A well-defined surface architecture is essential to generate water-dispersible UCNPs that are long-term stable and enable a wealth of bioanalytical applications.

Photon-upconverting nanoparticles (UCNPs) are lanthanide-doped nanocrystals that emit visible light under near-infrared excitation (anti-Stokes emission). This unique optical property precludes background fluorescence and light scattering from biological materials. The emission of multiple and narrow emission lines is an additional hallmark of UCNPs that opens up new avenues for optical encoding. Distinct emission signatures can be obtained if the multiple emission of UCNPs is tuned by their dopant composition or by surface modification with dyes. Tuning the intensity of only one of the multiple emission lines and using another one as a constant reference signal enables the design of ratiometric codes that are resistant to fluctuations in absolute signal intensities. Combining several UCNPs each displaying a distinct set of emission lines expands the coding capacity exponentially and lays the foundation for highly multiplexed analyte detection. This Review highlights the potential of UCNPs for labeling and encoding biomolecules, microspheres, and even whole cells.

Individual enzyme molecules have been observed to possess discrete and different turnover rates due to the presence of long-lived activity states. These stable activity states are thought to result from different molecular conformations or post-translational modifications. The distributions in kinetic activity observed in previous studies were obtained from small numbers of single enzyme molecules. Due to this limitation, it has not been possible to fully characterize the different kinetic and equilibrium binding parameters of single enzyme molecules. In this paper, we analyze hundreds of single beta-galactosidase molecules simultaneously; using a high-density array of 50,000 fL-reaction chambers, we confirm the presence of long-lived kinetic states within a population of enzyme molecules. Our analysis has isolated the source of kinetic variability to kcat. The results explain the kinetic variability within enzyme molecule populations and offer a deeper understanding of the unique properties of single enzyme molecules. Gaining a more fundamental understanding of how individual enzyme molecules work within a population should provide insight into how they affect downstream biochemical processes. If the results reported here can be generalized to other enzymes, then the stochastic nature of individual enzyme molecule kinetics should have a substantial impact on the overall metabolic activity within a cell.

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Photon upconverting nanoparticles convert near-infrared into visible light (anti-Stokes emission), which strongly reduces the background of autofluorescence and light scattering in biological materials. Hexagonal NaYF(4) nanocrystals doped with Yb(3+) as the sensitizer and Er(3+)/Ho(3+)/Tm(3+) as the activator display at least two emission lines that respond differently to temperature changes. The ratio of the main emission line intensities enables a self-referenced optical readout of the temperature in the physiologically relevant range from 20 to 45 °C. Upconverting nanoparticles of the type NaYF(4):Yb, Er covered by an inactive shell of NaYF(4) are bright and allow for resolving temperature differences of less than 0.5 °C in the physiological range. The optical readout of this nanoparticle-based thermometer offers many options for imaging the two-dimensional distribution of temperature.

Inhibition kinetics of single-␤-galactosidase molecules with the slow-binding inhibitor D-galactal have been characterized by segregating individual enzyme molecules in an array of 50,000 ultrasmall reaction containers and observing substrate turnover changes with fluorescence microscopy. Inhibited and active states of ␤-galactosidase could be clearly distinguished, and the large array size provided very good statistics. With a pre-steady-state experiment, we demonstrated the stochastic character of inhibitor release, which obeys first-order kinetics. Under steady-state conditions, the quantitative detection of substrate turnover changes over long time periods revealed repeated inhibitor binding and release events, which are accompanied by conformational changes of the enzyme's catalytic site. We proved that the rate constants of inhibitor release and binding derived from stochastic changes in the substrate turnover are consistent with bulk-reaction kinetics.␤-galactosidase ͉ enzyme kinetics ͉ fluorescence microscopy ͉ single molecule T he emergence of new assays for studying enzymes at the single-molecule level has profoundly extended our view of enzyme mechanisms. Whereas stochastic molecular behaviors are hidden by using bulk methods, single-molecule experiments have revealed that, in a population of enzymes, such as lactate dehydrogenase (1), phosphatase (2), or ␤-galactosidase (3), the catalytic rates of individual enzyme molecules are heterogeneous and do not interconvert quickly. Furthermore, it has been shown that the substrate turnover of individual ␤-galactosidase (4), cholesterol oxidase (5), or lipase (6) molecules undergoes dynamic fluctuations in sequential catalytic cycles. These two variations in enzyme activity are referred to as static and dynamic heterogeneity, respectively, and have both been attributed to different conformational states of the enzyme. Despite such heterogeneity, the Michaelis-Menten model derived from bulk enzyme experiments still holds for single-molecule experiments once a stochastic perspective is adopted (4,7,8).Traditionally, one of the most important tools to elucidate an enzyme's catalytic mechanism has been to study the enzyme in the presence of inhibitors. Here, we set out to correlate inhibition mechanisms established in bulk enzyme studies with singleenzyme molecule experiments. To date, inhibitors have been used in single-molecule studies to obtain information about conformational dynamics. Ha et al. (9) showed that it is possible to distinguish between free and inhibitor-bound states of a single-staphylococcal nuclease enzyme molecule. The binding of an inhibitor imposed a conformational constraint on the enzyme molecule resulting in a change of single-molecule polarization and intramolecular single-pair FRET. In this article, we report the direct observation of inhibitor release and binding from single-enzyme molecules by monitoring their substrate turnover.

Many individual horseradish peroxidase (HRP) molecules were isolated and observed simultaneously by fluorescence microscopy in an array of 50 000 femtoliter chambers chemically etched into the surface of a glass optical fiber bundle. The substrate turnovers of hundreds of individual HRP molecules were readily analyzed, and the large number of molecules observed provided excellent statistics. In contrast to other enzymes used for single-molecule studies, the rates of product formation in the femtoliter array were, on average, 10 times lower than in bulk solution. We attribute this phenomenon to the particular redox-reaction mechanism of HRP that involves two separate steps of product formation. HRP first oxidizes fluorogenic substrate molecules like Amplex Red to radical intermediates. Two radical molecules subsequently undergo an enzyme-independent dismutation reaction, the rate of which is decreased when confined to a femtoliter chamber resulting in less product. This two-step reaction mechanism of the widely used Amplex Red, as well as other fluorogenic substrates, is often overlooked. The mechanism not only affects single-molecule studies with HRP but also bulk reactions at low substrate turnover rates.

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