Wall-Immobilized Biocatalyst vs. Packed Bed in Miniaturized Continuous Reactors: Performances and Scale-Up

Sustainable biocatalysis syntheses have gained considerable popularity over the years. However, further optimizations - notably to reduce costs - are required if the methods are to be successfully deployed in a range of areas. As part of this drive, various enzyme immobilization strategies have been studied, alongside process intensification from batch to continuous production. The flow bioreactor portfolio mainly ranges between packed bed reactors and wall-immobilized enzyme miniaturized reactors. Because of their simplicity, packed bed reactors are the most frequently encountered at lab-scale. However, at industrial scale, the growing pressure drop induced by the increase in equipment size hampers their implementation for some applications. Wall-immobilized miniaturized reactors require less pumping power, but a new problem arises due to their reduced enzyme-loading capacity. This review starts with a presentation of the current technology portfolio and a reminder of the metrics to be applied with flow bioreactors. Then, a benchmarking of the most recent relevant works is presented. The scale-up perspectives of the various options are presented in detail, highlighting key features of industrial requirements. One of the main objectives of this review is to clarify the strategies on which future study should center to maximize the performance of wall-immobilized enzyme reactors.

A lava-inspired proteolytic enzyme therapy on cancer with a PEG-based hydrogel enhances tumor distribution and penetration of liposomes

The enhanced permeability and retention (EPR) effect has become the guiding principle for nanomedicine against cancer for a long time. However, several biological barriers severely resist therapeutic agents' penetration and retention into the deep tumor tissues, resulting in poor EPR effect and high tumor mortality. Inspired by lava, we proposed a proteolytic enzyme therapy to improve the tumor distribution and penetration of nanomedicine. A trypsin-crosslinked hydrogel (Trypsin@PSA Gel) was developed to maintain trypsin's activity. The hydrogel postponed trypsin's self-degradation and sustained the release. Trypsin promoted the cellular uptake of nanoformulations in breast cancer cells, enhanced the penetration through endothelial cells, and degraded total and membrane proteins. Proteomic analysis reveals that trypsin affected ECM components and down-regulated multiple pathways associated with cancer progression. Intratumoral injection of Trypsin@PSA Gel significantly increased the distribution of liposomes in tumors and reduced tumor vasculature. Combination treatment with intravenous injection of gambogic acid-loaded liposomes and intratumoral injection of Trypsin@PSA Gel inhibited tumor growth. The current study provides one of the first investigations into the enhanced tumor distribution of liposomes induced by a novel proteolytic enzyme therapy.

Stability of enzyme immobilized on the nanofluidic channel surface

The lifetime of an enzyme is critical to prevent system failure and optimize maintenance schedules in biological and analytical chemistry. The lifetime metrics of an enzyme can be evaluated from enzyme activity in terms of catalytic cycles per enzyme at various storage times. Trypsin, which is a gold-standard enzyme in proteomics, has been known to decrease activity due to self-digestion. To improve the activity of trypsin, enzyme reactors have developed by immobilizing in micro and nanospace. However, an evaluation method for the catalytic cycle has not been established due to major issues such as nonuniform space, unstable liquid transport, and self-digestion during immobilization in conventional work. To solve these issues, we have previously developed an ultra-fast enzyme reactor with a well-defined nanofabrication method, stable liquid transport, and partial enzyme modification. Here, we aimed to investigate catalytic cycles in a nanochannel. To extend enzyme lifetime efficiently, we have evaluated the optimal immobilization process and catalytic cycles of trypsin. As a result, immobilized enzyme densities by the trypsinogen immobilization process were increased at all concentrations compared to the trypsin immobilization process. To evaluate the lifetime of trypsin, the immobilized enzyme densities and activities were almost the same before and after 72 h of enzyme storage, and the calculated catalytic cycles were 1740. These results indicated that self-digestion of the immobilized enzyme was highly suppressed. Consequently, the reaction efficiency has been evaluated depending on the catalytic cycles from the substrate for the first time, while preventing self-digestion by trypsin.

Nanofluidic analytical system integrated with nanochannel open/close valves for enzyme-linked immunosorbent assay

There have been significant advances in the field of nanofluidics, and novel technologies such as single-cell analysis have been demonstrated. Despite the evident advantages of nanofluidics, fluid control in nanochannels for complicated analyses is extremely difficult because the fluids are currently manipulated by maintaining the balance of driving pressure. To address this issue, the use of valves will be essential. Our group previously developed a nanochannel open/close valve utilizing glass deformation, but this has not yet been integrated into nanofluidic devices for analytical applications. In the present study, a nanofluidic analytical system integrated with multiple nanochannel open/close valves was developed. This system consists of eight pneumatic pumps, seven nanochannel open/close valves combined with piezoelectric actuators, and an ultra-high sensitivity detector for non-fluorescent molecules. For simultaneous actuation of multiple valves, a device holder was designed that prevented deformation of the entire device caused by operating the valves. A system was subsequently devised to align each valve and actuator with a precision of better than 20 μm to permit the operation of valves. The developed analytical system was verified by analyzing IL-6 molecules using an enzyme-linked immunosorbent assay. Fluid operations such as sample injection, pL-level aliquot sampling and flow switching were accomplished in this device simply by opening/closing specific valves, and a sample consisting of approximately 1500 IL-6 molecules was successfully detected. This study is expected to significantly improve the usability of nanofluidic analytical devices and lead to the realization of sophisticated analytical techniques such as single-cell proteomics.

Femtoliter-Droplet Mass Spectrometry Interface Utilizing Nanofluidics for Ultrasmall and High-Sensitivity Analysis

In the fields of biology and medicine, comprehensive protein analysis at the single-cell level utilizing mass spectrometry (MS) with pL sample volumes and zmol to amol sensitivity is required. Our group has developed nanofluidic analytical pretreatment methods that exploit nanochannels for downsizing chemical unit operations to fL-pL volumes. In the field of analytical instruments, mass spectrometers have advanced to achieve ultrahigh sensitivity. However, a method to interface between fL-pL pretreatments and mass spectrometers without sample loss and dispersion is still challenging. In this study, we developed an MS interface utilizing nanofluidics to achieve high-sensitivity detection. After charging analyte molecules by an applied voltage through an electrode, the liquid sample was converted to fL droplets by a nanofluidic device. Considering the inertial force that acts on the droplets, the droplets were carried with a controlled trajectory, even in turbulent air flow, and injected into a mass spectrometer with 100% efficiency. A module for heat transfer was designed and constructed, by which all of the injected droplets were vaporized to produce gas-phase ions. The detection of caffeine ions was achieved at a limit of detection of 1.52 amol, which was 290 times higher than a conventional MS interface by electrospray ionization with sample dispersion combined with a similar mass spectrometer. Therefore, sensitivity that was 2 orders of magnitude higher could be realized due to the 100% sample injection rate. The present study provides a new methodology for the analysis of ultrasmall samples with high-sensitivity, such as protein molecules produced from a single cell.

Accelerated protein digestion and separation with picoliter volume utilizing nanofluidics

Single cell analyses can provide critical biological insight into cellular heterogeneity. In particular, the proteome, which governs cell functions, is much more difficult to analyze because it is principally impossible to amplify proteins compared to nucleic acids. The most promising approach to single cell proteomics is based on the liquid chromatography mass spectrometry (LC-MS) platform. However, pretreatments before MS detection have two critical issues for single cell analysis: analyte loss as a result of adsorption and artifacts due to the duration of analysis. This is a serious problem because single cells have a limited number of protein molecules and a small volume. To solve these issues, we developed an integrated nanofluidic device to manipulate samples on a femtoliter to picoliter (fL-pL) scale to achieve high-throughput analysis via suppressing analyte loss. This device can perform tryptic digestion, chromatographic separation, and non-labeled detection with high consistency. In addition, we introduced an open/close valve by physical deformation of glass on a nanometer scale to independently modify the nanochannel surfaces and control sample aliquots. The injection system equipped with this valve achieved an injection volume of 1.0 ± 0.1 pL. By using this integrated device, we found that the chromatogram of bulk-digestion for 12 hours resembled that of 15 min-digestion in the nanochannel, which indicated that these conditions reached a similar state of digestion. Therefore, an integrated device for ultra-fast protein analysis was developed on a 1 pL scale for the first time.

Microfluidic Immobilized Enzymatic Reactors for Proteomic Analyses—Recent Developments and Trends (2017–2021)

Given the strong interdisciplinary nature of microfluidic immobilized enzyme reactor (μ-IMER) technology, several branches of science contribute to its successful implementation. A combination of physical, chemical knowledge and engineering skills is often required. The development and application of μ-IMERs in the proteomic community are experiencing increasing importance due to their attractive features of enzyme reusability, shorter digestion times, the ability to handle minute volumes of sample and the prospect of on-line integration into analytical workflows. The aim of this review is to give an account of the current (2017–2021) trends regarding the preparation of microdevices, immobilization strategies, and IMER configurations. The different aspects of microfabrication (designs, fabrication technologies and detectors) and enzyme immobilization (empty and packed channels, and monolithic supports) are surveyed focusing on μ-IMERs developed for proteomic analysis. Based on the advantages and limitations of the published approaches and the different applications, a probable perspective is given.

Intraparticle Kinetics Unveil Crowding and Enzyme Distribution Effects on the Performance of Cofactor-Dependent Heterogeneous Biocatalysts

Multidimensional kinetic analysis of immobilized enzymes is essential to understand the enzyme functionality at the interface with solid materials. However, spatiotemporal kinetic characterization of heterogeneous biocatalysts on a microscopic level and under operando conditions has been rarely approached. As a case study, we selected self-sufficient heterogeneous biocatalysts where His-tagged cofactor-dependent enzymes (dehydrogenases, transaminases, and oxidases) are co-immobilized with their corresponding phosphorylated cofactors [nicotinamide adenine dinucleotide phosphate (NAD(P)H), pyridoxal phosphate (PLP), and flavin adenine dinucleotide (FAD)] on porous agarose microbeads coated with cationic polymers. These self-sufficient systems do not require the addition of exogenous cofactors to function, thus avoiding the extensive use of expensive cofactors. To comprehend the microscopic kinetics and thermodynamics of self-sufficient systems, we performed fluorescence recovery after photobleaching measurements, time-lapse fluorescence microscopy, and image analytics at both single-particle and intraparticle levels. These studies reveal a thermodynamic equilibrium that rules out the reversible interactions between the adsorbed phosphorylated cofactors and the polycations within the pores of the carriers, enabling the confined cofactors to access the active sites of the immobilized enzymes. Furthermore, this work unveils the relationship between the apparent Michaelis-Menten kinetic parameters and the enzyme density in the confined space, eliciting a negative effect of molecular crowding on the performance of some enzymes. Finally, we demonstrate that the intraparticle apparent enzyme kinetics are significantly affected by the enzyme spatial organization. Hence, multiscale characterization of immobilized enzymes serves as an instrumental tool to better understand the in operando functionality of enzymes within confined spaces.

Stable Formation of Aqueous/Organic Parallel Two-phase Flow in Nanochannels with Partial Surface Modification

In microfluidics, various chemical processes can be integrated utilizing parallel multiphase flows. Our group has extended this research to nanofluidics, and recently performed the extraction of lipids using parallel two-phase flow in nanochannels. Although this was achieved in surface-modified nanochannels, a stable condition of parallel two-phase flow remains unknown due to difficulties in device fabrication, for a suitable method of bonding surface-modified substrates is lacking. Therefore, research on parallel two-phase flow in nanochannels has been limited. Herein, a new bonding method which improves the wash process for the substrates and increases the bonding rate to ∼100% is described. The conditions to achieve parallel organic/aqueous two-phase flow were then studied. It was revealed that in nanochannels, higher capillary numbers for the organic phase flow were required compared to that in microchannels. The newly developed fabrication process and flow regimes will contribute to realize integrated nanofluidic devices capable of analyzing single molecules/cells.

Surface Patterning of Closed Nanochannel Using VUV Light and Surface Evaluation by Streaming Current

In nanofluidics, surface control is a critical technology because nanospaces are surface-governed spaces as a consequence of their extremely high surface-to-volume ratio. Various surface patterning methods have been developed, including patterning on an open substrate and patterning using a liquid modifier in microchannels. However, the surface patterning of a closed nanochannel is difficult. In addition, the surface evaluation of closed nanochannels is difficult because of a lack of appropriate experimental tools. In this study, we verified the surface patterning of a closed nanochannel by vacuum ultraviolet (VUV) light and evaluated the surface using streaming-current measurements. First, the C₁₈ modification of closed nanochannels was confirmed by Laplace pressure measurements. In addition, no streaming-current signal was detected for the C₁₈-modified surface, confirming the successful modification of the nanochannel surface with C₁₈ groups. The C₁₈ groups were subsequently decomposed by VUV light, and the nanochannel surface became hydrophilic because of the presence of silanol groups. In streaming-current measurements, the current signals increased in amplitude with increasing VUV light irradiation time, indicating the decomposition of the C₁₈ groups on the closed nanochannel surfaces. Finally, hydrophilic/hydrophobic patterning by VUV light was performed in a nanochannel. Capillary filling experiments confirmed the presence of a hydrophilic/hydrophobic interface. Therefore, VUV patterning in a closed nanochannel was demonstrated, and the surface of a closed nanochannel was successfully evaluated using streaming-current measurements.

Metal-Free Fabrication of Fused Silica Extended Nanofluidic Channel to Remove Artifacts in Chemical Analysis

In microfluidics, especially in nanofluidics, nanochannels with functionalized surfaces have recently attracted attention for use as a new tool for the investigation of chemical reaction fields. Molecules handled in the reaction field can reach the single-molecule level due to the small size of the nanochannel. In such surroundings, contamination of the channel surface should be removed at the single-molecule level. In this study, it was assumed that metal materials could contaminate the nanochannels during the fabrication processes; therefore, we aimed to develop metal-free fabrication processes. Fused silica channels 1000 nm-deep were conventionally fabricated using a chromium mask. Instead of chromium, electron beam resists more than 1000 nm thick were used and the lithography conditions were optimized. From the results of optimization, channels with 1000 nm scale width and depth were fabricated on fused silica substrates without the use of a chromium mask. In nanofluidic experiments, an oxidation reaction was observed in a device fabricated by conventional fabrication processes using a chromium mask. It was found that Cr⁶⁺ remained on the channel surfaces and reacted with chemicals in the liquid phase in the extended nanochannels; this effect occurred at least to the micromolar level. In contrast, the device fabricated with metal-free processes was free of artifacts induced by the presence of chromium. The developed fabrication processes and results of this study will be a significant contribution to the fundamental technologies employed in the fields of microfluidics and nanofluidics.

A simple and reversible glass-glass bonding method to construct a microfluidic device and its application for cell recovery

Compared with polymer microfluidic devices, glass microfluidic devices have advantages for diverse lab-on-a-chip applications due to their rigidity, optical transparency, thermal stability, and chemical/biological inertness. However, the bonding process to construct glass microfluidic devices usually involves treatment(s) like high temperature over 400 °C, oxygen plasma or piranha solution. Such processes require special skill, apparatus or harsh chemicals, and destroy molecules or cells in microchannels. Here, we present a simple method for glass-glass bonding to easily form microchannels. This method consists of two steps: placing water droplets on a glass substrate cleaned by neutral detergent, followed by fixing a cover glass plate on the glass substrate by binding clips for a few hours at room temperature. Surface analyses showed that the glass surface cleaned by neutral detergent had a higher ratio of SiOH over SiO than glass surfaces prepared by other cleaning steps. Thus, the suggested method could achieve stronger glass-glass bonding via dehydration condensation due to the higher density of SiOH. The pressure endurance reached over 600 kPa within 6 h of bonding, which is sufficient for practical microfluidic applications. Moreover, by exploiting the reversibility of this bonding method, cell recoveries after cultivating cells in a microchannel were demonstrated. This new bonding method can significantly improve both the productivity and the usability of glass microfluidic devices and extend the possibility of glass microfluidic applications in future.

Integration of sequential analytical processes into sub-100 nm channels: volumetric sampling, chromatographic separation, and label-free molecule detection

The progress of nanotechnology has developed nanofluidic devices utilizing nanochannels with a width and/or depth of sub-100 nm (10¹ nm channels), and several experiments have been implemented in ultra-small spaces comparable to DNAs and proteins. However, current experiments utilizing 10¹ nm channels focus on a single function or operation; integration of multiple analytical operations into 10¹ nm channels using nanofluidic circuits and fluidic control has yet to be realized despite the advantage of nanochannels. Herein, we report the establishment of a label-free molecule detection method for 10¹ nm channels and demonstration of sequential analytical processes using integrated nanofluidic devices. Our absorption-based detection method called photothermal optical diffraction (POD) enables non-invasive label-free molecule detection in 10¹ nm channels for the first time, and the limit of detection (LOD) of 1.8 μM is achieved in 70 nm wide and deep nanochannels, which corresponds to 7.5 molecules in the detection volume of 7 aL. As a demonstration of sampling in 10¹ nm channels, aL-fL volumetric sampling is performed using 90 nm deep cross-shaped nanochannels and pressure-driven fluidic control from three directions. Finally, the POD and volumetric sampling are combined with nanochannel chromatography, and separation analysis in 10¹ nm channels is demonstrated. The experimental results reported in this paper will contribute to the advances in 10¹ nm fluidic devices which have the potential to provide a novel platform for chemical/biological analyses.

Advanced Top-Down Fabrication for a Fused Silica Nanofluidic Device

Nanofluidics have recently attracted significant attention with regard to the development of new functionalities and applications, and producing new functional devices utilizing nanofluidics will require the fabrication of nanochannels. Fused silica nanofluidic devices fabricated by top-down methods are a promising approach to realizing this goal. Our group previously demonstrated the analysis of a living single cell using such a device, incorporating nanochannels having different sizes (102-103 nm) and with branched and confluent structures and surface patterning. However, fabrication of geometrically-controlled nanochannels on the 101 nm size scale by top-down methods on a fused silica substrate, and the fabrication of micro-nano interfaces on a single substrate, remain challenging. In the present study, the smallest-ever square nanochannels (with a size of 50 nm) were fabricated on fused silica substrates by optimizing the electron beam exposure time, and the absence of channel breaks was confirmed by streaming current measurements. In addition, micro-nano interfaces between 103 nm nanochannels and 101 μm microchannels were fabricated on a single substrate by controlling the hydrophobicity of the nanochannel surfaces. A micro-nano interface for a single cell analysis device, in which a nanochannel was connected to a 101 μm single cell chamber, was also fabricated. These new fabrication procedures are expected to advance the basic technologies employed in the field of nanofluidics.