Multiplexed, Tethered Particle Microscopy for Studies of DNA-Enzyme Dynamics.

DNA is the carrier of genetic information and, as such, is at the center of most essential cellular processes. To regulate its physiological function, specific proteins and motor enzymes constantly change conformational states with well-controlled dynamics. Twenty-five years ago, Schafer, Gelles, Sheetz, and Landick employed the tethered particle motion (TPM) technique for the first time to study transcription by RNA polymerase at the single-molecule level. TPM has since then remained one of the simplest, most affordable, and yet incisive single-molecule techniques available. It is an in vitro technique which allows investigation of DNA-protein interactions that change the effective length of a DNA tether. In this chapter, we will describe a recent strategy to multiplex TPM which substantially increases the throughput of TPM experiments, as well as a simulation to estimate the time resolution of experiments, such as transcriptional elongation assays, in which lengthy time averaging of the signal is impossible due to continual change of the DNA tether length. These improvements allow efficient study of several DNA-protein systems, including transcriptionally active DNA-RNA polymerase I complexes and DNA-gyrase complexes.

Foam drainage on the microscale II. Imaging flow through single Plateau borders.

The liquid in foam forms an interconnected network, which is composed of Plateau borders, nodes, and films. One of the dominant pathways for foam drainage is flow through Plateau borders, and we use confocal microscopy to obtain experimental results for the flow fields inside individual Plateau borders. For three types of surfactants detailed comparisons are made with a model based upon the influence of surface viscosity at free boundaries between the gas in the bubbles and the liquid in the Plateau borders. The model describes the flows well, and we find good agreement between the surface viscosity predicted by this model and representative values found in the literature. We also give a qualitative description of the flow in the nodes.

Rheological microscopy: local mechanical properties from microrheology.

We demonstrate how tracer microrheology methods can be extended to study submicron scale variations in the viscoelastic response of soft materials; in particular, a semidilute solution of lambda-DNA. The polymer concentration is depleted near the surfaces of the tracer particles, within a distance comparable to the polymer correlation length. The rheology of this microscopic layer alters the tracers' motion and can be precisely quantified using one- and two-point microrheology. Interestingly, we found this mechanically distinct layer to be twice as thick as the layer of depleted concentration, likely due to solvent drainage through the locally perturbed polymer structure.

Real-space imaging of nucleation and growth in colloidal crystallization.

Crystallization of concentrated colloidal suspensions was studied in real space with laser scanning confocal microscopy. Direct imaging in three dimensions allowed identification and observation of both nucleation and growth of crystalline regions, providing an experimental measure of properties of the nucleating crystallites. By following their evolution, we identified critical nuclei, determined nucleation rates, and measured the average surface tension of the crystal-liquid interface. The structure of the nuclei was the same as the bulk solid phase, random hexagonal close-packed, and their average shape was rather nonspherical, with rough rather than faceted surfaces.

Three-dimensional confocal microscopy of colloids.

Confocal microscopy is used in the study of colloidal gels, glasses, and binary fluids. We measure the three-dimensional positions of colloidal particles with a precision of approximately 50 nm (a small fraction of each particle's radius) and with a time resolution sufficient for tracking the thermal motions of several thousand particles at once. This information allows us to characterize the structure and the dynamics of these materials in qualitatively new ways, for example, by quantifying the topology of chains and clusters of particles as well as by measuring the spatial correlations between particles with high mobilities. We describe our experimental technique and describe measurements that complement the results of light scattering.

Two-point microrheology of inhomogeneous soft materials.

We demonstrate a novel method for measuring the microrheology of soft viscoelastic media, based on cross correlating the thermal motion of pairs of embedded tracer particles. The method does not depend on the exact nature of the coupling between the tracers and the medium, and yields accurate rheological data for highly inhomogeneous materials. We demonstrate the accuracy of this method with a guar solution, for which other microscopic methods fail due to the polymer's mesoscopic inhomogeneity. Measurements in an F-actin solution suggest conventional microrheology measurements may not reflect the true bulk behavior.