Single molecule kinetics of horseradish peroxidase exposed in large arrays of femtoliter-sized fused silica chambers

Functional analysis of single enzymes combining programmable molecular circuits with droplet-based microfluidics

The analysis of proteins at the single-molecule level reveals heterogeneous behaviours that are masked in ensemble-averaged techniques. The digital quantification of enzymes traditionally involves the observation and counting of single molecules partitioned into microcompartments via the conversion of a profluorescent substrate. This strategy, based on linear signal amplification, is limited to a few enzymes with sufficiently high turnover rate. Here we show that combining the sensitivity of an exponential molecular amplifier with the modularity of DNA-enzyme circuits and droplet readout makes it possible to specifically detect, at the single-molecule level, virtually any D(R)NA-related enzymatic activity. This strategy, denoted digital PUMA (Programmable Ultrasensitive Molecular Amplifier), is validated for more than a dozen different enzymes, including many with slow catalytic rate, and down to the extreme limit of apparent single turnover for Streptococcus pyogenes Cas9. Digital counting uniquely yields absolute molar quantification and reveals a large fraction of inactive catalysts in all tested commercial preparations. By monitoring the amplification reaction from single enzyme molecules in real time, we also extract the distribution of activity among the catalyst population, revealing alternative inactivation pathways under various stresses. Our approach dramatically expands the number of enzymes that can benefit from quantification and functional analysis at single-molecule resolution. We anticipate digital PUMA will serve as a versatile framework for accurate enzyme quantification in diagnosis or biotechnological applications. These digital assays may also be utilized to study the origin of protein functional heterogeneity.

Digital Cascade Assays for ADP- or ATP-Producing Enzymes Using a Femtoliter Reactor Array Device

Digital enzyme assays are emerging biosensing methods for highly sensitive quantitative analysis of biomolecules with single-molecule detection sensitivity. However, current digital enzyme assays require a fluorogenic substrate for detection, which limits the applicability of this method to certain enzymes. ATPases and kinases are representative enzymes for which fluorogenic substrates are not available; however, these enzymes form large domains and play a central role in biology. In this study, we implemented a fluorogenic cascade reaction in a femtoliter reactor array device to develop a digital bioassay platform for ATPases and kinases. The digital cascade assay enabled quantitative measurement of the single-molecule activity of F1-ATPase, the catalytic portion of ATP synthase. We also demonstrated a digital assay for human choline kinase α. Furthermore, we developed a digital cascade assay for ATP-synthesizing enzymes and demonstrated a digital assay for pyruvate kinase. These results show the high versatility of this assay platform. Thus, the digital cascade assay has great potential for the highly sensitive detection and accurate characterization of various ADP- and ATP-producing enzymes, such as kinases, which may serve as disease biomarkers.

Micro- and nanochamber array system for single enzyme assays

Arrays of small reaction containers, ranging from 624 femtoliters (10-15 L) to 270 attoliters (10-18 L), for capturing a single enzyme molecule and measuring the activity were developed along with a new reversible sealing system based on a pneumatic valve actuator made of polydimethylsiloxane (PDMS). The valve was actuated by PBS solution, effectively preventing evaporation of the solution from the micro- and nanochambers and allowing the assay to be performed over a long period of time. The hydrolysis rates of β-D-galactosidase (β-gal), kcat, were decreased according to the decrease of the chamber size, and the overall tendency seems to be symmetrically related to the specific surface area of the chambers even under the prevented condition of non-specific adsorption. The spatial localization of the protons in the chambers, which might could affect the dissociation state of the proteins, was also investigated to explain the decrease in the hydrolysis rate. The developed chamber system developed here may be useful for artificially reproducing the confined intracellular environment and molecular crowding conditions.

Disulfide Bonds Are Not Necessary for Intrinsic TNSALP Activity

Recent developments in single-molecule enzymology (SME) have allowed for the observation of subpopulations present in enzyme ensembles. Tissue-nonspecific alkaline phosphatase (TNSALP), a homodimeric monophosphate esterase central to bone metabolism, has become a model enzyme for SME studies. TNSALP contains two internal disulfide bonds that are critical for its effective dimerization; mutations in its disulfide bonding framework have been reported in patients with hypophosphatasia, a rare disease characterized by impaired bone and tooth mineralization. In this paper, we present the kinetics of these mutants and show that these disulfide bonds are not crucial for TNSALP enzymatic function. This surprising result reveals that the enzyme's active conformation does not rely on its disulfide bonds. We posit that the signs and symptoms seen in hypophosphatasia are likely not primarily due to impaired enzyme function, but rather decreased enzyme expression and trafficking.

Electrophoretic mobility of individual molecules of alkaline phosphatase

The electrophoretic mobilities and catalytic rates of individual molecules of bovine intestinal alkaline phosphatase were determined in CHES and borate buffers of identical pH using a capillary electrophoresis based method. Both properties were found to be heterogeneous. In the presence of CHES, the mobility and rate were found to be -1.9 ± 0.2 × 10^-9 m² V^-1 s^-1 and 9.8 ± 7.4 × 10⁴ min^-1 (N = 38), respectively. In the presence of borate, the mobility and rate were found to be -6.9 ± 0.5 × 10^-9 m² V^-1 s^-1 and 2.0 ± 1.3 × 10⁴ min^-1 (N = 41), respectively. The means and variances for both properties were found to differ significantly between the two buffers. The difference in average mobility was attributed to an increase in negative charge caused by borate complexing with the carbohydrate moieties attached to the enzyme. The difference in variance was attributed to heterogeneous complexation with borate due to heterogeneity in the glycosylation. The differences in mean values for the catalytic rate were attributed to the inhibitory effect of borate and the difference in variance may suggest that the K_I of this binding may also be heterogeneous.

A facile and rapid route to self-digitization of samples into a high density microwell array for digital bioassays

Digital bioassays are powerful methods to detect rare analytes from complex mixtures and study the temporal processes of individual entities within biological systems. In digital bioassays, a crucial first step is the discretization of samples into a large number of identical independent partitions. Here, we developed a rapid and facile sample partitioning method for versatile digital bioassays. This method is based on a detachable self-digitization (DSD) chip which couples a reversible assembly configuration and a predegassing-based self-pumping mechanism to achieve an easy, fast, and large-scale sample partitioning. The DSD chip consists of a channel layer used for loading the sample and a microwell layer used for holding the sample partitions. Benefitting from its detachability, the chip avoids a lengthy oil flushing process used to remove the excess sample in loading channels and can compartmentalize a sample into more than 100,000 wells of picoliter volume with densities up to 14,000 wells/cm² in less than 30 s. We also demonstrated the utility of the proposed method by applying it to digital PCR and digital microbial assays.

A hand-powered microfluidic system for portable and low-waste sample discretization

In this work, we present a simple and equipment-free system for discretizing samples into tens of thousands of discrete volumes in tens of seconds. Unlike conventional sample discretization systems that require bulky syringe pumps, pressure controllers, or vacuum equipment, our system requires only a sheet of water-soluble film, a hand-operated syringe, and a microfluidic device containing a high-density microchamber array. In this system, the water-soluble film seals the device inlet to form a closed channel-chamber system, while the syringe is used to create a vacuum in the closed system. Benefitting from the high negative pressure created by syringe-vacuum and the dissolution-triggered gating mechanism of the sealing water-soluble film, the aqueous sample loaded into the device inlet can be rapidly partitioned into tens of thousands of isolated chambers without the need for any expensive pumping systems. We demonstrated the utility of this system by exploiting it for digital PCR. We believe that this simple discretization system will find broad applications, such as in digital bioassays, single-cell analysis, and point-of-care diagnostics.

Elucidation and control of low and high active populations of alkaline phosphatase molecules for quantitative digital bioassay

Alkaline phosphatase (ALP), a homo‐dimeric enzyme has been widely used in various bioassays as disease markers and enzyme probes. Recent advancements of digital bioassay revolutionized ALP‐based diagnostic assays as seen in rapid growth of digital ELISA and the emerging multiplex profiling of single‐molecule ALP isomers. However, the intrinsic heterogeneity found among ALP molecules hampers the ALP‐based quantitative digital bioassays. This study aims quantitative analysis of single‐molecule activities of ALP from Escherichia coli and reveals the static heterogeneity in catalytic activity of ALP with two distinct populations: half‐active and fully‐active portions. Digital assays with serial buffer exchange uncovered single‐molecule Michaelis–Menten kinetics of ALP; half‐active molecules have halved values of the catalytic turnover rate, k_cat, and the rate constant of productive binding, k_on, of the fully active molecules. These findings suggest that half‐active ALP molecules are heterogenic dimers composed of inactive and active monomer units, while fully active ALP molecules comprise two active units. Static heterogeneity was also observed for ALP with other origins: calf intestine or shrimp, showing how the findings can be generalized across species. Cell‐free expression of ALP with disulfide bond enhancer and spiked zinc ion resulted in homogenous population of ALP of full activity, implying that inactive monomer units of ALP are deficient in correct disulfide bond formation and zinc ion coordination. These findings provide basis for further study on molecular mechanism and biogenesis of ALP, and also offer the way to prepare homogenous and active populations of ALP for highly quantitative and sensitive bioassays with ALP.

Monodisperse Liposomes with Femtoliter Volume Enable Quantitative Digital Bioassays of Membrane Transporters and Cell-Free Gene Expression

Digital bioassays have emerged as a new category of bioanalysis. However, digital bioassays for membrane transporter proteins have not been well established yet despite high demands in molecular physiology and molecular pharmacology due to the lack of biologically functional monodisperse liposomes with femtoliter volumes. Here, we established a simple and robust method to produce femtoliter-sized liposomes (femto-liposomes). We prepared 10⁶ monodispersed water-in-oil droplets stabilized by a lipid monolayer using a polyethylene glycol-coated femtoliter reactor array device. Droplets were subjected to the optimized emulsion transfer process for femto-liposome production. Liposomes were monodispersed (coefficient of variation = 5-15%) and had suitable diameter (0.6-5.3 μm) and uniform volumes of subfemtoliter or a few femtoliters; thus, they were termed uniform femto-liposomes. The unilamellarity of uniform femto-liposomes allowed quantitative single-molecule analysis of passive and active transporter proteins: α-hemolysin and F_oF₁-ATPase. Digital gene expression in uniform femto-liposomes (cell-free transcription and translation from single DNA molecules) was also demonstrated, showing the versatility of digital assays for membrane transporter proteins and cell-free synthetic biology.

Biologically-active unilamellar vesicles from red blood cells

We demonstrate a method to prepare giant unilamellar vesicles (GUVs) with biologically-active protein activity, by mixing erythrocyte (red blood cell) membrane extract with phospholipids and growing their mixture in a porous hydrogel matrix. This presents a pathway to retain protein biological activity without prior isolation and purification of the protein, though only the activity of the membrane protein GLUT1 is investigated to date. Using the cascade enzymatic reaction glucose oxidase and horseradish peroxidase to assay glucose concentration specifically within the GUV interior, we show that glucose is internalized by GLUT1 whereas adding cytochalasin B, a GLUT1 inhibitor, blocks glucose transport. The method presented here operates at biological ionic strength and is both simple and potentially generalizable.

Probing conformational dynamics of an enzymatic active site by an in situ single fluorogenic probe under piconewton force manipulation

Unraveling the conformational details of an enzyme during the essential steps of a catalytic reaction (i.e., enzyme-substrate interaction, enzyme-substrate active complex formation, nascent product formation, and product release) is challenging due to the transient nature of intermediate conformational states, conformational fluctuations, and the associated complex dynamics. Here we report our study on the conformational dynamics of horseradish peroxidase using single-molecule multiparameter photon time-stamping spectroscopy with mechanical force manipulation, a newly developed single-molecule fluorescence imaging magnetic tweezers nanoscopic approach. A nascent-formed fluorogenic product molecule serves as a probe, perfectly fitting in the enzymatic reaction active site for probing the enzymatic conformational dynamics. Interestingly, the product releasing dynamics shows the complex conformational behavior with multiple product releasing pathways. However, under magnetic force manipulation, the complex nature of the multiple product releasing pathways disappears and more simplistic conformations of the active site are populated.

Enzyme Kinetics in Femtoliter Arrays

Over the last decade, femtoliter arrays have been used as a simple and robust way to encapsulate and monitor the kinetics of single enzyme molecules. Encapsulating individual enzyme molecules within a femtoliter-sized reaction chamber does not require immobilization of the enzyme molecules or fluorescent tagging of the enzyme molecules, which offers the unique advantage of observing unmodified single enzyme molecules free in solution. Several fascinating details about enzyme kinetics have been revealed using these femtoliter arrays, which were unattainable from traditional ensemble experiments. Here, we discuss various considerations to take into account when developing single-molecule enzyme assays in femtoliter arrays and the advantages and disadvantages of various protocols.

A single-molecule digital enzyme assay using alkaline phosphatase with a cumarin-based fluorogenic substrate

Digitalization of fluorogenic enzymatic assays through the use of femtoliter chamber array technology is an emerging approach to realizing highly quantitative bioassays with single-molecule sensitivity. However, only a few digital fluorogenic enzyme assays have been reported, and the variations of the digital enzyme assays are basically limited to fluorescein- and resorufin-based fluorogenic assays. This limitation hampers the realization of a multiplex digital enzyme assay such as a digital enzyme-linked immunosorbent assay (ELISA). In this study, after optimization of buffer conditions, we achieved a single-molecule digital enzyme alkaline phosphatase (ALP) assay with a cumarin-based fluorogenic substrate, 4-methylunbelliferyl phosphate (4-MUP). When ALP molecules were encapsulated in a 44-femtoliter chamber array at a low ratio of less than 1 molecule per chamber, each chamber showed a discrete fluorescence signal in an all-or-none manner, allowing the digital counting of the number of active enzyme molecules. The fraction of fluorescent chambers linearly decreased with the enzyme concentration, obeying the Poisson distribution as expected. We also demonstrated a dual-color digital enzyme assay with a ALP/4-MUP and β-galactosidase (β-gal)/resorufin-β-d-galactopyranoside combination. The activities of single ALP and β-gal molecules were clearly detected simultaneously. The method developed in this study will enable us to carry out a parallelized, multiplex digital ELISA.

Enzyme molecules in solitary confinement

Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

A single molecule perspective on the functional diversity of in vitro evolved β-glucuronidase

The mechanisms that drive the evolution of new enzyme activity have been investigated by comparing the kinetics of wild-type and in vitro evolved β-glucuronidase (GUS) at the single molecule level. Several hundred single GUS molecules were separated in large arrays of 62,500 ultrasmall reaction chambers etched into the surface of a fused silica slide to observe their individual substrate turnover rates in parallel by fluorescence microscopy. Individual GUS molecules feature long-lived but divergent activity states, and their mean activity is consistent with classic Michaelis-Menten kinetics. The large number of single molecule substrate turnover rates is representative of the activity distribution within an entire enzyme population. Partially evolved GUS displays a much broader activity distribution among individual enzyme molecules than wild-type GUS. The broader activity distribution indicates a functional division of work between individual molecules in a population of partially evolved enzymes that-as so-called generalists-are characterized by their promiscuous activity with many different substrates.