Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription

Two different molecular mechanisms, sliding and hopping, are employed by DNA-binding proteins for their one-dimensional facilitated diffusion on nonspecific DNA regions until reaching their specific target sequences. While it has been controversial whether RNA polymerases (RNAPs) use one-dimensional diffusion in targeting their promoters for transcription initiation, two recent single-molecule studies discovered that post-terminational RNAPs use one-dimensional diffusion for their reinitiation on the same DNA molecules. Escherichia coli RNAP, after synthesizing and releasing product RNA at intrinsic termination, mostly remains bound on DNA and diffuses in both forward and backward directions for recycling, which facilitates reinitiation on nearby promoters. However, it has remained unsolved which mechanism of one-dimensional diffusion is employed by recycling RNAP between termination and reinitiation. Single-molecule fluorescence measurements in this study reveal that post-terminational RNAPs undergo hopping diffusion during recycling on DNA, as their one-dimensional diffusion coefficients increase with rising salt concentrations. We additionally find that reinitiation can occur on promoters positioned in sense and antisense orientations with comparable efficiencies, so reinitiation efficiency depends primarily on distance rather than direction of recycling diffusion. This additional finding confirms that orientation change or flipping of RNAP with respect to DNA efficiently occurs as expected from hopping diffusion.

A Fractal-Based Correlation for Time-Dependent Surface Diffusivity in Porous Adsorbents

Fluid–solid adsorption processes are mostly governed by the adsorbate transport in the solid phase and surface diffusion is often the limiting step of the overall process in microporous materials such as zeolites. This work starts from a concise review of concepts and models for surface transport and variable surface diffusivity. It emerges that the phenomenon of hindered surface diffusion for monolayer adsorption, which is common in zeolites, and models able to fit a non-monotonic trend of surface diffusivity against adsorbate solid phase concentration, have received limited attention. This work contributes to the literature of hindered diffusion by formulating a time-dependent equation for surface diffusivity based on fractal dynamics concepts. The proposed equation takes into account the contributions of both fractal-like diffusion (a time-decreasing term) and hopping diffusion (a time-increasing term). The equation is discussed and numerically analyzed to testify its ability to reproduce the possible different patterns of surface diffusivity vs. time.

Probing inhomogeneous diffusion in the microenvironments of phase-separated polymers under confinement

Biopolymer condensates formed by liquid-liquid phase separation of proteins and nucleic acids have been recently discovered to be prevalent in biology. These dynamic condensates behave like biochemical reaction vessels but little is known about their structural organization and properties. Their biophysical properties and catalytic functions are likely related to condensate size, and thus it is critical that we study them on scales found in vivo. However, previous in vitro studies of condensate assembly and physical properties have involved condensates up to 1000 times larger than those found in vivo. Here, we report the application of confinement microscopy to visualize condensates and control their sizes by creating appropriate confinement length scales relevant to the cell environment. We observe anomalous diffusion of probe particles embedded within confined condensates, as well as heterogeneous dynamics in condensates formed from PEG/dextran and in ribonucleoprotein complexes of RNA and the RNA-binding protein Dhh1. We propose that the non-Gaussian dynamics we observe may indicate a hopping diffusion mechanism inside condensates. We also observe that for dextran-rich condensates, but not for ribonucleo condensates, probe particle diffusion depends on condensate size.

Microkinetic model for reaction and diffusion of titanium interstitial atoms near a TiO2(110) surface

For Ti interstitials in rutile, model yields kinetic parameters for surface injection, site-hopping diffusion, and reaction with extended defects.