Probing the catalytic activity and heterogeneity of Au-nanoparticles at the single-molecule level.

Nanoparticles can catalyze many important chemical transformations in organic synthesis, pollutant removal, and energy production. Characterizing their catalytic properties is essential for understanding the fundamental principles governing their activities, but is challenging in ensemble measurements due to their intrinsic heterogeneity from their structural dispersions, heterogeneous surface sites, and surface restructuring dynamics. To remove ensemble averaging, we recently developed a single-particle approach to study the redox catalysis of individual Au-nanoparticles in solution. By detecting the fluorescence of the catalytic product at the single-molecule level, we followed the catalytic turnovers of single Au-nanoparticles in real time at single-turnover resolution. Here we extend our single-nanoparticle studies to examine in detail the activity and heterogeneity of 6 nm spherical Au-nanoparticles. By analyzing the statistical properties of single-particle reaction waiting times across a range of substrate concentrations, we directly determine the distributions of kinetic parameters of individual Au-nanoparticles, including the rate constants and the equilibrium constants of substrate adsorption, and quantify their heterogeneity. Large activity heterogeneity is observed among the Au-nanoparticles in both the catalytic conversion reaction and the product dissociation reaction, which are typically hidden in ensemble-averaged measurements. Analyzing the temporal fluctuation of catalytic activity of individual Au-nanoparticles further reveals that these nanoparticles have two types of surface sites with different catalytic properties-one type-a with lower activity but higher substrate binding affinity, and the other type-b with higher activity but lower substrate binding affinity. Each Au-nanoparticle exhibits type-a behavior at low substrate concentrations and switches to type-b behavior at a higher substrate concentration, and the switching concentration varies largely from one nanoparticle to another. The heterogeneous and dynamic behavior of Au-nanoparticle catalysts highlight the intricate interplay between catalysis, structural dispersion, variable surface sites, and surface restructuring dynamics in nanocatalysis.

Single-molecule nanocatalysis reveals heterogeneous reaction pathways and catalytic dynamics.

Nanoparticles are important catalysts for many chemical transformations. However, owing to their structural dispersions, heterogeneous distribution of surface sites and surface restructuring dynamics, nanoparticles are intrinsically heterogeneous and challenging to characterize in ensemble measurements. Using a single-nanoparticle single-turnover approach, we study the redox catalysis of individual colloidal Au nanoparticles in solution, using single-molecule detection of fluorogenic reactions. We find that for product generation, all Au nanoparticles follow a Langmuir-Hinshelwood mechanism but with heterogeneous reactivity; and for product dissociation, three nanoparticle subpopulations are present that show heterogeneous reactivity between multiple dissociation pathways with distinct kinetics. Correlation analyses of single-turnover waiting times further reveal activity fluctuations of individual Au nanoparticles, attributable to both catalysis-induced and spontaneous dynamic surface restructuring that occurs at different timescales at the surface catalytic and product docking sites. The results exemplify the power of the single-molecule approach in revealing the interplay of catalysis, heterogeneous reactivity and surface structural dynamics in nanocatalysis.

Engineered holliday junctions as single-molecule reporters for protein-DNA interactions with application to a MerR-family regulator.

Protein-DNA interactions are essential for gene maintenance, replication, and expression. Characterizing how proteins interact with and change the structure of DNA is crucial in elucidating the mechanisms of protein function. Here, we present a novel and generalizable method of using engineered DNA Holliday junctions (HJs) that contain specific protein-recognition sequences to report protein-DNA interactions in single-molecule FRET measurements, utilizing the intrinsic structural dynamics of HJs. Because the effects of protein binding are converted to the changes in the structure and dynamics of HJs, protein-DNA interactions that involve small structural changes of DNA can be studied. We apply this method to investigate how the MerR-family regulator PbrR691 interacts with DNA for transcriptional regulation. Both apo- and holo-PbrR691 bind the stacked conformers of the engineered HJ, change their structures, constrain their conformational distributions, alter the kinetics, and shift the equilibrium of their structural dynamics. The information obtained maps the potential energy surfaces of HJ before and after PbrR691 binding and reveals the protein actions that force DNA structural changes for transcriptional regulation. The ability of PbrR691 to bind both HJ conformers and still allow HJ structural dynamics also informs about its conformational flexibility that may have significance for its regulatory function. This method of using engineered HJs offers quantification of the changes both in structure and in dynamics of DNA upon protein binding and thus provides a new tool to elucidate the correlation of structure, dynamics, and function of DNA-binding proteins.