that uses a differential dynamic microscopy system, combined with an adjustable optical field. We use this technique to study Brownian motion of colloidal particles in weak optical fields. CDDM can quantitatively measure both the intensity and the pattern of the weak optical field and the diffusion coefficient of the particles. While the light paths of both the weak optical field and the illumination are coaxially incident on the sample cell, they remain independent. The optical field can be designed to have any pattern and adjusted to any intensity, while the measurements' sample illumination requirements are also satisfied. To verify the accuracy of the technique, we measured particle diffusion in weak Gaussian optical fields of different strengths. The diffusion coefficient was found to decrease with increasing field strength. These experimental results agree well with those results predicted using the Fokker-Planck equation and Euler algorithm simulations. This technique is expected to provide an efficient tool for research into particle manipulation by using weak optical fields, particularly for delicate systems, such as colloidal particles and biological cells.

A vector holographic optical trap

The invention of optical tweezers almost forty years ago has triggered applications spanning multiple disciplines and has also found its way into commercial products. A major breakthrough came with the invention of holographic optical tweezers (HOTs), allowing simultaneous manipulation of many particles, traditionally done with arrays of scalar beams. Here we demonstrate a vector HOT with arrays of digitally controlled Higher-Order Poincaré Sphere (HOPS) beams. We employ a simple set-up using a spatial light modulator and show that each beam in the array can be manipulated independently and set to an arbitrary HOPS state, including replicating traditional scalar beam HOTs. We demonstrate trapping and tweezing with customized arrays of HOPS beams comprising scalar orbital angular momentum and cylindrical vector beams, including radially and azimuthally polarized beams simultaneously in the same trap. Our approach is general enough to be easily extended to arbitrary vector beams, could be implemented with fast refresh rates and will be of interest to the structured light and optical manipulation communities alike.

Alleviating Distortion and Improving the Young's Modulus in Two-Photon Polymerization Fabrications

Two-photon polymerization enables the extremely high resolution three-dimensional printing of micro-structures. To know the mechanical properties, and better still, to be able to adjust them is of paramount importance to ensuring the proper structural integrity of the printed products. In this work, the Young’s modulus is measured on two-photon polymerized micro-cantilever bars. Optimizing the scanning trajectory of the laser focus points is important in alleviating distortion of the printed bars. By increasing the laser power and decreasing the inter-voxel distances we can double the Young’s modulus. Post-curing with ultraviolet light can approximately quadruple the Young’s modulus. However, the resulting modulus is still only about 0.3% of that of the bulk polymerized material.

Optical Trapping and Manipulation of Superparamagnetic Beads Using Annular-Shaped Beams

We propose an optical tweezers setup based on an annular-shaped laser beam that is efficient to trap 2.8 μm-diameter superparamagnetic particles. The optical trapping of such particles was fully characterized, and a direct absolute comparison with a geometrical optics model was performed. With this comparison, we were able to show that light absorption by the superparamagnetic particles is negligible for our annular beam tweezers, differing from the case of conventional Gaussian beam tweezers, in which laser absorption by the beads makes stable trapping difficult. In addition, the trap stiffness of the annular beam tweezers increases with the laser power and with the bead distance from the coverslip surface. While this first result is expected and similar to that achieved for conventional Gaussian tweezers, which use ordinary dielectric beads, the second result is quite surprising and different from the ordinary case, suggesting that spherical aberration is much less important in our annular beam geometry. The results obtained here provide new insights into the development of hybrid optomagnetic tweezers, which can apply simultaneously optical and magnetic forces on the same particles.

Single-Nanoparticle Tracking with Angstrom Localization Precision and Microsecond Time Resolution

Gold nanoparticles (AuNPs) have been used as a contrast agent for optical imaging of various single biomolecules. Because AuNPs have high scattering efficiency without photobleaching, biomolecular dynamics have been observed with nanometer localization precision and sub-millisecond time resolution. To understand the working principle of biomolecular motors in greater detail, further improvement of the localization precision and time resolution is necessary. Here, we investigated the lower limit of localization precision achievable with AuNPs and the fundamental law, which determines the localization precision. We first used objective-lens-type total internal reflection dark-field microscopy to obtain a scattering signal from an isolated AuNP. The localization precision was inversely proportional to the square root of the photon number, which is consistent with theoretical estimation. The lower limit of precision for a 40 nm AuNP was ∼0.3 nm with 1 ms time resolution and was restricted by detector saturation. To achieve higher localization precision, we designed and constructed an annular illumination total internal reflection dark-field microscopy system with an axicon lens, which can illuminate the AuNPs at high laser intensity without damaging the objective lens. In addition, we used high image magnification to avoid detector saturation. Consequently, we achieved 1.3 Å localization precision for 40 nm AuNPs and 1.9 Å localization precision for 30 nm AuNPs at 1 ms time resolution. Furthermore, even at 33 μs time resolution, localization precisions at 5.4 Å for 40 nm AuNPs and at 1.7 nm for 30 nm AuNPs were achieved. We then observed motion of head of kinesin-1 labeled with AuNP at microsecond time resolution. Transition cycles of bound/unbound states and tethered diffusion of unbound head during stepping motion on microtubule were clearly captured with higher time resolution or smaller AuNP than those used in previous studies, indicating applicability to single-molecule imaging of biomolecular motors.

Demodulated standing solitary wave and DNA-RNA transcription

Nonlinear dynamics of DNA molecule at segments where DNA-RNA transcription occurs is studied. Our basic idea is that the solitary wave, moving along the chain, transforms into a demodulated one at these segments. The second idea is that the wave becomes a standing one due to interaction with DNA surrounding, e.g., RNA polymerase molecules. We explain why this is biologically convenient and show that our results match the experimental ones. In addition, we suggest how to experimentally determine crucial constant describing covalent bonds within DNA.

Dynamics of individual molecular shuttles under mechanical force

Molecular shuttles are the basis of some of the most advanced synthetic molecular machines. In these devices a macrocycle threaded onto a linear component shuttles between different portions of the thread in response to external stimuli. Here, we use optical tweezers to measure the mechanics and dynamics of individual molecular shuttles in aqueous conditions. Using DNA as a handle and as a single molecule reporter, we measure thousands of individual shuttling events and determine the force-dependent kinetic rates of the macrocycle motion and the main parameters governing the energy landscape of the system. Our findings could open avenues for the real-time characterization of synthetic devices at the single molecule level, and provide crucial information for designing molecular machinery able to operate under physiological conditions.

Molecular shuttles are bi-stable and stimuli-responsive systems that are considered potential elements for molecular machinery. Here, the authors use optical tweezers to measure the force dependent real-time kinetics of individual molecular shuttles under aqueous conditions.

Nanoscale fiber-optic force sensors for mechanical probing at the molecular and cellular level

There is an ongoing need to develop ultrasensitive nanomechanical instrumentation that has high spatial and force resolution, as well as an ability to operate in various biological environments. Here, we present a compact nanofiber optic force transducer (NOFT) with sub-piconewton force sensitivity and a nanoscale footprint that paves the way to the probing of complex mechanical phenomena inside biomolecular systems. The NOFT platform comprises a SnO₂ nanofiber optic equipped with a thin, compressible polymer cladding layer studded with plasmonic nanoparticles (NPs). This combination allows angstrom-level movements of the NPs to be quantified by tracking the optical scattering of the NPs as they interact with the near-field of the fiber. The distance-dependent optical signals can be converted to force once the mechanical properties of the compressible cladding are fully characterized. In this protocol, the details of the synthesis, characterization, and calibration of the NOFT system are described. The overall protocol, from the synthesis of the nanofiber optic devices to acquisition of nanomechanical data, takes ~72 h.

Nanoradiator-Mediated Deterministic Opto-Thermoelectric Manipulation

Optical manipulation of colloidal nanoparticles and molecules is significant in numerous fields. Opto-thermoelectric nanotweezers exploiting multiple coupling among light, heat, and electric fields enables the low-power optical trapping of nanoparticles on a plasmonic substrate. However, the management of light-to-heat conversion for the versatile and precise manipulation of nanoparticles is still elusive. Herein, we explore the opto-thermoelectric trapping at plasmonic antennas that serve as optothermal nanoradiators to achieve the low-power (∼0.08 mW/μm2) and deterministic manipulation of nanoparticles. Specifically, precise optical manipulation of nanoparticles is achieved via optical control of the subwavelength thermal hot spots. We employ a femtosecond laser beam to further improve the heat localization and the precise trapping of single ∼30 nm semiconductor quantum dots at the antennas where the plasmon-exciton coupling can be tuned. With its low-power, precise, and versatile particle control, the opto-thermoelectric manipulation can have applications in photonics, life sciences, and colloidal sciences.

Inequivalence of fixed-force and fixed-extension statistical ensembles for a flexible polymer tethered to a planar substrate

Recent advances in single macromolecule experiments have sparked interest in the ensemble dependence of force-extension relations. The thermodynamic limit may not be attainable for such systems, which leads to inequivalence of the fixed-force and the fixed-extension ensembles. We consider an ideal Gaussian chain described by the Edwards Hamiltonian with one end tethered to a rigid planar substrate. We analytically calculate the force-extension relation in the two ensembles and we show their inequivalence, which is caused by the confinement of the polymer to half space. The inequivalence is quite remarkable for strong compressional forces. We also perform Monte-Carlo simulations of a tethered wormlike chain with contour length 20 times its persistence length, which corresponds to experiments measuring the conformations of DNA tethered to a wall. The simulations confirm the ensemble inequivalence and qualitatively agree with the analytical predictions of the Gaussian model. Our analysis shows that confinement due to tethering causes ensemble inequivalence, irrespective of the polymer model.

Calibration of force detection for arbitrarily shaped particles in optical tweezers

Force measurement with an optical trap requires calibration of it. With a suitable detector, such as a position-sensitive detector (PSD), it is possible to calibrate the detector so that the force can be measured for arbitrary particles and arbitrary beams without further calibration; such a calibration can be called an "absolute calibration". Here, we present a simple method for the absolute calibration of a PSD. Very often, paired position and force measurements are required, and even if synchronous measurements are possible with the position and force detectors used, knowledge of the force-position curve for the particle in the trap can be highly beneficial. Therefore, we experimentally demonstrate methods for determining the force-position curve with and without synchronous force and position measurements, beyond the Hookean (linear) region of the trap. Unlike the absolute calibration of the force and position detectors, the force-position curve depends on the particle and the trapping beam, and needs to be determined in each individual case. We demonstrate the robustness of our absolute calibration by measuring optical forces on microspheres as commonly trapped in optical tweezers, and other particles such a birefringent vaterite microspheres, red blood cells, and a deformable "blob".

Optical tweezers for trapping in a microfluidic environment

Optical tweezers use the force from a light beam to implement a precise gripping tool. Based purely on an optical principle, it works without any bodily contact with the object. In this paper we describe an optical tweezers that targets an application within the framework of nuclear magnetic resonance (NMR) spectroscopy of small objects, which are embedded inside a microfluidic channel that will be integrated in a micro-NMR detector. In the project's final stages, the whole system will be installed within the wide bore of a superconducting magnet. The aim is to precisely maintain the position of the object to be measured, without the use of susceptibility disturbing materials or geometries. In this contribution we focus on the design and construction of the tweezers. For the optical force simulation of the system we used a geometrical optics approach, which we combined with a ray fan description of the output beam of an optical system. By embedding both techniques within an iterative design process, we were able to design efficient optical tweezers that met the numerous constraints. Based on details of the constraints and requirements given by the application, different system concepts were derived and studied. Next, a highly adapted and efficient optical trapping system was designed and manufactured. After the components were characterized using vertical scanning interferometry, the system was assembled to achieve a monolithic optical component. The proper function of the optical tweezers was successfully tested by optical trapping of fused silica particles.

Non-invasive Neurite Mechanics in Differentiated PC12 Cells

Thermal Fluctuations Spectroscopy (TFS) in combination with novel optical-based instrumentation was used to study mechanical properties of cell-cultured neurites with a spatial resolution limited only by the light diffraction. The analysis of thermal fluctuations together with a physical model of cellular elasticity allow us to determine relevant mechanical properties of neurite as axial tension σ, flexural rigidity B, plasma membrane tension γ, membrane bending rigidity K, and cytoskeleton to membrane-coupling ρ_bk, whose values are consistent with previously reported values measured using invasive approaches. The value obtained for the membrane-coupling parameter was used to estimate the average number of coupling elements between the plasma membrane and the cytoskeleton that fell in the range of 30 elements per area of the laser spot used to record the fluctuations. Furthermore, to expand the TFS analysis, we investigate the correlation between F-actin linear density and the mechanical features of PC12 neurites. Using a hybrid instrument that combines TFS and a simple fluorescent technique, our results show that the fluctuations are related with the F-actin concentration. These measurements have an advantage of not requiring the application of an external force, allowing as to directly establish a correlation between changes in the mechanical parameters and cytoskeleton-protein concentrations. The sensibility of our method was also tested by the application of TFS technique to PC12 neurite under Paraformaldehyde and Latrunculin-A effect. These results show a dramatic modification in the fluctuations that are consistent with the reported effect of these drugs, confirming the high sensitivity of this technique. Finally, the thermal fluctuation approach was applied to DRG axons to show that its utility is not limited to studies of PC12 neurites, but it is suitable to measure the general characteristic of various neuron-like cells.

Microrheology, advances in methods and insights

Microrheology is an emerging technique that probes mechanical response of soft material at micro-scale. Generally, microrheology technique can be divided into active and passive versions. During last two decades, extensive efforts have been paid to improve both the experiment techniques and data analysis methods, especially about how to link consequential particle positions into trajectories. We review the recent advances in microrheology, including improvements in labeling, imaging, data acquiring, data processing and data interpretation. Some of the recent insights in soft matter and living systems gained by using this technique are given. Before these, we also give a very brief description of the basic principles of both active and passive microrheology techniques, and some details about optical particle tracking and DWS.

Direct Visualization of Barrier Crossing Dynamics in a Driven Optical Matter System

A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are inferred from ensemble measurements or the position of a transducer ( e. g., an AFM cantilever) as a surrogate variable. Direct visualization is highly desirable. Here, we achieve the direct measurement of barrier crossing trajectories by using optical microscopy to observe position and orientation changes of pairs of Ag nanoparticles, i. e. passing events, in an optical ring trap. A two-step mechanism similar to a bimolecular exchange reaction or the Michaelis-Menten scheme is revealed by analysis that combines detailed knowledge of each trajectory, a statistically significant number of repetitions of the passing events, and the driving force dependence of the process. We find that while the total event rate increases with driving force, this increase is due to an increase in the rate of encounters. There is no drive force dependence on the rate of barrier crossing because the key motion for the process involves a random (thermal) radial fluctuation of one particle allowing the other to pass. This simple experiment can readily be extended to study more complex barrier crossing processes by replacing the spherical metal nanoparticles with anisotropic ones or by creating more intricate optical trapping potentials.

Phase-shift feedback control for dielectrophoretic micromanipulation

In this paper, we present a novel approach to noncontact micromanipulation by controlled dielectrophoresis (DEP). To steer micro-objects in the desired way, the solutions reported in the literature use either DEP cages or amplitude modulation of the voltages applied to the electrodes. In contrast, we modulate the phases, that is, we control the phase shifts of the voltages applied to the electrodes, which simplifies the hardware implementation and extends the set of feasible forces. Furthermore, we introduce an innovative micro-electrode array layout, composed of four sectors with parallel (colinear) electrodes, which is capable of inducing an arbitrary movement in the manipulation area and is easy to fabricate using just an affordable one-layer technology. We then propose a closed-loop cascade control strategy based on real-time numerical optimization and deploy it to our experimental set-up. Numerical simulations and laboratory experiments demonstrate the manipulation capabilities such as positioning and steering of one or several microscopic objects (microspheres with a diameter of 50 μm) and even bringing two objects together and then separating them again. The results from simulations and experiments are compared and the positioning accuracy is evaluated in the whole manipulation area. The error in position is 8 μm in the worst case, which corresponds to 16% of the microsphere size or 0.7% of the manipulation range.

Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance

Single-molecule manipulation techniques have provided unprecedented insights into the structure, function, interactions, and mechanical properties of biological macromolecules. Recently, the single-molecule toolbox has been expanded by techniques that enable measurements of rotation and torque, such as the optical torque wrench (OTW) and several different implementations of magnetic (torque) tweezers. Although systematic analyses of the position and force precision of single-molecule techniques have attracted considerable attention, their angle and torque precision have been treated in much less detail. Here, we propose Allan deviation as a tool to systematically quantitate angle and torque precision in single-molecule measurements. We apply the Allan variance method to experimental data from our implementations of (electro)magnetic torque tweezers and an OTW and find that both approaches can achieve a torque precision better than 1 pN · nm. The OTW, capable of measuring torque on (sub)millisecond timescales, provides the best torque precision for measurement times ≲10 s, after which drift becomes a limiting factor. For longer measurement times, magnetic torque tweezers with their superior stability provide the best torque precision. Use of the Allan deviation enables critical assessments of the torque precision as a function of measurement time across different measurement modalities and provides a tool to optimize measurement protocols for a given instrument and application.

A Horizontal Magnetic Tweezers and Its Use for Studying Single DNA Molecules

We report the development of a magnetic tweezers that can be used to micromanipulate single DNA molecules by applying picoNewton (pN)-scale forces in the horizontal plane. The resulting force–extension data from our experiments show high-resolution detection of changes in the DNA tether’s extension: ~0.5 pN in the force and <10 nm change in extension. We calibrate our instrument using multiple orthogonal techniques including the well-characterized DNA overstretching transition. We also quantify the repeatability of force and extension measurements, and present data on the behavior of the overstretching transition under varying salt conditions. The design and experimental protocols are described in detail, which should enable straightforward reproduction of the tweezers.

Quantifying Local Molecular Tension Using Intercalated DNA Fluorescence

The ability to measure mechanics and forces in biological nanostructures, such as DNA, proteins and cells, is of great importance as a means to analyze biomolecular systems. However, current force detection methods often require specialized instrumentation. Here, we present a novel and versatile method to quantify tension in molecular systems locally and in real time, using intercalated DNA fluorescence. This approach can report forces over a range of at least ∼0.5-65 pN with a resolution of 1-3 pN, using commercially available intercalating dyes and a general-purpose fluorescence microscope. We demonstrate that the method can be easily implemented to report double-stranded (ds)DNA tension in any single-molecule assay that is compatible with fluorescence microscopy. This is particularly useful for multiplexed techniques, where measuring applied force in parallel is technically challenging. Moreover, tension measurements based on local dye binding offer the unique opportunity to determine how an applied force is distributed locally within biomolecular structures. Exploiting this, we apply our method to quantify the position-dependent force profile along the length of flow-stretched DNA and reveal that stretched and entwined DNA molecules-mimicking catenated DNA structures in vivo-display transient DNA-DNA interactions. The method reported here has obvious and broad applications for the study of DNA and DNA-protein interactions. Additionally, we propose that it could be employed to measure forces in any system to which dsDNA can be tethered, for applications including protein unfolding, chromosome mechanics, cell motility, and DNA nanomachines.

The Role of Single-Molecule Force Spectroscopy in Unraveling Typical and Autoimmune Heparin-induced Thrombocytopenia

For the last two decades, heparins have been widely used as anticoagulants. Besides numerous advantages, up to 5% patients with heparin administration suffer from a major adverse drug effect known as heparin-induced thrombocytopenia (HIT). This typical HIT can result in deep vein thrombosis, pulmonary embolism, occlusion of a limb artery, acute myocardial infarct, stroke, and a systemic reaction or skin necrosis. The basis of HIT may lead to clinical insights. Recent studies using single-molecule force spectroscopy (SMFS)-based atomic force microscopy revealed detailed binding mechanisms of the interactions between platelet factor 4 (PF4) and heparins of different lengths in typical HIT. Especially, SMFS results allowed identifying a new mechanism of the autoimmune HIT caused by a subset of human-derived antibodies in patients without heparin exposure. The findings proved that not only heparin but also a subset of antibodies induce thrombocytopenia. In this review, the role of SMFS in unraveling a major adverse drug effect and insights into molecular mechanisms inducing thrombocytopenia by both heparins and antibodies will be discussed.

Fundamental Limits of Optical Tweezer Nanoparticle Manipulation Speeds

Optical tweezers are a noncontact method of 3D positioning applicable to the fields of micro- and nanomanipulation and assembly, among others. In these applications, the ability to manipulate particles over relatively long distances at high speed is essential in determining overall process efficiency and throughput. In order to maximize manipulation speeds, it is necessary to increase the trapping laser power, which is often accompanied by undesirable heating effects due to material absorption. As such, the majority of previous studies focus primarily on trapping large dielectric microspheres using slow movement speeds at low laser powers, over relatively short translation distances. In contrast, we push nanoparticle manipulation beyond the region in which maximum lateral movement speed is linearly proportional to laser power, and investigate the fundamental limits imposed by material absorption, thus quantifying maximum possible speeds attainable with optical tweezers. We find that gold and silver nanospheres of diameter 100 nm are limited to manipulation speeds of ∼0.15 mm/s, while polystyrene spheres of diameter 160 nm can reach speeds up to ∼0.17 mm/s, over distances ranging from 0.1 to 1 mm. When the laser power is increased beyond the values used for these maximum manipulation speeds, the nanoparticles are no longer stably trapped in 3D due to weak confinement as a result of material absorption, heating, microbubble formation, and enhanced Brownian motion. We compared this result to our theoretical model, incorporating optical forces in the Rayleigh regime, Stokes' drag, and absorption effects, and found good agreement. These results show that optical tweezers can be fast enough to compete with other common, serial rapid prototyping and nanofabrication approaches.

Self-Induced Backaction Optical Pulling Force

We achieve long-range and continuous optical pulling in a periodic photonic crystal background, which supports a unique Bloch mode with the self-collimation effect. Most interestingly, the pulling force reported here is mainly contributed by the intensity gradient force originating from the self-induced backaction of the object to the self-collimation mode. This force is sharply distinguished from the widely held conception of optical tractor beams based on the scattering force. Also, this pulling force is insensitive to the angle of incidence and can pull multiple objects simultaneously.

Single-molecule manipulation and detection

Compared to conventional ensemble methods, studying macromolecules at single-molecule level can reveal extraordinary clear and even surprising views for a biological reaction. In the past 20 years, single-molecule techniques have been undergoing a very rapid development, and these cutting edge technologies have revolutionized the biological research by facilitating single-molecule manipulation and detection. Here we give a brief review about these advanced techniques, including optical tweezers, magnetic tweezers, atomic force microscopy (AFM), hydrodynamic flow-stretching assay, and single-molecule fluorescence resonance energy transfer (smFRET). We are trying to describe their basic principles and provide a few examples of applications for each technique. This review aims to give a rather introductory survey of single-molecule techniques for audiences with biological or biophysical background.