Enzyme Kinetics in Femtoliter Arrays

Development of fluorogenic substrates for colorectal tumor-related neuropeptidases for activity-based diagnosis

The M3 metalloproteases, neurolysin and THOP1, are neuropeptidases that are expressed in various tissues and metabolize neuropeptides, such as neurotensin. The biological roles of these enzymes are not well characterized, partially because the chemical tools to analyse their activities are not well developed. Here, we developed a fluorogenic substrate probe for neurolysin and thimet oligopeptidase 1 (THOP1), which enabled the analysis of enzymatic activity changes in tissue and plasma samples. In particular, the probe was useful for studying enzyme activities in a single-molecule enzyme assay platform, which can detect enzyme activity with high sensitivity. We detected the activity of neurolysin in plasma samples and revealed higher enzyme activity in the blood samples of patients with colorectal tumor. The result indicated that single-molecule neurolysin activity is a promising candidate for a blood biomarker for colorectal cancer diagnosis.

Enzyme-based digital bioassay technology - key strategies and future perspectives

Digital bioassays based on single-molecule enzyme reactions represent a new class of bioanalytical methods that enable the highly sensitive detection of biomolecules in a quantitative manner. Since the first reports of these methods in the 2000s, there has been significant growth in this new bioanalytical strategy. The principal strategy of this method is to compartmentalize target molecules in micron-sized reactors at the single-molecule level and count the number of microreactors showing positive signals originating from the target molecule. A representative application of digital bioassay is the digital enzyme-linked immunosorbent assay (ELISA). Owing to their versatility, various types of digital ELISAs have been actively developed. In addition, some disease markers and viruses possess catalytic activity, and digital bioassays for such enzymes and viruses have, thus, been developed. Currently, with the emergence of new microreactor technologies, the targets of this methodology are expanding from simple enzymes to more complex systems, such as membrane transporters and cell-free gene expression. In addition, multiplex or multiparametric digital bioassays have been developed to assess precisely the heterogeneities in sample molecules/systems that are obscured by ensemble measurements. In this review, we first introduce the basic concepts of digital bioassays and introduce a range of digital bioassays. Finally, we discuss the perspectives of new classes of digital bioassays and emerging fields based on digital bioassay technology.

Multiplexed single-molecule enzyme activity analysis for counting disease-related proteins in biological samples

We established an ultrasensitive method for identifying multiple enzymes in biological samples by using a multiplexed microdevice-based single-molecule enzymatic assay. We used a paradigm in which we "count" the number of enzyme molecules by profiling their single enzyme activity characteristics toward multiple substrates. In this proof-of-concept study of the single enzyme activity-based protein profiling (SEAP), we were able to detect the activities of various phosphoric ester-hydrolyzing enzymes such as alkaline phosphatases, tyrosine phosphatases, and ectonucleotide pyrophosphatases in blood samples at the single-molecule level and in a subtype-discriminating manner, demonstrating its potential usefulness for the diagnosis of diseases based on ultrasensitive detection of enzymes.

Redox Cycling in Individually Encapsulated Attoliter-Volume Nanopores

Redox cycling electrochemistry in arrays of individually encapsulated attoliter-volume ( V ∼ 10 aL) nanopores is investigated and reported here. These nanopore electrode array (NEA) structures exhibit distinctive electrochemical behaviors not observed in open NEAs, which allow free diffusion of redox couples between the nanopore interior and bulk solution. Confined nanopore environments, generated by sealing NEAs with a layer of poly(dimethylsiloxane), are characterized by enhanced currents-up to 250-fold compared with open NEAs-owing to effective trapping of the redox couple inside the nanopores and to enhanced mass transport effects. In addition, electrochemical rectification ( ca. 1.5-6.3) was observed and is attributed to ion migration. Finite-element simulations were performed to characterize the concentration and electric potential gradients associated with the disk electrode, aqueous medium, and ring electrode inside the nanopores, and the results are consistent with experimental observations. The additional signal enhancement and redox-cycling-based rectification behaviors produced in these self-confined attoliter-volume nanopores are potentially useful in devising ultrasensitive sensors and molecular-based iontronic devices.