Nanomechanics of negatively supercoiled diaminopurine-substituted DNA

Single molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. The particular sequence of a DNA segment defines both base stacking and hydrogen bonding that affect the partitioning and conformations of the two phases. Naturally or artificially modified bases alter H-bonds and base stacking and DNA with diaminopurine (DAP) replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded DAP:T base pairs. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiological conditions of mild tension and unwinding. This transition avoids writhing and the ease of this transition may prevent cumbersome topological rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length than B-DNA. However, left-handed DAP-substituted DNA was twice as stiff as unmodified L-DNA. Unmodified DNA and DAP-substituted DNA have very distinct mechanical characteristics at physiological levels of negative supercoiling and tension.

Mechanistic Insights From Single-Molecule Studies of Repair of Double Strand Breaks

DNA double strand breaks (DSBs) are among some of the most deleterious forms of DNA damage. Left unrepaired, they are detrimental to genome stability, leading to high risk of cancer. Two major mechanisms are responsible for the repair of DSBs, homologous recombination (HR) and nonhomologous end joining (NHEJ). The complex nature of both pathways, involving a myriad of protein factors functioning in a highly coordinated manner at distinct stages of repair, lend themselves to detailed mechanistic studies using the latest single-molecule techniques. In avoiding ensemble averaging effects inherent to traditional biochemical or genetic methods, single-molecule studies have painted an increasingly detailed picture for every step of the DSB repair processes.

In vitro single-molecule manipulation studies of viral DNA replication

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

Topological and physical links in soft matter systems

Linking, or multicomponent topological entanglement, is ubiquitous in soft matter systems, from mixtures of polymers and DNA filaments packedin vivoto interlocked line defects in liquid crystals and intertwined synthetic molecules. Yet, it is only relatively recently that theoretical and experimental advancements have made it possible to probe such entanglements and elucidate their impact on the physical properties of the systems. Here, we review the state-of-the-art of this rapidly expanding subject and organize it as follows. First, we present the main concepts and notions, from topological linking to physical linking and then consider the salient manifestations of molecular linking, from synthetic to biological ones. We next cover the main physical models addressing mutual entanglements in mixtures of polymers, both linear and circular. Finally, we consider liquid crystals, fluids and other non-filamentous systems where topological or physical entanglements are observed in defect or flux lines. We conclude with a perspective on open challenges.

Where Biology and Traditional Polymers Meet: The Potential of Associating Sequence-Defined Polymers for Materials Science

Polymers with precisely defined monomeric sequences present an exquisite tool for controlling material properties by harnessing both the robustness of synthetic polymers and the ability to tailor the inter- and intramolecular interactions so crucial to many biological materials. While polymer scientists traditionally synthesized and studied the physics of long molecules best described by their statistical nature, many biological polymers derive their highly tailored functions from precisely controlled sequences. Therefore, significant effort has been applied toward developing new methods of synthesizing, characterizing, and understanding the physics of non-natural sequence-defined polymers. This perspective considers the synergistic advantages that can be achieved via tailoring both precise sequence control and attributes of traditional polymers in a single system. Here, we focus on the potential of sequence-defined polymers in highly associating systems, with a focus on the unique properties, such as enhanced proton conductivity, that can be attained by incorporating sequence. In particular, we examine these materials as key model systems for studying previously unresolvable questions in polymer physics including the role of chain shape near interfaces and how to tailor compatibilization between dissimilar polymer blocks. Finally, we discuss the critical challenges-in particular, truly scalable synthetic approaches, characterization and modeling tools, and robust control and understanding of assembly pathways-that must be overcome for sequence-defined polymers to attain their potential and achieve ubiquity.

A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules

Single molecule force spectroscopy is a powerful approach to probe the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. However, common approaches to apply forces to biomolecules require expensive and cumbersome equipment and relatively large probes such as beads or cantilevers, which limits their use for many environments and makes integrating with other methods challenging. Furthermore, existing methods have key limitations such as an inability to apply compressive forces on single molecules. We report a nanoscale DNA force spectrometer (nDFS), which is based on a DNA origami hinge with tunable mechanical and dynamic properties. The angular free energy landscape of the nDFS can be engineered across a wide range through substitution of less than 5% of the strand components. We further incorporate a removable strut that enables reversible toggling of the nDFS between open and closed states to allow for actuated application of tensile and compressive forces. We demonstrate the ability to apply compressive forces by inducing a large bend in a 249bp DNA molecule, and tensile forces by inducing DNA unwrapping of a nucleosome sample. These results establish a versatile tool for force spectroscopy and robust methods for designing nanoscale mechanical devices with tunable force application.

Design and operation of magnetophoretic systems at microscale: Device and particle approaches

Combining both device and particle designs are the essential concepts to be considered in magnetophoretic system development. Researcher efforts are often dedicated to only one of these design aspects and neglecting the interplay between them. Herein, to bring out importance of the idea of integration between device and particle, we reviewed the working principle of magnetophoretic system (includes both device and particle design concepts). Since, the magnetophoretic force is influenced by both field gradient and magnetization volume, hence, accurate prediction of the magnetophoretic force is relying on the availability of information on both parameters. In device design, we focus on the different strategies used to create localized high-field gradient. For particle design, we emphasize on the scaling between hydrodynamic size and magnetization volume. Moreover, we also briefly discussed the importance of magnetoshape anisotropy related to particle design aspect of magnetophoretic systems. Next, we illustrated the need for integration between device and particle design using microscale applications of magnetophoretic systems, include magnetic tweezers and microfluidic systems, as our working example. On the basis of our discussion, we highlighted several promising examples of microscale magnetophoretic systems which greatly utilized the interplay between device and particle design. Further, we concluded the review with several factors that possibly resulted in the lack of research efforts related to device and particle design integration.

Nanomechanics of G-quadruplexes within the promoter of the KIT oncogene

G-quadruplexes (G4s) are tetrahelical DNA structures stabilized by four guanines paired via Hoogsteen hydrogen bonds into quartets. While their presence within eukaryotic DNA is known to play a key role in regulatory processes, their functional mechanisms are still under investigation. In the present work, we analysed the nanomechanical properties of three G4s present within the promoter of the KIT proto-oncogene from a single-molecule point of view through the use of magnetic tweezers (MTs). The study of DNA extension fluctuations under negative supercoiling allowed us to identify a characteristic fingerprint of G4 folding. We further analysed the energetic contribution of G4 to the double-strand denaturation process in the presence of negative supercoiling, and we observed a reduction in the energy required for strands separation.

Surface-modified elastomeric nanofluidic devices for single nanoparticle trapping

Our work focuses on the development of simpler and effective production of nanofluidic devices for high-throughput charged single nanoparticle trapping in an aqueous environment. Single nanoparticle confinement using electrostatic trapping has been an effective approach to study the fundamental properties of charged molecules under a controlled aqueous environment. Conventionally, geometry-induced electrostatic trapping devices are fabricated using SiOx-based substrates and comprise nanochannels imbedded with nanoindentations such as nanopockets, nanoslits and nanogrids. These geometry-induced electrostatic trapping devices can only trap negatively charged particles, and therefore, to trap positively charged particles, modification of the device surface is required. However, the surface modification process of a nanofluidic device is cumbersome and time consuming. Therefore, here, we present a novel approach for the development of surface-modified geometry-induced electrostatic trapping devices that reduces the surface modification time from nearly 5 days to just a few hours. We utilized polydimethylsiloxane for the development of a surface-modified geometry-induced electrostatic trapping device. To demonstrate the device efficiency and success of the surface modification procedure, a comparison study between a PDMS-based geometry-induced electrostatic trapping device and the surface-modified polydimethylsiloxane-based device was performed. The device surface was modified with two layers of polyelectrolytes (1: poly(ethyleneimine) and 2: poly(styrenesulfonate)), which led to an overall negatively charged surface. Our experiments revealed the presence of a homogeneous surface charge density inside the fluidic devices and equivalent trapping strengths for the surface-modified and native polydimethylsiloxane-based geometry-induced electrostatic trapping devices. This work paves the way towards broader use of geometry-induced electrostatic trapping devices in the fields of biosensing, disease diagnosis, molecular analysis, fluid quality control and pathogen detection.

Statistical Learning from Single-Molecule Experiments: Support Vector Machines and Expectation-Maximization Approaches to Understanding Protein Unfolding Data

Single-molecule force spectroscopy has become a powerful tool for the exploration of dynamic processes that involve proteins; yet, meaningful interpretation of the experimental data remains challenging. Owing to low signal-to-noise ratio, experimental force-extension spectra contain force signals due to nonspecific interactions, tip or substrate detachment, and protein desorption. Unravelling of complex protein structures results in the unfolding transitions of different types. Here, we test the performance of Support Vector Machines (SVM) and Expectation Maximization (EM) approaches in statistical learning from dynamic force experiments. When the output from molecular modeling in silico (or other studies) is used as a training set, SVM and EM can be applied to understand the unfolding force data. The maximal margin or maximum likelihood classifier can be used to separate experimental test observations into the unfolding transitions of different types, and EM optimization can then be utilized to resolve the statistics of unfolding forces: weights, average forces, and standard deviations. We designed an EM-based approach, which can be directly applied to the experimental data without data classification and division into training and test observations. This approach performs well even when the sample size is small and when the unfolding transitions are characterized by overlapping force ranges.

Simple way to correct the drift in surface-coupled optical tweezers using the laser reflection pattern

The surface-coupled optical tweezers are widely used to resolve small units of motion in biology. However, such motions could readily be interfered by the drift between the trap and surface. We present a simple and low-cost method to correct the drift both actively and passively based on video tracking the distance between the laser reflection pattern and the reference bead. As a result, we achieved sub-nanometer resolution and stability for the stuck bead over a broad range of averaging time (0.002-100 s) as demonstrated by the Allan deviation analysis. The sub-nanometer resolution was further manifested with step measurement. Finally, in double-stranded DNA and DNA hairpin stretching experiments, an extension resolution of 1-2 nm with the stability over 120 s has been demonstrated under a constant force. This work thus provides an easy way to bring the benefit of nanometer resolution and long-term stability to the surface-coupled optical tweezers.

Highly-Parallel Microfluidics-Based Force Spectroscopy on Single Cytoskeletal Motors

Cytoskeletal motors transform chemical energy into mechanical work to drive essential cellular functions. Optical trapping experiments have provided crucial insights into the operation of these molecular machines under load. However, the throughput of such force spectroscopy experiments is typically limited to one measurement at a time. Here, a highly-parallel, microfluidics-based method that allows for rapid collection of force-dependent motility parameters of cytoskeletal motors with two orders of magnitude improvement in throughput compared to currently available methods is introduced. Tunable hydrodynamic forces to stepping kinesin-1 motors via DNA-tethered beads and utilize a large field of view to simultaneously track the velocities, run lengths, and interaction times of hundreds of individual kinesin-1 molecules under varying resisting and assisting loads are applied. Importantly, the 16 µm long DNA tethers between the motors and the beads significantly reduces the vertical component of the applied force pulling the motors away from the microtubule. The approach is readily applicable to other molecular systems and constitutes a new methodology for parallelized single-molecule force studies on cytoskeletal motors.

Nanopores: a versatile tool to study protein dynamics

Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now readily available, observing the functional cycle of proteins - involving conformational changes and interactions - remains very challenging, e.g., due to ensemble averaging. However, time-resolved information is crucial to gain a mechanistic understanding of protein function. Single-molecule techniques such as FRET and force spectroscopies provide answers but can be limited by the required labelling, a narrow time bandwidth, and more. Here, we describe electrical nanopore detection as a tool for probing protein dynamics. With a time bandwidth ranging from microseconds to hours, nanopore experiments cover an exceptionally wide range of timescales that is very relevant for protein function. First, we discuss the working principle of label-free nanopore experiments, various pore designs, instrumentation, and the characteristics of nanopore signals. In the second part, we review a few nanopore experiments that solved research questions in protein science, and we compare nanopores to other single-molecule techniques. We hope to make electrical nanopore sensing more accessible to the biochemical community, and to inspire new creative solutions to resolve a variety of protein dynamics - one molecule at a 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.

Bubbles in microfluidics: an all-purpose tool for micromanipulation

In recent decades, the integration of microfluidic devices and multiple actuation technologies at the microscale has greatly contributed to the progress of related fields. In particular, microbubbles are playing an increasingly important role in microfluidics because of their unique characteristics that lead to specific responses to different energy sources and gas-liquid interactions. Many effective and functional bubble-based micromanipulation strategies have been developed and improved, enabling various non-invasive, selective, and precise operations at the microscale. This review begins with a brief introduction of the morphological characteristics and formation of microbubbles. The theoretical foundations and working mechanisms of typical micromanipulations based on acoustic, thermodynamic, and chemical microbubbles in fluids are described. We critically review the extensive applications and the frontline advances of bubbles in microfluidics, including microflow patterns, position and orientation control, biomedical applications, and development of bubble-based microrobots. We lastly present an outlook to provide directions for the design and application of microbubble-based micromanipulation tools and attract the attention of relevant researchers to the enormous potential of microbubbles in microfluidics.

Tornado-inspired acoustic vortex tweezer for trapping and manipulating microbubbles

Spatially concentrating and manipulating biotherapeutic agents within the circulatory system is a longstanding challenge in medical applications due to the high velocity of blood flow, which greatly limits drug leakage and retention of the drug in the targeted region. To circumvent the disadvantages of current methods for systemic drug delivery, we propose tornado-inspired acoustic vortex tweezer (AVT) that generates net forces for noninvasive intravascular trapping of lipid-shelled gaseous microbubbles (MBs). MBs are used in a diverse range of medical applications, including as ultrasound contrast agents, for permeabilizing vessels, and as drug/gene carriers. We demonstrate that AVT can be used to successfully trap MBs and increase their local concentration in both static and flow conditions. Furthermore, MBs signals within mouse capillaries could be locally improved 1.7-fold and the location of trapped MBs could still be manipulated during the initiation of AVT. The proposed AVT technique is a compact, easy-to-use, and biocompatible method that enables systemic drug administration with extremely low doses.

Particle Manipulation with External Field; From Recent Advancement to Perspectives

Physical forces, such as dielectric, magnetic, electric, optical, and acoustic force, provide useful principles for the manipulation of particles, which are impossible or difficult with other approaches. Microparticles, including polymer particles, liquid droplets, and biological cells, can be trapped at a particular position and are also transported to arbitrary locations in an appropriate external physical field. Since the force can be externally controlled by the field strength, we can evaluate physicochemical properties of particles from the shift of the particle location. Most of the manipulation studies are conducted for particles of sub-micrometer or larger dimensions, because the force exerted on nanomaterials or molecules is so weak that their direct manipulation is generally difficult. However, the behavior, interactions, and reactions of such small substances can be indirectly evaluated by observing microparticles, on which the targets are tethered, in a physical field. We review the recent advancements in the manipulation of particles using a physical force and discuss its potentials, advantages, and limitations from fundamental and practical perspectives.

Wi-Fi Live-Streaming Centrifuge Force Microscope for Benchtop Single-Molecule Experiments

The ability to apply controlled forces to individual molecules has been revolutionary in shaping our understanding of biophysics in areas as diverse as dynamic bond strength, biological motor operation, and DNA replication. However, the methodology to perform single-molecule experiments remains relatively inaccessible because of cost and complexity. In 2010, we introduced the centrifuge force microscope (CFM) as a platform for accessible and high-throughput single-molecule experimentation. The CFM consists of a rotating microscope with which prescribed centrifugal forces can be applied to microsphere-tethered biomolecules. In this work, we develop and demonstrate a next-generation Wi-Fi CFM that offers unprecedented ease of use and flexibility in design. The modular CFM unit fits within a standard benchtop centrifuge and connects by Wi-Fi to an external computer for live control and streaming at near gigabit speeds. The use of commercial wireless hardware allows for flexibility in programming and provides a streamlined upgrade path as Wi-Fi technology advances. To facilitate ease of use, detailed build and setup instructions, as well as LabVIEW-based control software and MATLAB-based analysis software, are provided. We demonstrate the instrument’s performance by analysis of force-dependent dissociation of short DNA duplexes of 7, 8, and 9 bp. We showcase the sensitivity of the approach by resolving distinct dissociation kinetic rates for a 7 bp duplex in which one G-C basepair is mutated to an A-T basepair.

Mechanical Characterization for Cellular Mechanobiology: Current Trends and Future Prospects

Accurate mechanical characterization of adherent cells and their substrates is important for understanding the influence of mechanical properties on cells themselves. Recent mechanobiology studies outline the importance of mechanical parameters, such as stress relaxation and strain stiffening on the behavior of cells. Numerous techniques exist for probing mechanical properties and it is vital to understand the benefits of each technique and how they relate to each other. This mini review aims to guide the reader through the toolbox of mechanical characterization techniques by presenting well-established and emerging methods currently used to assess mechanical properties of substrates and cells.

Contactless acoustic micro/nano manipulation: a paradigm for next generation applications in life sciences

Acoustic actuation techniques offer a promising tool for contactless manipulation of both synthetic and biological micro/nano agents that encompass different length scales. The traditional usage of sound waves has steadily progressed from mid-air manipulation of salt grains to sophisticated techniques that employ nanoparticle flow in microfluidic networks. State-of-the-art in microfabrication and instrumentation have further expanded the outreach of these actuation techniques to autonomous propulsion of micro-agents. In this review article, we provide a universal perspective of the known acoustic micromanipulation technologies in terms of their applications and governing physics. Hereby, we survey these technologies and classify them with regards to passive and active manipulation of agents. These manipulation methods account for both intelligent devices adept at dexterous non-contact handling of micro-agents, and acoustically induced mechanisms for self-propulsion of micro-robots. Moreover, owing to the clinical compliance of ultrasound, we provide future considerations of acoustic manipulation techniques to be fruitfully employed in biological applications that range from label-free drug testing to minimally invasive clinical interventions.

Real-time compaction of nanoconfined DNA by an intrinsically disordered macromolecular counterion

We demonstrate how a recently developed nanofluidic device can be used to study protein-induced compaction of genome-length DNA freely suspended in solution. The protein we use in this study is the hepatitis C virus core protein (HCVcp), which is a positively charged, intrinsically disordered protein. Using nanofluidic devices in combination with fluorescence microscopy, we observe that protein-induced compaction preferentially begins at the ends of linear DNA. This observation would be difficult to make with many other single-molecule techniques, which generally require the DNA ends to be anchored to a substrate. We also demonstrate that this protein-induced compaction is reversible and can be dynamically modulated by exposing the confined DNA molecules to solutions containing either HCVcp (to promote compaction) or Proteinase K (to disassemble the compact nucleo-protein complex). Although the natural binding partner for HCVcp is genomic viral RNA, the general biophysical principles governing protein-induced compaction of DNA are likely relevant for a broad range of nucleic acid-binding proteins and their targets.

Point spread function in interferometric scattering microscopy (iSCAT). Part I: aberrations in defocusing and axial localization

Interferometric scattering (iSCAT) microscopy is an emerging label-free technique optimized for the sensitive detection of nano-matter. Previous iSCAT studies have approximated the point spread function in iSCAT by a Gaussian intensity distribution. However, recent efforts to track the mobility of nanoparticles in challenging speckle environments and over extended axial ranges has necessitated a quantitative description of the interferometric point spread function (iPSF). We present a robust vectorial diffraction model for the iPSF in tandem with experimental measurements and rigorous FDTD simulations. We examine the iPSF under various imaging scenarios to understand how aberrations due to the experimental configuration encode information about the nanoparticle. We show that the lateral shape of the iPSF can be used to achieve nanometric three-dimensional localization over an extended axial range on the order of 10 µm either by means of a fit to an analytical model or calibration-free unsupervised machine learning. Our results have immediate implications for three-dimensional single particle tracking in complex scattering media.

Streaming-enhanced, chip-based biosensor with acoustically active, biomarker-functionalized micropillars: A case study of thrombin detection

Enzyme-linked immunosorbent assay is a widely used analytical technique for detecting and quantifying disease-specific protein biomarkers. Despite recent progresses in disease-specific protein biomarkers detection with microfluidic chips, many devices still suffer from the limited mass transport of target molecules, and consequently low detection efficiency or long incubation time. In this work, we present a novel strategy to significantly enhance the sensing efficiency of a chip-based biosensor by exploiting micro-streaming in an acoustofluidic device, which boosts intermolecular interactions and a hybridization chain reaction to increase the fluorescent signals. This device was made of a microfluidic chip that contains an array of PDMS micropillars in a ship-shaped microchannel. And the inner surface of the channel was functionalized with capture aptamers that bind with thrombin, chosen as a model target molecule. An ultrasonic transducer underneath the chip operating at 150 kHz generates circular micro-streaming flows around the pillars that significantly improves the binding efficiency of thrombin with capture aptamers by 1) increasing the retention time and 2) enhancing mass transport via local convection versus diffusion. The effects of ultrasound parameters, such as operating frequencies and voltages, on the distribution and magnitude of flows were optimized to obtain a better performance of the sensor chip. Under the optimized conditions, the detection limit was increased by one order of magnitude. Although this work has focused on the detection of thrombin as a model molecule, this streaming-enhanced, microstructure-based sensing strategy can be applied to detect a wide range of molecules or even cells.

Capture and elongation of single chromosomal DNA molecules using optically driven microchopsticks

DNA analysis based on the observation of single DNA molecules has been a key technology in molecular biology. Several techniques for manipulating single DNA molecules have been proposed for this purpose; however, these techniques have limits on the manipulatable DNA. To overcome this, we demonstrate a method of DNA manipulation using microstructures captured by optical tweezers that allow the manipulation of a chromosomal DNA molecule. For proper DNA handling, we developed microstructures analogous to chopsticks to capture and elongate single DNA molecules under an optical microscope. Two microstructures (i.e., microchopsticks) were captured by two focused laser beams to pinch a single yeast chromosomal DNA molecule between them and thereby manipulate it. The experiments demonstrated successful DNA manipulation and revealed that the size and geometry of the microchopsticks are important factors for effective DNA handling. This technique allows a high degree of freedom in handling single DNA molecules, potentially leading to applications in the study of chromosomal DNA.

Pitch-rotational manipulation of single cells and particles using single-beam thermo-optical tweezers

3D pitch rotation of microparticles and cells assumes importance in a wide variety of applications in biology, physics, chemistry and medicine. Applications such as cell imaging and injection benefit from pitch-rotational manipulation. Generation of such motion in single beam optical tweezers has remained elusive due to the complexities of generating high enough ellipticity perpendicular to the direction of propagation. Further, trapping a perfectly spherical object at two locations and subsequent pitch rotation hasn't yet been demonstrated to be possible. Here, we use hexagonal-shaped upconverting particles and single cells trapped close to a gold-coated glass cover slip in a sample chamber to generate complete 360 degree and continuous pitch motion even with a single optical tweezer beam. The tweezers beam passing through the gold surface is partially absorbed and generates a hot-spot to produce circulatory convective flows in the vicinity which rotates the objects. The rotation rate can be controlled by the intensity of the laser light. Thus such a simple configuration can turn the particle in the pitch sense. The circulatory flows in this technique have a diameter of about 5 μm which is smaller than those reported using acousto-fluidic techniques.

Optical Sorting at the Single-Particle Level with Single-Nanometer Precision Using Coordinated Intensity and Phase Gradient Forces

Position-controlled sorting of colloidal nanoparticles (NPs) at the single-particle level is a challenge in nanoscience. Optofluidic potential wells can partially address this challenge, but they have limited flexibility, reconfigurability, and precision. Here we introduce a strategy by feedback-controlled manipulation of NPs using reconfigurable optical traps with designed intensity and phase gradient. Spatiotemporal patterns of these optical traps coordinatively manipulate the NPs based on machine vision of their positions and differentiated scattering intensities. The NPs are always kept inside the optical field during the manipulation and stably trapped once the sorting is accomplished. To substantiate the key advantages of our approach, we present position-controlled optical sorting of single Ag and Au NPs of the same size (150 nm diameter) and ordering of monodisperse Au NPs (80 ± 9 nm diameter) according to their sub-10 nm radius variation, which can hardly be done via other approaches.

Force spectra of single bacterial amyloid CsgA nanofibers

CsgA is a major protein subunit of Escherichia coli biofilms and plays key roles in bacterial adhesion and invasion. CsgA proteins can self-assemble into amyloid nanofibers, characterized by their hierarchical structures across multiple length scales, outstanding strength and their structural robustness under harsh environments. Here, magnetic tweezers were used to study the force spectra of CsgA protein at fibril levels. The two ends of a single nanofiber were directly connected between a magnetic bead and a glass slide using a previously reported tag-free method. We showed that a wormlike chain model could be applied to fit the typical force–extension curves of CsgA nanofibers and to estimate accordingly the mechanical properties. The bending stiffness of nanofibers increased with increasing diameters. The changes in extension of single CsgA fibers were found to be up to 17 fold that of the original length, indicating exceptional tensile properties. Our results provide new insights into the tensile properties of bacterial amyloid nanofibers and highlight the ultrahigh structural stability of the Escherichia coli biofilms.

Magnetic tweezers were used to study the force spectra of CsgA, a major protein subunit of Escherichia coli biofilms, at fibril level.

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.

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.

Irreversible hydrodynamic trapping by surface rollers

A colloidal particle driven by externally actuated rotation can self-propel parallel to a rigid boundary by exploiting the hydrodynamic coupling that surfaces induce between translation and rotation. As such a roller moves along the boundary it generates local vortical flows, which can be used to trap and transport passive cargo particles. However, the details and conditions for this trapping mechanism have not yet been fully understood. Here, we show that the trapping of cargo is accomplished through time-irreversible interactions between the cargo and the boundary, leading to its migration across streamlines into a steady flow vortex next to the roller. The trapping mechanism is explained analytically with a two dimensional model, investigated numerically in three dimensions for a wide range of parameters and is shown to be analogous to the deterministic lateral displacement (DLD) technique used in microfluidics for the separation of differently sized particles. The several geometrical parameters of the problem are analysed and we predict that thin, disc-like rollers offer the most favourable trapping conditions.

Acoustic tweezers based on circular, slanted-finger interdigital transducers for dynamic manipulation of micro-objects

Acoustic tweezing technologies are gaining significant attention from the scientific communities due to their versatility and biocompatibility. This study presents acoustic tweezers based on circular, slanted-finger interdigital transducers (CSFITs), which can steer the propagation direction of surface acoustic waves (SAWs) by tuning the excitation frequency. The CSFITs based acoustic tweezers enable dynamic and reconfigurable manipulation of micro-objects using multi-tone excitation signals. Compared to traditional interdigital transducers that generate and control SAWs along one axis, the CSFITs allow for simultaneously generating and independently controlling SAWs propagating along multiple axes by changing the frequency composition and the phase information in a multi-tone excitation signal. Moreover, the CSFITs based acoustic tweezers can be used for patterning cells/particles in various distributions and translating them along complex paths. We believe that our design is valuable for cellular-scale biological applications, in which on-chip, contactless, biocompatible handling of bioparticles is needed.

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.

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.

Model-free 3D localization with precision estimates for brightfield-imaged particles

Volumetric imaging and 3D particle tracking are becoming increasingly common and have a variety of microscopy applications including in situ fluorescent imaging, in-vitro single-molecule characterization, and analysis of colloidal systems. While recent interest has generated discussion of optimal schemes for localizing diffraction-limited fluorescent puncta, there have been relatively few published routines for tracking particles imaged with bright-field illumination. To address this, we outline a simple, look-up-table based 3D tracking strategy, which can be adapted to most commercially available wide-field microscopes, and present two image processing algorithms that together yield high-precision localization and return estimates of statistical accuracy. Under bright-field illumination, a particle's depth can be determined based on the size and shape of its diffractive pattern due to Mie scattering. Contrary to typical "super-resolution" fluorescence tracking routines, which typically fit a diffraction-limited spot to a model point-spread-function, the lateral (XY) tracking routine relies on symmetry to locate a particle without prior knowledge of the form of the particle. At low noise levels (signal:noise > 1000), the symmetry routine estimates particle positions with accuracy better than 0.01 pixel. Depth localization is accomplished by matching images of particles to those in a pre-recorded look-up-table. The routine presented here optimally interpolates between LUT entries with better than 0.05 step accuracy. Both routines are tolerant of high levels of image noise, yielding sub-pixel/step accuracy with signal-to-noise ratios as small as 1, and, by design, return confidence intervals indicating the expected accuracy of each calculated position. The included implementations operate extremely quickly and are amenable to real-time analysis at frame rates exceeding several hundred frames per second.

3D steerable, acoustically powered microswimmers for single-particle manipulation

The ability to precisely maneuver micro/nano objects in fluids in a contactless, biocompatible manner can enable innovative technologies and may have far-reaching impact in fields such as biology, chemical engineering, and nanotechnology. Here, we report a design for acoustically powered bubble-based microswimmers that are capable of autonomous motion in three dimensions and selectively transporting individual synthetic colloids and mammalian cells in a crowded group without labeling, surface modification, or effect on nearby objects. In contrast to previously reported microswimmers, their motion does not require operation at acoustic pressure nodes, enabling propulsion at low power and far from an ultrasonic transducer. In a megahertz acoustic field, the microswimmers are subject to two predominant forces: the secondary Bjerknes force and a locally generated acoustic streaming propulsive force. The combination of these two forces enables the microswimmers to independently swim on three dimensional boundaries or in free space under magnetical steering.

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.

A Toolbox for Organelle Mechanobiology Research-Current Needs and Challenges

Mechanobiology studies from the last decades have brought significant insights into many domains of biological research, from development to cellular signaling. However, mechano-regulation of subcellular components, especially membranous organelles, are only beginning to be unraveled. In this paper, we take mitochondrial mechanobiology as an example to discuss recent advances and current technical challenges in this field. In addition, we discuss the needs for future toolbox development for mechanobiological research of intracellular organelles.

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.

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.

Wave number-spiral acoustic tweezers for dynamic and reconfigurable manipulation of particles and cells

Acoustic tweezers have recently raised great interest across many fields including biology, chemistry, engineering, and medicine, as they can perform contactless, label-free, biocompatible, and precise manipulation of particles and cells. Here, we present wave number-spiral acoustic tweezers, which are capable of dynamically reshaping surface acoustic wave (SAW) wavefields to various pressure distributions to facilitate dynamic and programmable particle/cell manipulation. SAWs propagating in multiple directions can be simultaneously and independently controlled by simply modulating the multitone excitation signals. This allows for dynamic reshaping of SAW wavefields to desired distributions, thus achieving programmable particle/cell manipulation. We experimentally demonstrated the multiple functions of wave number-spiral acoustic tweezers, among which are multiconfiguration patterning; parallel merging; pattern translation, transformation, and rotation; and dynamic translation of single microparticles along complex paths. This wave number-spiral design has the potential to revolutionize future acoustic tweezers development and advance many applications, including microscale assembly, bioprinting, and cell-cell interaction research.

Translation of a Coated Rigid Spherical Inclusion in an Elastic Matrix: Exact Solution, and Implications for Mechanobiology

The displacement of relatively rigid beads within a relatively compliant, elastic matrix can be used to measure the mechanical properties of the matrix. For example, in mechanobiological studies, magnetic or reflective beads can be displaced with a known external force to estimate the matrix modulus. Although such beads are generally rigid compared to the matrix, the material surrounding the beads typically differs from the matrix in one or two ways. The first case, as is common in mechanobiological experimentation, is the situation in which the bead must be coated with materials such as protein ligands that enable adhesion to the matrix. These layers typically differ in stiffness relative to the matrix material. The second case, common for uncoated beads, is the situation in which the beads disrupt the structure of the hydrogel or polymer, leading to a region of enhanced or reduced stiffness in the neighborhood of the bead. To address both cases, we developed the first analytical solution of the problem of translation of a coated, rigid spherical inclusion displaced within an isotropic elastic matrix by a remotely applied force. The solution is applicable to cases of arbitrary coating stiffness and size of the coating. We conclude by discussing applications of the solution to mechanobiology.

Ephemeral states in protein folding under force captured with a magnetic tweezers design

Magnetic tape heads are ubiquitously used to read and record on magnetic tapes in technologies as diverse as old VHS tapes, modern hard-drive disks, or magnetic bands on credit cards. Their design highlights the ability to convert electric signals into fluctuations of the magnetic field at very high frequencies, which is essential for the high-density storage demanded nowadays. Here, we twist this conventional use of tape heads to implement one in a magnetic tweezers design, which offers the unique capability of changing the force with a bandwidth of ∼10 kHz. We calibrate our instrument by developing an analytical expression that predicts the magnetic force acting on a superparamagnetic bead based on the Karlqvist approximation of the magnetic field created by a tape head. This theory is validated by measuring the force dependence of protein L unfolding/folding step sizes and the folding properties of the R3 talin domain. We demonstrate the potential of our instrument by carrying out millisecond-long quenches to capture the formation of the ephemeral molten globule state in protein L, which has never been observed before. Our instrument provides the capability of interrogating individual molecules under fast-changing forces with a control and resolution below a fraction of a piconewton, opening a range of force spectroscopy protocols to study protein dynamics under force.

Single-molecule approach for studying RNAP II transcription initiation using magnetic tweezers

The initiation of transcription underlies the ability of cells to modulate genome expression as a function of both internal and external signals and the core process of initiation has features that are shared across all domains of life. Specifically, initiation can be sub-divided into promoter recognition, promoter opening, and promoter escape. However, the molecular players and mechanisms used are significantly different in Eukaryotes and Bacteria. In particular, bacterial initiation requires only the formation of RNA polymerase (RNAP) holoenzyme and proceeds as a series of spontaneous conformational changes while eukaryotic initiation requires the formation of the 31-subunit pre-initiation complex (PIC) and often requires ATP hydrolysis by the Ssl2/XPB subunit of the general transcription factor TFIIH. Our mechanistic view of this process in Eukaryotes has recently been improved through a combination of structural and single-molecule approaches which are providing a detailed picture of the structural dynamics that lead to the production of an elongation competent RNAP II and thus, an RNA transcript. Here we provide the methodological details of our single-molecule magnetic tweezers studies of transcription initiation using purified factors from Saccharomyces cerevisiae.