Magnetic tweezers

Many biologically important macromolecules undergo motions that are essential to their function. Biophysical techniques can now resolve the motions of single molecules down to the nanometer scale or even below, providing new insights into the mechanisms that drive molecular movements. This review outlines the principal approaches that have been used for high-resolution measurements of single-molecule motion, including centroid tracking, fluorescence resonance energy transfer, magnetic tweezers, atomic force microscopy, and optical traps. For each technique, the principles of operation are outlined, the capabilities and typical applications are examined, and various practical issues for implementation are considered. Extensions to these methods are also discussed, with an eye toward future application to outstanding biological problems. related to motor processivity and load-bearing ability , and the kinetics and thermodynamics of mechanical response and folding transitions . However, deeper questions about the mechanism of molecular motion can also be addressed by singlemolecule methods. These include the coupling between chemical and mechanical cycles (1, 20,80), mechanisms of translocation , folding pathways and the properties of transition states , and issues of enzyme stochasticity and population heterogeneity .

This study evaluates the influence of vinculin in closed conformation on the mechanical properties of cells. We demonstrate that MEFvin À/À cells transfected with the eGFP-vinculin mutant A50I (talin-binding-deficient-vinculin in a constitutively closed conformation) show 2-fold lower stiffness and focal adhesion density compared to MEFvin +/+ and MEF Rescue cells. MEF A50I cells are as stiff as MEFvin À/À cells with similar focal adhesion density. Further, 2D traction microscopy indicates that MEF A50I and MEFvin À/ À cells generate 3-to 4-fold less strain energy than MEFvin +/+ and MEF Rescue cells. These results demonstrate that vinculin's mechano-coupling function is dependent on its conformational state.

Escherichia coli single-stranded DNA (ssDNA) binding protein (SSB) is the defining bacterial member of ssDNA binding proteins essential for DNA maintenance. SSB binds ssDNA with a variable footprint of ~30-70 nucleotides, reflecting partial or full wrapping of ssDNA around a tetramer of SSB. We directly imaged single molecules of SSB-coated ssDNA using total internal reflection fluorescence (TIRF) microscopy and observed intramolecular condensation of nucleoprotein complexes exceeding expectations based on simple wrapping transitions. We further examined this unexpected property by single-molecule force spectroscopy using magnetic tweezers. In conditions favoring complete wrapping, SSB engages in long-range reversible intramolecular interactions resulting in condensation of the SSB-ssDNA complex. RecO and RecOR, which interact with SSB, further condensed the complex. Our data support the idea that RecOR--and possibly other SSB interacting proteins--function(s) in part to alter long-range, macroscopic interactions between or throughout nucleoprotein complexes by microscopically altering wrapping and bridging distant sites.

Initiation is a highly regulated, rate-limiting step in transcription. We employed a series of approaches to examine the kinetics of RNA polymerase (RNAP) transcription initiation in greater detail. Quenched kinetics assays, in combination with magnetic tweezer experiments and other methods, showed that, contrary to expectations, RNAP exit kinetics from later stages of initiation (e.g. from a 7-base transcript) was markedly slower than from earlier stages. Further examination implicated a previously unidentified intermediate in which RNAP adopted a long-lived backtracked state during initiation. In agreement, the RNAP-GreA endonuclease accelerated transcription kinetics from otherwise delayed initiation states and prevented RNAP backtracking. Our results indicate a previously uncharacterized RNAP initiation state that could be exploited for therapeutic purposes and may reflect a conserved intermediate among paused, initiating eukaryotic enzymes.Significance:Transcription initiation ...

The commonly used fluorescent dye YOYO-1 (YOYO) has, using bulk techniques, been demonstrated to stain DNA heterogeneously at substoichiometric concentrations. We here, using nanofluidic channels and fluorescence microscopy, investigate the heterogeneous staining on the single DNA molecule level and demonstrate that the dye distribution is continuous. The equilibration of YOYO on DNA is extremely slow but can be accelerated by increasing the ionic strength and/or the temperature. Furthermore, we demonstrate how to use the heterogeneous staining as a tool for detailed and time-efficient studies of how fluorescent dyes affect the physical properties of DNA. We show that the relative increase in extension of DNA with increasing amount of YOYO bound is higher at low ionic strengths and also extrapolate the extension of native DNA. Our study reveals important information on how YOYO affects the physical properties of DNA, but it also has broader applications. First, it reveals how cationic intercalators, such as potential DNA drugs, affect DNA under strong confinement. Second, the strategy of using heterogeneous staining is of general use for single molecule studies of DNA interacting with proteins or ligands.

Initiation is a highly regulated, rate-limiting step in transcription. We used a series of approaches to examine the kinetics of RNA polymerase (RNAP) transcription initiation in greater detail. Quenched kinetics assays, in combination with gel-based assays, showed that RNAP exit kinetics from complexes stalled at later stages of initiation (e.g., from a 7-base transcript) were markedly slower than from earlier stages (e.g., from a 2- or 4-base transcript). In addition, the RNAP–GreA endonuclease accelerated transcription kinetics from otherwise delayed initiation states. Further examination with magnetic tweezers transcription experiments showed that RNAP adopted a long-lived backtracked state during initiation and that the paused–backtracked initiation intermediate was populated abundantly at physiologically relevant nucleoside triphosphate (NTP) concentrations. The paused intermediate population was further increased when the NTP concentration was decreased and/or when an imbalan...

In many cases, initiation is rate limiting to transcription. This due in part to the multiple cycles of abortive transcription that delay promoter escape and the transition from initiation to elongation. Pausing of transcription in initiation can further delay promoter escape. The previously hypothesized pausing in initiation was confirmed by two recent studies from Duchi et al. 1 and from Lerner, Chung et al. 2 In both studies, pausing is attributed to a lack of forward translocation of the nascent transcript during initiation. However, the two works report on different pausing mechanisms. Duchi et al. report on pausing that occurs during initiation predominantly on-pathway of transcript synthesis. Lerner, Chung et al. report on pausing during initiation as a result of RNAP backtracking, which is off-pathway to transcript synthesis. Here, we discuss these studies, together with additional experimental results from single-molecule FRET focusing on a specific distance within the transcription bubble. We show that the results of these studies are complementary to each other and are consistent with a model involving two types of pauses in initiation: a short-lived pause that occurs in the translocation of a 6-mer nascent transcript and a long-lived pause that occurs as a result of 1-2 nucleotide backtracking of a 7-mer transcript.

In many cases, initiation is rate limiting to transcription. This due in part to the multiple cycles of abortive transcription that delay promoter escape and the transition from initiation to elongation. Pausing of transcription in initiation can further delay promoter escape. The previously hypothesized pausing in initiation was confirmed by two recent studies from Duchi et al. 1 and from Lerner, Chung et al. 2 In both studies, pausing is attributed to a lack of forward translocation of the nascent transcript during initiation. However, the two works report on different pausing mechanisms. Duchi et al. report on pausing that occurs during initiation predominantly on-pathway of transcript synthesis. Lerner, Chung et al. report on pausing during initiation as a result of RNAP backtracking, which is off-pathway to transcript synthesis. Here, we discuss these studies, together with additional experimental results from single-molecule FRET focusing on a specific distance within the transcription bubble. We show that the results of these studies are complementary to each other and are consistent with a model involving two types of pauses in initiation: a short-lived pause that occurs in the translocation of a 6-mer nascent transcript and a long-lived pause that occurs as a result of 1-2 nucleotide backtracking of a 7-mer transcript.

Magnetomotive microscopy techniques are introduced to investigate cell dynamics and biomechanics. These techniques are based on magnetomotive transducers present in cells and optical coherence imaging techniques. In this study, magnetomotive transducers include magnetic nanoparticles (MNPs) and fluorescently labeled magnetic microspheres, while the optical coherence imaging techniques include integrated optical coherence (OCM)and multiphoton (MPM) microscopy,and diffraction phase microscopy (DPM). Samples used in this study are murine macrophage cells in culture that were incubated with magnetomotive transducers. MPMis used to visualize multifunctional microspheres based on their fluorescence, while magnetomotive OCM detects sinusoidal displacements of the sample induced by a magnetic field. DPM is used to image single cells at a lower frequency magnetic excitation, and with its Fourier transform light scattering (FTLS) analysis, oscillation amplitude is obtained, indicating the relative biomechanical properties of macrophage cells. These magnetomotive microscopy method shave potential to be used to image and measure cell dynamics and biomechanical properties. The ability to measure and understand biomechanical properties of cells and their microenvironments, especially for tumor cells, is of great importance and may provide insight for diagnostic and subsequently therapeutic interventions.

Magnetomotive microscopy techniques are introduced to investigate cell dynamics and biomechanics. These techniques are based on magnetomotive transducers present in cells and optical coherence imaging techniques. In this study, magnetomotive transducers include magnetic nanoparticles (MNPs) and fluorescently labeled magnetic microspheres, while the optical coherence imaging techniques include integrated optical coherence (OCM)and multiphoton (MPM) microscopy,and diffraction phase microscopy (DPM). Samples used in this study are murine macrophage cells in culture that were incubated with magnetomotive transducers. MPMis used to visualize multifunctional microspheres based on their fluorescence, while magnetomotive OCM detects sinusoidal displacements of the sample induced by a magnetic field. DPM is used to image single cells at a lower frequency magnetic excitation, and with its Fourier transform light scattering (FTLS) analysis, oscillation amplitude is obtained, indicating the relative biomechanical properties of macrophage cells. These magnetomotive microscopy method shave potential to be used to image and measure cell dynamics and biomechanical properties. The ability to measure and understand biomechanical properties of cells and their microenvironments, especially for tumor cells, is of great importance and may provide insight for diagnostic and subsequently therapeutic interventions.