Getting the Most Out of Fluorogenic Probes: Challenges and Opportunities in Using Single-Molecule Fluorescence to Image Electro- and Photocatalysis

Single-molecule fluorescence microscopy enables the direct observation of individual reaction events at the surface of a catalyst. It has become a powerful tool to image in real time both intra- and interparticle heterogeneity among different nanoscale catalyst particles. Single-molecule fluorescence microscopy of heterogeneous catalysts relies on the detection of chemically activated fluorogenic probes that are converted from a nonfluorescent state into a highly fluorescent state through a reaction mediated at the catalyst surface. This review article describes challenges and opportunities in using such fluorogenic probes as proxies to develop structure-activity relationships in nanoscale electrocatalysts and photocatalysts. We compare single-molecule fluorescence microscopy to other microscopies for imaging catalysis in situ to highlight the distinct advantages and limitations of this technique. We describe correlative imaging between super-resolution activity maps obtained from multiple fluorogenic probes to understand the chemical origins behind spatial variations in activity that are frequently observed for nanoscale catalysts. Fluorogenic probes, originally developed for biological imaging, are introduced that can detect products such as carbon monoxide, nitrite, and ammonia, which are generated by electro- and photocatalysts for fuel production and environmental remediation. We conclude by describing how single-molecule imaging can provide mechanistic insights for a broader scope of catalytic systems, such as single-atom catalysts.

How Heterogeneity Affects Cooperative Communications within Single Nanocatalysts

Catalysis remains one of the most essential methods in chemical research and industry. Recent experiments have discovered an unusual phenomenon of catalytic cooperativity, when a reaction at one active site can stimulate reactions at neighboring sites within single nanoparticles. While theoretical analysis established that the transport of charged holes is responsible for this phenomenon, it does not account for inhomogeneity in the structural and dynamic properties of single nanocatalysts. Here, we investigate the effect of heterogeneity on catalytic communications by extending a discrete-state stochastic framework to random distributions of the transition rates. Our explicit calculations of spatial and temporal properties of heterogeneous systems in comparison with homogeneous systems predict that the strength of cooperativity increases, while the communication lifetimes and distances decrease. Monte Carlo computer simulations support theoretical calculations, and microscopic arguments to explain these observations are also presented. Our theoretical analysis clarifies some important aspects of molecular mechanisms of catalytic processes.

Machine learning of atomic dynamics and statistical surface identities in gold nanoparticles

It is known that metal nanoparticles (NPs) may be dynamic and atoms may move within them even at fairly low temperatures. Characterizing such complex dynamics is key for understanding NPs' properties in realistic regimes, but detailed information on, e.g., the stability, survival, and interconversion rates of the atomic environments (AEs) populating them are non-trivial to attain. In this study, we decode the intricate atomic dynamics of metal NPs by using a machine learning approach analyzing high-dimensional data obtained from molecular dynamics simulations. Using different-shape gold NPs as a representative example, an AEs' dictionary allows us to label step-by-step the individual atoms in the NPs, identifying the native and non-native AEs and populating them along the MD simulations at various temperatures. By tracking the emergence, annihilation, lifetime, and dynamic interconversion of the AEs, our approach permits estimating a "statistical equivalent identity" for metal NPs, providing a comprehensive picture of the intrinsic atomic dynamics that shape their properties.

Investigating Plasmonic Catalysis Kinetics on Hot-Spot Engineered Nanoantennae

Strong hot-spots can facilitate photocatalytic reactions potentially providing effective solar-to-chemical energy conversion pathways. Although it is well-known that the local electromagnetic field in plasmonic nanocavities increases as the cavity size reduces, the influence of hot-spots on photocatalytic reactions remains elusive. Herein, we explored hot-spot dependent catalytic behaviors on a highly controlled platform with varying interparticle distances. Plasmon-meditated dehalogenation of 4-iodothiophenol was employed to observe time-resolved catalytic behaviors via in situ surface-enhanced Raman spectroscopy on dimers with 5, 10, 20, and 30 nm interparticle distances. As a result, we show that by reducing the gap from 20 to 10 nm, the reaction rate can be sped up more than 2 times. Further reduction in the interparticle distance did not improve reaction rate significantly although the maximum local-field was ∼2.3-fold stronger. Our combined experimental and theoretical study provides valuable insights in designing novel plasmonic photocatalytic platforms.

Dynamics of chemical reactions on single nanocatalysts with heterogeneous active sites

Modern chemical science and industries critically depend on the application of various catalytic methods. However, the underlying molecular mechanisms of these processes still remain not fully understood. Recent experimental advances that produced highly-efficient nanoparticle catalysts allowed researchers to obtain more quantitative descriptions, opening the way to clarify the microscopic picture of catalysis. Stimulated by these developments, we present a minimal theoretical model that investigates the effect of heterogeneity in catalytic processes at the single-particle level. Using a discrete-state stochastic framework that accounts for the most relevant chemical transitions, we explicitly evaluated the dynamics of chemical reactions on single heterogeneous nanocatalysts with different types of active sites. It is found that the degree of stochastic noise in nanoparticle catalytic systems depends on several factors that include the heterogeneity of catalytic efficiencies of active sites and distinctions between chemical mechanisms on different active sites. The proposed theoretical approach provides a single-molecule view of heterogeneous catalysis and also suggests possible quantitative routes to clarify some important molecular details of nanocatalysts.

In situ quantitative single-molecule study of site-specific photocatalytic activity and dynamics on ultrathin g-C3N4 nanosheets

Graphitic carbon nitride (g-C₃N₄) has attracted extensive research attention in recent years due to its unique layered structure, facile synthetic route, visible-light-responsive nature, and excellent photocatalytic performance. However, an insightful investigation of site-specific catalytic activities and kinetics on g-C₃N₄ is still warranted. Here, we fabricated ultrathin g-C₃N₄ nanosheets through thermal exfoliation. The optimized sample exhibits a high specific surface area of 307.35 m² g^-1 and a remarkable H₂ generation activity of 2008 μmol h^-1 g^-1 with an apparent quantum efficiency of 4.62% at λ = 420 nm. Single-molecule fluorescence microscopy was applied for the first time to spatially resolve the reaction heterogeneities with nanometer precision (∼10 nm). The catalytic kinetics (i.e., reactant adsorption, conversion, and product dissociation) and temporal activity fluctuations were in situ quantified at individual structural features (i.e., wrinkles, edges, and basal planes) of g-C₃N₄. It was found that the wrinkle and edge exhibited superior photocatalytic activity due to the intrinsic band modulation, which are 20 times and 14.8 times that of the basal plane, respectively. Moreover, due to the steric effect, the basal plane showed the highest adsorption constant and the lowest direct dissociation constant. Density functional theory (DFT) simulations unveiled the adsorption energies of reactant and product molecules on each structure of g-C₃N₄, which support our experimental results. Such investigation would shed more light on the fundamental understanding of site-specific catalytic dynamics on g-C₃N₄, which benefits the rational design of 2D layered materials for efficient solar-to-chemical energy conversion.

Microscopic mechanisms of cooperative communications within single nanocatalysts

Catalysis is an experimental approach to accelerate chemical reactions. It plays a critical role in modern industries. Recent experimental studies uncovered striking observations of cooperative communications for reactions on nanocatalysts. In these experiments, it was shown that the chemical reactions observed at specific active sites might effectively stimulate the same reactions at the neighboring sites. We developed a theoretical model to investigate the microscopic mechanisms of these phenomena. Our idea is that the catalytic communication is the result of the complex dynamics of charged holes. Explicit calculations are able to quantitatively explain all experimental observations, clarifying the molecular origin of cooperative communications. The presented theoretical framework might be utilized for developing efficient catalytic systems with better control over chemical reactions.

Catalysis is a method of accelerating chemical reactions that is critically important for fundamental research as well as for industrial applications. It has been recently discovered that catalytic reactions on metal nanoparticles exhibit cooperative effects. The mechanism of these observations, however, remains not well understood. In this work, we present a theoretical investigation on possible microscopic origin of cooperative communications in nanocatalysts. In our approach, the main role is played by positively charged holes on metal surfaces. A corresponding discrete-state stochastic model for the dynamics of holes is developed and explicitly solved. It is shown that the observed spatial correlation lengths are given by the average distances migrated by the holes before they disappear, while the temporal memory is determined by their lifetimes. Our theoretical approach is able to explain the universality of cooperative communications as well as the effect of external electric fields. Theoretical predictions are in agreement with experimental observations. The proposed theoretical framework quantitatively clarifies some important aspects of the microscopic mechanisms of heterogeneous catalysis.

Understanding the Reaction Dynamics on Heterogeneous Catalysts Using a Simple Stochastic Approach

Recent experimental advances on investigating nanoparticle catalysts with multiple active sites provided a large amount of quantitative information on catalytic processes. These observations stimulated significant theoretical efforts, but the underlying molecular mechanisms are still not well-understood. We introduce a simple theoretical method to analyze the reaction dynamics on catalysts with multiple active sites based on a discrete-state stochastic description and obtain a comprehensive description of the dynamics of chemical reactions on such catalysts. We explicitly determine how the dynamics of catalyzed chemical reactions depend on the number of active sites, on the number of intermediate chemical transitions, and on the topology of underlying chemical reactions. It is argued that the theory provides quantitative bounds for realistic dynamic properties of catalytic processes that can be directly applied to analyze the experimental observations. In addition, this theoretical approach clarifies several important aspects of the molecular mechanisms of chemical reactions on catalysts.

Design and engineering of a dual-mode absorption/emission molecular switch for all-optical encryption

Photochemical reactions that produce a detectable change in the spectroscopic properties of organic chromophores can be exploited to harness the principles of Boolean algebra and design molecule-based logic circuits. Moreover, the logic processing capabilities of these photoactive molecules can be directed to protect, encode, and conceal information at the molecular level. We have designed a photochemical strategy to read, write and encrypt data in the form of optical signals. We have synthesized a supramolecular system based on the known dye resazurin, and investigated a series of photochemical transformations that can be used to regulate its absorption and emission properties upon illumination with ultraviolet or visible light. We have then examined the logic behaviour of the photochemistry involved, and illustrated its potential application in data encryption.

Single-molecule photocatalytic dynamics at individual defects in two-dimensional layered materials

The insightful comprehension of in situ catalytic dynamics at individual structural defects of two-dimensional (2D) layered material, which is crucial for the design of high-performance catalysts via defect engineering, is still missing. Here, we resolved single-molecule trajectories resulted from photocatalytic activities at individual structural features (i.e., basal plane, edge, wrinkle, and vacancy) in 2D layered indium selenide (InSe) in situ to quantitatively reveal heterogeneous photocatalytic dynamics and surface diffusion behaviors. The highest catalytic activity was found at vacancy in a four-layer InSe, up to ~30× higher than that on the basal plane. Moreover, lower adsorption strength of reactant and slower dissociation/diffusion rates of product were found at more photocatalytic active defects. These distinct dynamic properties are determined by lattice structures/electronic energy levels of defects and layer thickness of supported InSe. Our findings shed light on the fundamental understanding of photocatalysis at defects and guide the rational defect engineering.

Stochastic Kinetics of Nanocatalytic Systems

Catalytic reaction events occurring on the surface of a nanoparticle constitute a complex stochastic process. Although advances in modern single-molecule experiments enable direct measurements of individual catalytic turnover events occurring on a segment of a single nanoparticle, we do not yet know how to measure the number of catalytic sites in each segment or how the catalytic turnover counting statistics and the catalytic turnover time distribution are related to the microscopic dynamics of catalytic reactions. Here, we address these issues by presenting a stochastic kinetics for nanoparticle catalytic systems. We propose a new experimental measure of the number of catalytic sites in terms of the mean and variance of the catalytic event count. By considering three types of nanocatalytic systems, we investigate how the mean, the variance, and the distribution of the catalytic turnover time depend on the catalytic reaction dynamics, the heterogeneity of catalytic activity, and communication among catalytic sites. This work enables accurate quantitative analyses of single-molecule experiments for nanocatalytic systems and enzymes with multiple catalytic sites.

Theoretical Investigations of the Dynamics of Chemical Reactions on Nanocatalysts with Multiple Active Sites

Recent synthetic advances led to the development of new catalytic particles with well-defined atomic structures and multiple active sites, which are called nanocatalysts. Experimental studies of processes at nanocatalysts uncovered a variety of surprising effects, but the molecular mechanisms of these phenomena remain not well understood. We propose a theoretical method to investigate the dynamics of chemical reactions on catalytic particles with multiple active sites. It is based on a discrete-state stochastic description that allows us to explicitly evaluate dynamic properties of the system. It is found that for independently occurring chemical reactions, the mean turnover times are inversely proportional to the number of active sites, showing no stochastic effects. However, the molecular details of reactions and the number of active sites influence the higher moments of reaction times. Our theoretical method provides a way to quantify the molecular mechanisms of processes at nanocatalysts.

Laser illumination-induced dramatic catalytic activity change on Au nanospheres

Understanding morphology dependent catalytic kinetics from a single nanoparticle plays a significant role in the development of robust nano-catalysts with high efficiency. Unfortunately, detailed knowledge of the morphology dependent catalytic properties of single nanoparticles after shape transitions is lacking. In this work, the distinct catalytic properties of a single gold nanoparticle (GNP) after symmetry breaking were disclosed at the single-particle level for the first time. The morphology of the spherical GNP was elongated into a rod shape (i.e., gold nanorod, GNR) with a tightly focused Gaussian laser beam based on the photothermal effect. By using the fluorogenic oxidation reaction (i.e., amplex red to resorufin) as a model reaction, noticeable variation in catalytic efficiency after the shape modulation process was found at the single-particle level. The GNP displays noticeably higher catalytic efficiency which might be ascribed to the heterogeneous lattice structure on the particle surface as confirmed by transmission electron microscopy (TEM) characterization. Rearrangement of surface atoms after shape modulation normally generates a more ordered crystal structure, resulting in a lower surface energy for catalytic reaction. However, both of these nanoparticles still exhibit dynamic activity fluctuation in a temporal dependent route, indicating a distinct spontaneous dynamic surface restructuring process. These kinetic evidences might facilitate the development nanoparticle-based heterogeneous catalysts, particularly based on the morphology effect.

Revealing the thermodynamics of individual catalytic steps based on temperature-dependent single-particle nanocatalysis

Due to the intrinsic heterogeneity of nanocatalysis, many underlying catalytic details on nanocatalysts are hidden in ensemble-averaged measurements.

Imaging Catalytic Hotspots on Single Plasmonic Nanostructures via Correlated Super-Resolution and Electron Microscopy

Surface-plasmon (SP) enhanced catalysis on plasmonic nanostructures brings opportunities to increase catalytic efficiency and alter catalytic selectivity. Understanding the underlying mechanism requires quantitative measurements of catalytic enhancement on these nanostructures, whose intrinsic structural heterogeneity presents experimental challenges. Using correlated super-resolution fluorescence microscopy and electron microscopy, here we report a quantitative visualization of SP-enhanced catalytic activity at the nanoscale within single plasmonic nanostructures. We focus on two Au- and Ag-based linked nanostructures that present plasmonic hotspots at nanoscale gaps. Spatially localized higher reaction rates at these gaps vs nongap regions report the SP-induced catalytic enhancements, which show direct correlations with the nanostructure geometries and local electric field enhancements. Furthermore, the catalytic enhancement scales quadratically with the local actual light intensity, attributable to hot electron involvement in the catalytic enhancement mechanism. These discoveries highlight the effectiveness of correlated super-resolution and electron microscopy in interrogating nanoscale catalytic properties.

Size-dependent catalytic kinetics and dynamics of Pd nanocubes: a single-particle study

Due to the well-known significant effect of the size on the catalytic activity of nanocatalysts, here we use single-molecule fluorescence microscopy to study the size-dependent catalytic kinetics and dynamics of individual Pd nanocubes. A series of size-dependent catalytic properties were revealed in both product formation and product desorption processes. It was found that, due to the different adsorption mechanisms of substrate molecules on Pd nanocubes, H2 adsorption is independent of the size of Pd nanocubes, while the large flat resazurin molecules show stronger adsorption on larger sized Pd nanocubes. Apparently, the Pd nanocubes can be divided into three types: when the size of the Pd nanocube is small, substrate binding can prohibit product desorption and product desorption prefers the direct pathway; when the size is in an appropriate range, the product desorption process could be independent of substrate binding and shows no selectivity between two parallel desorption pathways; if the size is large enough, substrate binding can promote product desorption and product desorption prefers the indirect pathway. We also observed the surface-restructuring-induced dynamic heterogeneity of individual Pd nanocubes in both product formation and desorption processes with timescales of about tens to one hundred seconds. The activity fluctuation of individual Pd nanocubes was found to be mainly due to the spontaneous surface-restructuring rather than the catalysis. Furthermore, we estimated the size-dependent activation energies and time scales of spontaneous dynamic surface restructuring, which are fundamental to heterogeneous catalysis. The work presented here reveals new insight into nanocatalysis and exemplifies the advantages of the single-molecule approach in probing the catalytic properties of nanocatalysts.

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles

Molecular dynamics simulations of ubiquitin in water/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a dynamics similar to 'surface-melted' inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a 'glassy' state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations ('colored' or 'pink' noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes. On the other hand, we find the dynamics of ubiquitin to be even more like a polycrystalline material in which the α-helix and β-sheet regions of the protein are similar to crystal grains so that the string-like collective atomic motion is concentrated in regions between the α-helix and β-sheet domains.

Microfluidic-based controllable synthesis of Pt nanocatalysts supported on carbon for fuel cells

A simple custom-made microfluidic reactor is used to synthesize Pt nanoparticles supported on carbon continuously as electrocatalysts for fuel cells.

X-ray spectroscopy for chemical and energy sciences: the case of heterogeneous catalysis

Heterogeneous catalysis is the enabling technology for much of the current and future processes relevant for energy conversion and chemicals synthesis. The development of new materials and processes is greatly helped by the understanding of the catalytic process at the molecular level on the macro/micro-kinetic time scale and on that of the actual bond breaking and bond making. The performance of heterogeneous catalysts is inherently the average over the ensemble of active sites. Much development aims at unravelling the structure of the active site; however, in general, these methods yield the ensemble-average structure. A benefit of X-ray-based methods is the large penetration depth of the X-rays, enabling in situ and operando measurements. The potential of X-ray absorption and emission spectroscopy methods (XANES, EXAFS, HERFD, RIXS and HEROS) to directly measure the structure of the catalytically active site at the single nanoparticle level using nanometer beams at diffraction-limited storage ring sources is highlighted. The use of pump-probe schemes coupled with single-shot experiments will extend the time range from the micro/macro-kinetic time domain to the time scale of bond breaking and making.

Origin and nature of spontaneous shape fluctuations in "small" nanoparticles

Normally chemically inert materials such as Au have been found to be catalytically active in the form of particles whose size is about 1 nm. Direct and indirect observations of various types of metal nanoparticles (NPs) in this size range, under catalytically relevant conditions for fuel-cell operation and catalysis, have indicated that such "small" particles can exhibit large spontaneous shape fluctuations and significant changes in shape and chemical activity in response to alterations in environmental conditions. NPs also normally exhibit facile coalescence when in proximity, impacting their stability and reactivity in applications. We perform molecular dynamics simulations on Ni nanoparticles, a commonly used NP in catalytic applications and carbon nanotube growth, in the ≈1 nm size regime where large-scale shape fluctuations have been observed experimentally. An analysis of the large-scale shape fluctuations observed in our simulations of these "small" NPs indicates that they are accompanied by collective motion of Ni atoms through the NP center, and we quantify these dynamic structures and their impact on NP shape. In contrast, stringlike collective atomic motion is confined to the NP interfacial region of NPs having a diameter greater than a few nanometers, and correspondingly, the overall NP shape remains roughly spherical, a case studied in our prior Ni NP simulations. Evidently, the large spontaneous NP shape fluctuations reflect a change in character of the collective atomic dynamics when the NPs become critically small in size.

Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions

In recent years, single-molecule and single-particle fluorescence microscopy has emerged as a tool to investigate chemical systems. After an initial lag of over a decade with respect to biophysical studies, this powerful imaging technique is now revealing mechanisms of 'classical' organic reactions, spatial distribution of chemical reactivity on surfaces and the phase of active catalysts. The recent advance into commercial imaging systems obviates the need for home-built laser systems and thus opens this technique to traditionally trained synthetic chemists. We discuss the requisite photophysical and chemical properties of fluorescent reporters and highlight the main challenges in applying single-molecule techniques to chemical questions. The goal of this Perspective is to provide a snapshot of an emerging multidisciplinary field and to encourage broader use of this young experimental approach that aids the observation of chemical reactions as depicted in many textbooks: molecule by molecule.

Glassy Interfacial Dynamics of Ni Nanoparticles: Part II Discrete Breathers as an Explanation of Two-Level Energy Fluctuations

Recent studies of the dynamics of diverse condensed amorphous materials have indicated significant heterogeneity in the local mobility and a progressive increase in collective particle motion upon cooling that takes the form of string-like particle rearrangements. In a previous paper (Part I), we examined the possibility that fluctuations in potential energy E and particle mobility μ associated with this 'dynamic heterogeneity' might offer information about the scale of collective motion in glassy materials based on molecular dynamics simulations of the glassy interfacial region of Ni nanoparticles (NPs) at elevated temperatures. We found that the noise exponent associated with fluctuations in the Debye-Waller factor, a mobility related quantity, was directly proportional to the scale of collective motion L under a broad range of conditions, but the noise exponent associated with E(t) fluctuations was seemingly unrelated to L. In the present work, we focus on this unanticipated difference between potential energy and mobility fluctuations by examining these quantities at an atomic scale. We find that the string atoms exhibit a jump-like motion between two well-separated bands of energy states and the rate at which these jumps occur seems to be consistent with the phenomenology of the 'slow-beta' relaxation process of glass-forming liquids. Concurrently with these local E(t) jumps, we also find 'quake-like' particle displacements having a power-law distribution in magnitude so that particle displacement fluctuations within the strings are strikingly different from local E(t) fluctuations. An analysis of these E(t) fluctuations suggests that we are dealing with 'discrete breather' excitations in which large energy fluctuations develop in arrays of non-linear oscillators by virtue of large anharmonicity in the interparticle interactions and discreteness effects associated with particle packing. We quantify string collective motions on a fast caging times scale (picoseconds) and explore the significance of these collective motions for understanding the Boson peak of glass-forming materials.

How does a single Pt nanocatalyst behave in two different reactions? A single-molecule study

Using single-molecule microscopy of fluorogenic reactions we studied Pt nanoparticle catalysis at single-particle, single-turnover resolution for two reactions: one an oxidative N-deacetylation and the other a reductive N-deoxygenation. These Pt nanoparticles show distinct catalytic kinetics in these two reactions: one following noncompetitive reactant adsorption and the other following competitive reactant adsorption. In both reactions, single nanoparticles exhibit temporal activity fluctuations attributable to dominantly spontaneous surface restructuring. Depending on the reaction sequence, single Pt nanoparticles may or may not show activity correlations in catalyzing both reactions, reflecting the structure insensitivity of the N-deacetylation reaction and the structure sensitivity of the N-deoxygenation reaction.

Interpreting single turnover catalysis measurements with constrained mean dwell times

Observation of a chemical transformation at the single-molecule level yields a detailed view of kinetic pathways contributing to the averaged results obtained in a bulk measurement. Studies of a fluorogenic reaction catalyzed by gold nanoparticles have revealed heterogeneous reaction dynamics for these catalysts. Measurements on single nanoparticles yield binary trajectories with stochastic transitions between a dark state in which no product molecules are adsorbed and a fluorescent state in which one product molecule is present. The mean dwell time in either state gives information corresponding to a bulk measurement. Quantifying fluctuations from mean kinetics requires identifying properties of the fluorescence trajectory that are selective in emphasizing certain dynamic processes according to their time scales. We propose the use of constrained mean dwell times, defined as the mean dwell time in a state with the constraint that the immediately preceding dwell time in the other state is, for example, less than a variable time. Calculations of constrained mean dwell times for a kinetic model with dynamic disorder demonstrate that these quantities reveal correlations among dynamic fluctuations at different active sites on a multisite catalyst. Constrained mean dwell times are determined from measurements of single nanoparticle catalysis. The results indicate that dynamical fluctuations at different active sites are correlated, and that especially rapid reaction events produce particularly slowly desorbing product molecules.

Exploring both sequence detection and restriction endonuclease cleavage kinetics by recognition site via single-molecule microfluidic trapping

We demonstrate the feasibility of a single-molecule microfluidic approach to both sequence detection and obtaining kinetic information for restriction endonucleases on dsDNA. In this method, a microfluidic stagnation point flow is designed to trap, hold, and linearize double-stranded (ds) genomic DNA to which a restriction endonuclease has been pre-bound sequence-specifically. By introducing the cofactor magnesium, we determine the binding location of the enzyme by the cleavage process of dsDNA as in optical restriction mapping, however here the DNA need not be immobilized on a surface. We note that no special labeling of the enzyme is required, which makes it simpler than our previous scheme using stagnation point flows for sequence detection. Our accuracy in determining the location of the recognition site is comparable to or better than other single molecule techniques due to the fidelity with which we can control the linearization of the DNA molecules. In addition, since the cleavage process can be followed in real time, information about the cleavage kinetics, and subtle differences in binding and cleavage frequencies among the recognition sites, may also be obtained. Data for the five recognition sites for the type II restriction endonuclease EcoRI on λ-DNA are presented as a model system. While the roles of the varying fluid velocity and tension along the chain backbone on the measured kinetics remain to be determined, we believe this new method holds promise for a broad range of studies of DNA-protein interactions, including the kinetics of other DNA cleavage processes, the dissociation of a restriction enzyme from the cleaved substrate, and other macromolecular cleavage processes.