Magnetic tweezers

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 ...

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...

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.