High-precision measurements of light-induced torque on absorbing microspheres

High-Speed Optical Tweezers for the Study of Single Molecular Motors

Mechanical transitions in molecular motors often occur on a submillisecond time scale and rapidly follow binding of the motor with its cytoskeletal filament. Interactions of nonprocessive molecular motors with their filament can be brief and last for few milliseconds or fraction of milliseconds. The investigation of such rapid events and their load dependence requires specialized single-molecule tools. Ultrafast force-clamp spectroscopy is a constant-force optical tweezers technique that allows probing such rapid mechanical transitions and submillisecond kinetics of biomolecular interactions, which can be particularly valuable for the study of nonprocessive motors, single heads of processive motors, or stepping dynamics of processive motors. Here we describe a step-by-step protocol for the application of ultrafast force-clamp spectroscopy to myosin motors. We give indications on optimizing the optical tweezers setup, biological constructs, and data analysis to reach a temporal resolution of few tens of microseconds combined with subnanometer spatial resolution. The protocol can be easily generalized to other families of motor proteins.

Dissecting myosin-5B mechanosensitivity and calcium regulation at the single molecule level

Myosin-5B is one of three members of the myosin-5 family of actin-based molecular motors. Despite its fundamental role in recycling endosome trafficking and in collective actin network dynamics, the molecular mechanisms underlying its motility are inherently unknown. Here we combine single-molecule imaging and high-speed laser tweezers to dissect the mechanoenzymatic properties of myosin-5B. We show that a single myosin-5B moves processively in 36-nm steps, stalls at ~2 pN resistive forces, and reverses its directionality at forces >2 pN. Interestingly, myosin-5B mechanosensitivity differs from that of myosin-5A, while it is strikingly similar to kinesin-1. In particular, myosin-5B run length is markedly and asymmetrically sensitive to force, a property that might be central to motor ensemble coordination. Furthermore, we show that Ca2+ does not affect the enzymatic activity of the motor unit, but abolishes myosin-5B processivity through calmodulin dissociation, providing important insights into the regulation of postsynaptic cargoes trafficking in neuronal cells.

Sliding of a single lac repressor protein along DNA is tuned by DNA sequence and molecular switching

In any living cell, genome maintenance is carried out by DNA-binding proteins that recognize specific sequences among a vast amount of DNA. This includes fundamental processes such as DNA replication, DNA repair, and gene expression and regulation. Here, we study the mechanism of DNA target search by a single lac repressor protein (LacI) with ultrafast force-clamp spectroscopy, a sub-millisecond and few base-pair resolution technique based on laser tweezers. We measure 1D-diffusion of proteins on DNA at physiological salt concentrations with 20 bp resolution and find that sliding of LacI along DNA is sequence dependent. We show that only allosterically activated LacI slides along non-specific DNA sequences during target search, whereas the inhibited conformation does not support sliding and weakly interacts with DNA. Moreover, we find that LacI undergoes a load-dependent conformational change when it switches between sliding and strong binding to the target sequence. Our data reveal how DNA sequence and molecular switching regulate LacI target search process and provide a comprehensive model of facilitated diffusion for LacI.

Optical manipulation from the microscale to the nanoscale: fundamentals, advances and prospects

Since the invention of optical tweezers, optical manipulation has advanced significantly in scientific areas such as atomic physics, optics and biological science. Especially in the past decade, numerous optical beams and nanoscale devices have been proposed to mechanically act on nanoparticles in increasingly precise, stable and flexible ways. Both the linear and angular momenta of light can be exploited to produce optical tractor beams, tweezers and optical torque from the microscale to the nanoscale. Research on optical forces helps to reveal the nature of light-matter interactions and to resolve the fundamental aspects, which require an appropriate description of momenta and the forces on objects in matter. In this review, starting from basic theories and computational approaches, we highlight the latest optical trapping configurations and their applications in bioscience, as well as recent advances down to the nanoscale. Finally, we discuss the future prospects of nanomanipulation, which has considerable potential applications in a variety of scientific fields and everyday life.

Optical trapping performance of dielectric-metallic patchy particles

We demonstrate a series of simulation experiments examining the optical trapping behavior of composite micro-particles consisting of a small metallic patch on a spherical dielectric bead. A full parameter space of patch shapes, based on current state of the art manufacturing techniques, and optical properties of the metallic film stack is examined. Stable trapping locations and optical trap stiffness of these particles are determined based on the particle design and potential particle design optimizations are discussed. A final test is performed examining the ability to incorporate these composite particles with standard optical trap metrology technologies.

Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level

The maintenance of intact genetic information, as well as the deployment of transcription for specific sets of genes, critically rely on a family of proteins interacting with DNA and recognizing specific sequences or features. The mechanisms by which these proteins search for target DNA are the subject of intense investigations employing a variety of methods in biology. A large interest in these processes stems from the faster-than-diffusion association rates, explained in current models by a combination of 3D and 1D diffusion. Here, we present a review of the single-molecule approaches at the forefront of the study of protein-DNA interaction dynamics and target search in vitro and in vivo. Flow stretch, optical and magnetic manipulation, single fluorophore detection and localization as well as combinations of different methods are described and the results obtained with these techniques are discussed in the framework of the current facilitated diffusion model.

Ultrafast force-clamp spectroscopy of single molecules reveals load dependence of myosin working stroke

We describe a dual-trap force-clamp configuration that applies constant loads between a binding protein and an intermittently interacting biological polymer. The method has a measurement delay of only ∼10 μs, allows detection of interactions as brief as ∼100 μs and probes sub-nanometer conformational changes with a time resolution of tens of microseconds. We tested our method on molecular motors and DNA-binding proteins. We could apply constant loads to a single motor domain of myosin before its working stroke was initiated (0.2-1 ms), thus directly measuring its load dependence. We found that, depending on the applied load, myosin weakly interacted (<1 ms) with actin without production of movement, fully developed its working stroke or prematurely detached (<5 ms), thus reducing the working stroke size with load. Our technique extends single-molecule force-clamp spectroscopy and opens new avenues for investigating the effects of forces on biological processes.

Soft magnetic tweezers: a proof of principle

We present here the principle of soft magnetic tweezers which improve the traditional magnetic tweezers allowing the simultaneous application and measurement of an arbitrary torque to a deoxyribonucleic acid (DNA) molecule. They take advantage of a nonlinear coupling regime that appears when a fast rotating magnetic field is applied to a superparamagnetic bead immersed in a viscous fluid. In this work, we present the development of the technique and we compare it with other techniques capable of measuring the torque applied to the DNA molecule. In this proof of principle, we use standard electromagnets to achieve our experiments. Despite technical difficulties related to the present implementation of these electromagnets, the agreement of measurements with previous experiments is remarkable. Finally, we propose a simple way to modify the experimental design of electromagnets that should bring the performances of the device to a competitive level.

Cellular strategies for regulating DNA supercoiling: a single-molecule perspective

Entangling and twisting of cellular DNA (i.e., supercoiling) are problems inherent to the helical structure of double-stranded DNA. Supercoiling affects transcription, DNA replication, and chromosomal segregation. Consequently the cell must fine-tune supercoiling to optimize these key processes. Here, we summarize how supercoiling is generated and review experimental and theoretical insights into supercoil relaxation. We distinguish between the passive dissipation of supercoils by diffusion and the active removal of supercoils by topoisomerase enzymes. We also review single-molecule studies that elucidate the timescales and mechanisms of supercoil removal.

Torque detection using Brownian fluctuations

We report the statistical analysis of the movement of a submicron particle confined in a harmonic potential in the presence of a torque. The absolute value of the torque can be found from the auto- and cross-correlation functions of the particle's coordinates. We experimentally prove this analysis by detecting the torque produced onto an optically trapped particle by an optical beam with orbital angular momentum.

Exploring molecular motors and switches at the single-molecule level

Single-molecule techniques have propelled an impressive number of biophysical studies during the last decade. From relatively simple video-microscopy techniques, to sophisticated manipulation and detection apparata, single-molecule techniques are capable of tracking the movements and the reaction trajectories of single enzymatic units. By observing microspheres attached to biomolecules it is possible to follow the motion of molecular motors, or to detect conformational "switching" induced by regulatory proteins. Micromanipulation tools like optical tweezers have been widely applied to understand the mechanisms of linear molecular motors, and have allowed the measurement of the elementary steps and the forces produced by several motor proteins, including myosin, kinesin, and dynein. New experimental assays based on magnetic or optical "wrenches," which are able to apply and detect torques on rotary motors and biopolymers, are opening new possibilities in this field. Here, established and emerging magneto-optical manipulation and video-tracking techniques are reviewed, in the perspective of single molecular motors and regulatory proteins studies.