Magneto-optical tweezers built around an inverted microscope

Bessel beam optical tweezers for manipulating superparamagnetic beads

We propose a Bessel beam optical tweezers setup that can stably trap superparamagnetic beads. The trap stiffness measured is practically independent of the radius of the Bessel beam and of the bead height (distance from the coverlip of the sample chamber), indicating that the beads can be trapped with high accuracy within a wide range of such parameters. On the other hand, the trap stiffness exhibits the expected linear increase with the laser power, despite the non-negligible absorption coefficient of the superparamagnetic beads. A geometrical optics model that considers spherical aberration and light absorption by the beads was used to predict the optical forces and trap stiffness, showing excellent agreement with the experimental data. We believe the results presented here advance the field of optical trapping manipulation of absorbing magnetic particles, and future applications will involve, for example, the design of new hybrid optomagnetic tweezers.

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-molecule techniques in biophysics: a review of the progress in methods and applications

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k _B T, where k _B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Mechanical determination of particle–cell interactions and the associated biomedical applications

Mechanical determination of particle–cell interactions and the associated biomedical applications.

Electromagnetic tweezers with independent force and torque control

Magnetic tweezers are powerful tools to manipulate and study the mechanical properties of biological molecules and living cells. In this paper we present a novel, bona fide electromagnetic tweezer (EMT) setup that allows independent control of the force and torque applied via micrometer-sized magnetic beads to a molecule under study. We implemented this EMT by combining a single solenoid that generates force (f-EMT) with a set of four solenoids arranged into a symmetric quadrupole to generate torque (τ-EMT). To demonstrate the capability of the tweezers, we attached optically asymmetric Janus beads to single, tethered DNA molecules. We show that tension in the piconewton force range can be applied to single DNA molecules and the molecule can simultaneously be twisted with torques in the piconewton-nanometer range. Furthermore, the EMT allows the two components to be independently controlled. At various force levels applied to the Janus bead, the trap torsional stiffness can be continuously changed simply by varying the current magnitude applied to the τ-EMT. The flexible and independent control of force and torque by the EMT makes it an ideal tool for a range of measurements where tensional and torsional properties need to be studied simultaneously on a molecular or cellular level.

Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube and in a computer

DNA-interacting proteins have roles in multiple processes, many operating as molecular machines which undergo dynamic meta-stable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and the proteins that bind to it must ideally be interrogated at a single molecule level in their native in vivo environments, in a time-resolved manner, fast enough to sample the molecular transitions across the free-energy landscape. Progress has been made over the past decade in utilizing cutting-edge tools of the physical sciences to address challenging biological questions concerning the function and modes of action of several different proteins which bind to DNA. These physiologically relevant assays are technically challenging but can be complemented by powerful and often more tractable in vitro experiments which confer advantages of the chemical environment with enhanced detection signal-to-noise of molecular signatures and transition events. In the present paper, we discuss a range of techniques we have developed to monitor DNA-protein interactions in vivo, in vitro and in silico. These include bespoke single-molecule fluorescence microscopy techniques to elucidate the architecture and dynamics of the bacterial replisome and the structural maintenance of bacterial chromosomes, as well as new computational tools to extract single-molecule molecular signatures from live cells to monitor stoichiometry, spatial localization and mobility in living cells. We also discuss recent developments from our laboratory made in vitro, complementing these in vivo studies, which combine optical and magnetic tweezers to manipulate and image single molecules of DNA, with and without bound protein, in a new super-resolution fluorescence microscope.

Structure and dynamics of single DNA molecules manipulated by magnetic tweezers and or flow

Here we describe the use of magnetic tweezers and or microfluidics to manipulate single DNA molecules. We describe experiment which employ magnetic tweezers coupled to an inverted microscope as well as the use of a magnetic tweezers setup with an upright microscope. Using a chamber prepared via soft lithography, we also describe a microfluidic device for the manipulation of individual DNA molecules. Finally, we present some past successful examples of using these approaches to elucidate unique information about protein-nucleic acid interactions.

Fast dynamics of supercoiled DNA revealed by single-molecule experiments

The dynamics of supercoiled DNA play an important role in various cellular processes such as transcription and replication that involve DNA supercoiling. We present experiments that enhance our understanding of these dynamics by measuring the intrinsic response of single DNA molecules to sudden changes in tension or torsion. The observed dynamics can be accurately described by quasistatic models, independent of the degree of supercoiling initially present in the molecules. In particular, the dynamics are not affected by the continuous removal of the plectonemes. These results set an upper bound on the hydrodynamic drag opposing plectoneme removal, and thus provide a quantitative baseline for the dynamics of bare DNA.

Single molecule studies of DNA binding proteins using optical tweezers

Optical tweezers have become a versatile tool in the biological sciences. Combined with various types of optical microscopy, they are being successfully used to discover the fundamental mechanism of biological processes. Recently, the study of proteins acting on DNA was aggressively undertaken at the single-molecule level. Here, we review the most recent studies which have revealed the dynamic behavior of individual protein molecules at work on DNA, providing detailed mechanistic insight that could not be revealed, at least not easily, using bulk-phase or ensemble approaches.