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Schematic layout of a magnetic tweezers device with horn-shaped yokes. Letters represent different parameterized variables in the geometry. Table I lists each geometric parameter and indicates the effect of varying that parameter on the ∇ x B ⇀ . The line labeled Δx represents the contour along which the B ⇀ values are tabulated. A sample would be placed normal to the distal end of this contour.
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We present the design methodology for arrays of neodymium iron boron (NdFeB)-based magnets for use in magnetic tweezers devices. Using finite element analysis (FEA), we optimized the geometry of the NdFeB magnet as well as the geometry of iron yokes designed to focus the magnetic fields toward the sample plane. Together, the magnets and yokes form...
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Context 1
... understand the effects of magnet and yoke geometry on device performance, we parameterized every aspect of the magnet and yoke geometry, then systematically tested the effects of changing each parameter independently (Fig. 1). To qualitatively compare the various simulations, the magnitude of the ⇀ B field was plotted as a 2-D density plot, providing insight into how the magnet and yoke geometry influence the distribution of field lines around the device (for example, in Figs. 2(a)-2(c)). Additionally, quantitative values of the magnitude of the ⇀ B field ...Context 2
... of field lines around the device (for example, in Figs. 2(a)-2(c)). Additionally, quantitative values of the magnitude of the ⇀ B field were plotted for a 1-cm long path extending from the midpoint between the tips of the magnetic tweezers device and extending away from the magnets into the area where a sample would be located (given by ∆x, as in Fig. 1). From these data, a figure of merit was developed to quantitatively compare the performance of each magnet and yoke configuration based on a linear fit to ⇀ B versus the magnet-sample separation distance ∆x (Fig. 1). The slope of the fitted line provides a locally averaged estimate of ∇ x ⇀ B , which in the limit of large magnetic ...Context 3
... of the magnetic tweezers device and extending away from the magnets into the area where a sample would be located (given by ∆x, as in Fig. 1). From these data, a figure of merit was developed to quantitatively compare the performance of each magnet and yoke configuration based on a linear fit to ⇀ B versus the magnet-sample separation distance ∆x (Fig. 1). The slope of the fitted line provides a locally averaged estimate of ∇ x ⇀ B , which in the limit of large magnetic fields (when the bead magnetic moment saturates to a constant value) is directly proportional to the applied force. The calculation of ∇ x ⇀ B also provides an estimate of the distance over which the applied force ...Similar publications
All living cells constantly experience and respond to mechanical stresses. The molecular networks that activate in cells in response to mechanical stimuli are yet not well-understood. Our limited knowledge stems partially from the lack of available tools that are capable of exerting controlled mechanical stress to individual cells and at the same t...
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds between monomers or of entire groups of monomers to tension is governed by the activation of statistically interac...
Submicrometer elasticity of double-stranded DNA (dsDNA) governs nanoscale bending of DNA segments and their interactions with proteins. Single-molecule force spectroscopy, including magnetic tweezers (MTs), is an important tool for studying DNA mechanics. However, its application to short DNAs under 1 μm is limited. We developed an MT-based method...
The metal ion-DNA interaction is key to biochemical processes and has applications in areas such as metal ion sensors and DNA nanomachines. For example, the formation of the T-Hg ²⁺ -T structure has been used in technologies such as DNA-based mercuric ion sensors. Though the interaction is widely used for practical purposes, the underlying mechanis...
Loops are ubiquitous topological elements formed when proteins simultaneously bind to two non-contiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the ext...
Citations
... In this case, the magnetic field amplitude and gradient are determined by the specific magnetic material selection and array design, and the field values are fixed with respect to the magnet rest frame. 18,19 The field gradients, and thus forces, can be easily and robustly varied with respect to the specimen plane using motorized stages that change the separation distance between the magnet array and the sample. 20 Although the use of precision linear stages, rather than current control, significantly simplifies the design, eliminates the possibility of hysteretic responses, and removes the need for cooling and complex electronics, 17,21 it also introduces several implementation challenges, including the disruption of the light path, an inability to apply true step forces due to the finite translation time of the heavy magnets, and noise associated with the motion and settling of the magnet into position. ...
... The key innovation in this design is the use of a diametrically opposed cylindrical magnet (RX04X0DIA, K&J Magnetics) that is oriented with respect to a fixed iron yoke with tips that focus and direct the magnetic field toward the sample (see Fig. 1, inset). 18 Rotating the cylindrical magnet about its central axis changes its alignment with respect to the focusing yoke and thereby creates a time-varying magnetic field at the sample, which varies from zero to about 0.1 T in our design. We used a servo motor (AKM23F, Kollmorgen) to drive this rotation and control the rotation speed. ...
Here we present a new, compact magnetic tweezers design that enables precise application of a wide range of dynamic forces to soft materials without the need to raise or lower the magnet height above the sample. This is achieved through the controlled rotation of the permanent magnet array with respect to the fixed symmetry axis defined by a custom-built iron yoke. These design improvements increase the portability of the device and can be implemented within existing microscope setups without the need for extensive modification of the sample holders or light path. This device is particularly well-suited to active microrheology measurements using either creep analysis, in which a step force is applied to a micron-sized magnetic particle that is embedded in a complex fluid, or oscillatory microrheology, in which the particle is driven with a periodic waveform of controlled amplitude and frequency. In both cases, the motions of the particle are measured and analyzed to determine the local dynamic mechanical properties of the material.
... Magnetic tweezers are uniquely suited for studying the mechanical response of biopolymers under controlled forces-such experiments are said to be performed in the constant force ensemble in which the DNA's thermally-averaged extension is measured as a function of externally-generated forces. Technical advances now allow applied forces in the 0.1-100 pN range and extensions down to angstroms to be reliably measured (although typical setups are limited to detecting extension changes in the order of 1-10 nm) [5][6][7][8][9][10][11][12]. In addition to a pulling force, the DNA's twist (or, more generally, linking number) [13] can also be modulated or, in a fixed-torque assay, direct, simultaneous and independent control of forces and torques on the DNA is also possible [14][15][16]. ...
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.
... This is a key factor that defines performance of the tweezers. The generated force is proportional to the gradient of magnetic field and directed toward the area with the strongest field [1,[15][16][17]. As a result, magnetic tweezers display different properties depending on the configuration of the field. ...
Magnetic force spectroscopy is a rapidly developing single molecule technique that has found numerous applications at the interface of physics and biology. Since the invention of the first magnetic tweezers, a number of modifications to the approach have helped to relieve the limitations of the original design while amplifying its strengths. Inventive molecular biology solutions further advanced the technique by expanding its possible applications. In its present form, the method can be applied to both single molecules and live cells without resorting to intense irradiation, can be easily multiplexed, accommodates multiple DNAs, displays impressive resolution, and allows a remarkable ease in the stretching and twisting of macromolecules. In this review, we describe the architecture of magnetic tweezers, key requirements for experimental design and analysis of data, and outline several applications of the method that illustrate its versatility.
... Tethers have superparamagnetic particles attached to one end that are subject to forces in the 0.1 piconewton (pN) to 100 nanonewton (nN) range when placed in non-uniform magnetic fields (sufficient to saturate the particles) (3,9,10). The magnetic fields are produced using permanent magnets or electromagnets (11,12). The twist of DNA can also be manipulated by rotating the magnets (2). ...
We report the development of a simple-to-implement magnetic force transducer that can apply a wide range of piconewton (pN) scale forces on single DNA molecules and DNA–protein complexes in the horizontal plane. The resulting low-noise force-extension data enable very high-resolution detection of changes in the DNA tether’s extension: ~0.05 pN in force and <10 nm change in extension. We have also verified that we can manipulate DNA in near equilibrium conditions through the wide range of forces by ramping the force from low to high and back again, and observing minimal hysteresis in the molecule’s force response. Using a calibration technique based on Stokes’ drag law, we have confirmed our force measurements from DNA force-extension experiments obtained using the fluctuation-dissipation theorem applied to transverse fluctuations of the magnetic microsphere. We present data on the force-distance characteristics of a DNA molecule complexed with histones. The results illustrate how the tweezers can be used to study DNA binding proteins at the single molecule level.
In order to generate homogeneous magnetophoretic forces, current magnetic tweezer devices operate placing electromagnetic inductors far enough from the sample. Consequently, high-power supplies are needed to reach sufficiently large forces. We demonstrate that both magnetophoretic force magnitude and homogeneity can be increased at will in this kind of devices by simply placing appropriate magnetic materials between the inductors and the sample. Choice of these material shape and location is made upon an extensive optimization process performed with finite element method simulations. Optimal configuration is shown to create large and homogeneous magnetophoretic forces over areas extensive enough to perform multiplexed microrheology tests with different values of force and pulse duration. A good correspondence is obtained between the experiment and the results from the simulations.
Single-molecule technologies have expanded our ability to detect biological events individually, in contrast to ensemble biophysical technologies, where the result provides averaged information. Recent developments in atomic force microscopy have not only enabled us to distinguish the heterogeneous phenomena of individual molecules, but also allowed us to view up to the resolution of a single covalent bond. Similarly, optical tweezers, due to their versatility and precisions, have emerged as a potent technique to dissect a diverse range of complex biological processes, from nanomechanics of ClpXP protease–dependent degradation to force-dependent processivity of motor proteins. Despite the advantages of optical tweezers, the time scales used in this technology were inconsistent with physiological scenarios, which led to the development of magnetic tweezers, where proteins are covalently linked with the glass surface, which in turn increases the observation window of a single biomolecule from minutes to weeks. Unlike optical tweezers, magnetic tweezers use magnetic fields to impose torque, which makes them convenient for studying DNA topology and topoisomerase functioning. Using modified magnetic tweezers, researchers were able to discover the mechanical role of chaperones, which support their substrate proteins by pulling them during translocation and assist their native folding as a mechanical foldase. In this article, we provide a focused review of many of these new roles of single-molecule technologies, ranging from single bond breaking to complex chaperone machinery, along with the potential to design mechanomedicine, which would be a breakthrough in pharmacological interventions against many diseases.
Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Although high strain and strain-rate impacts to the human body have been the subject of substantial research at both the systemic and tissue levels, little is known about the cell-level ramifications of such assaults. This is largely due to the lack of high throughput, dynamic compression devices capable of simulating such traumatic loading conditions on individual cells. To fill this gap, we developed and characterized a high speed, high actuation force, magnetically driven MEMS chip to apply stress to biological cells at unprecedented strain (10% to 90%), strain rate (30,000 to 200,000 s⁻¹, and throughput (12,000 cells/min). To demonstrate the capabilities of the μHammer, we applied biologically relevant strains and strain rates to human leukemic K562 cells and then monitored their viability for up to 8 days. We observed significantly repressed proliferation of the hit cells compared to both unperturbed and sham-hit control cells, accompanied by minimal cell death. This indicates success in applying cellular damage without compromising the overall viability of the population, allowing us to conclude that this device is well suited to study the subtle effects of impact on large populations of inherently heterogeneous cells. [2019-0132]
