IR-Compatible PDMS microfluidic devices for monitoring of enzyme kinetics

A spectIR-fluidic reactor for monitoring fast chemical reaction kinetics with on-chip attenuated total reflection Fourier transform infrared spectroscopy

Microfluidics has emerged as a powerful technology with diverse applications in microbiology, medicine, chemistry, and physics. While its potential for controlling and studying chemical reactions is well recognized, the extraction and analysis of useful chemical information generated within microfluidic devices remain challenging. This is mainly due to the limited tools available for in situ measurements of chemical reactions. In this study, we present a proof-of-concept spectIR-fluidic reactor design that combines microfluidics with Fourier transform infrared (FTIR) spectroscopy for in situ kinetic studies of fast reactions. By integrating a multi-ridge silicon attenuated total reflection (ATR) wafer into the microfluidic device, we enable multi-point measurements for precise reaction time monitoring. As such, this work establishes a validated foundation for studying fast chemical reactions using on-chip ATR-FTIR spectroscopy in a microfluidic reactor environment, which enables simultaneous monitoring of reagents, intermediates, and products using a phosphate proton transfer reaction. The spectIR-fluidic reactor platform offers customizable designs, allowing for the investigation of reactions with various time scales, and has the potential to significantly advance studies exploring reaction mechanisms and optimization.

Microfabrication Process Development for a Polymer-Based Lab-on-Chip Concept Applied in Attenuated Total Reflection Fourier Transform Infrared Spectroelectrochemistry

Micro electro-mechanical systems (MEMS) combining sensing and microfluidics functionalities, as are common in Lab-on-Chip (LoC) devices, are increasingly based on polymers. Benefits of polymers include tunable material properties, the possibility of surface functionalization, compatibility with many micro and nano patterning techniques, and optical transparency. Often, additional materials, such as metals, ceramics, or silicon, are needed for functional or auxiliary purposes, e.g., as electrodes. Hybrid patterning and integration of material composites require an increasing range of fabrication approaches, which must often be newly developed or at least adapted and optimized. Here, a microfabrication process concept is developed that allows one to implement attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and electrochemistry on an LoC device. It is designed to spatially resolve chemical sensitivity and selectivity, which are instrumental for the detection of chemical distributions, e.g., during on-flow chemical and biological reaction chemistry. The processing sequence involves (i) direct-write and soft-contact UV lithography in SUEX dry resist and replication in polydimethylsiloxane (PDMS) elastomers as the fluidic structure; (ii) surface functionalization of PDMS with oxygen plasma, 3-aminopropyl-triethoxysilane (APTES), and a UV-curable glue (NOA 73) for bonding the fluidic structure to the substrate; (iii) double-sided patterning of silicon nitride-coated silicon wafers serving as the ATR-FTIR-active internal reflection element (IRE) on one side and the electrode-covered substrate for microfluidics on the back side with lift-off and sputter-based patterning of gold electrodes; and (iv) a custom-designed active vacuum positioning and alignment setup. Fluidic channels of 100 μm height and 600 μm width in 5 mm thick PDMS were fabricated on 2" and 4" demonstrators. Electrochemistry on-chip functionality was demonstrated by cyclic voltammetry (CV) of redox reactions involving iron cyanides in different oxidation states. Further, ATR-FTIR measurements of laminar co-flows of H₂O and D₂O demonstrated the chemical mapping capabilities of the modular fabrication concept of the LoC devices.

Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments

Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >10⁷-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >10⁷ variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.

Chemical Imaging of Mass Transport Near the No-Slip Interface of a Microfluidic Device using Attenuated Total Reflection-Fourier Transform Infrared Spectroscopy

Mass transport in geometrically confined environments is fundamental to microfluidic applications. Measuring the distribution of chemical species on flow requires the use of spatially resolved analytical tools compatible with microfluidic materials and designs. Here, the implementation of an attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) imaging (macro-ATR) approach for chemical mapping of species in microfluidic devices is described. The imaging method is configurable between a large field of view, single-frame imaging, and the use of image stitching to build composite chemical maps. Macro-ATR is used to quantify transverse diffusion in the laminar streams of coflowing fluids in dedicated microfluidic test devices. It is demonstrated that the ATR evanescent wave, which primarily probes the fluid within ∼500 nm of the channel surface, provides accurate quantification of the spatial distribution of species in the entire microfluidic device cross section. This is the case when flow and channel conditions promote vertical concentration contours in the channel as verified by three-dimensional numeric simulations of mass transport. Furthermore, the validity of treating the mass transport problem in a simplified and faster approach using reduced dimensionality numeric simulations is described. Simplified one-dimensional simulations, for the specific parameters used herein, overestimate diffusion coefficients by a factor of approximately 2, whereas full three-dimensional simulations accurately agree with experimental results.

Infrared compatible rapid mixer to probe millisecond chemical kinetics

Fast microfluidic mixers are a valuable tool for studying solution-phase chemical reaction kinetics and molecular processes with spectroscopy. However, microfluidic mixers that are compatible with infrared vibrational spectroscopy have seen only limited development due to the poor infrared transparency of the current microfabrication material. We describe the design, fabrication, and characterization of CaF₂-based continuous flow turbulent mixers, which are capable of measuring kinetics in the millisecond time window with infrared spectroscopy, when integrated into an infrared microscope. Kinetics measurements demonstrate the ability to resolve relaxation processes with 1 millisecond time resolution, and straightforward improvements are described that should result in sub-100 µs time-resolution.

Validation of HepG2/C3A Cell Cultures in Cyclic Olefin Copolymer Based Microfluidic Bioreactors

Organ-on-chip (OoC) technology is one of the most promising in vitro tools to replace the traditional animal experiment-based paradigms of risk assessment. However, the use of OoC in drug discovery and toxicity studies remain still limited by the low capacity for high-throughput production and the incompatibility with standard laboratory equipment. Moreover, polydimethylsiloxanes, the material of choice for OoC, has several drawbacks, particularly the high absorption of drugs and chemicals. In this work, we report the development of a microfluidic device, using a process adapted for mass production, to culture liver cell line in dynamic conditions. The device, made of cyclic olefin copolymers, was manufactured by injection moulding and integrates Luer lock connectors compatible with standard medical and laboratory instruments. Then, the COC device was used for culturing HepG2/C3a cells. The functionality and behaviour of cultures were assessed by albumin secretion, cell proliferation, viability and actin cytoskeleton development. The cells in COC device proliferated well and remained functional for 9 days of culture. Furthermore, HepG2/C3a cells in the COC biochips showed similar behaviour to cells in PDMS biochips. The present study provides a proof-of-concept for the use of COC biochip in liver cells culture and illustrate their potential to develop OoC.

Scanning Aperture Approach for Spatially Selective ATR-FTIR Spectroscopy: Application to Microfluidics

We present a novel spectroscopy accessory that can easily convert any Fourier transform infrared (FTIR) spectrometer into a fully automated mapping and assaying system. The accessory uses a multiridge attenuated total reflection (ATR) wafer as the sensing element coupled with a moving aperture that is used to select the regions of interest on the wafer. In this demonstration, the accessory is combined with a series of parallel micropatterned channels, which are positioned co-linear with the light-coupling ridges on the opposite side of the ATR wafer. The ATR spectroscopy microfluidic assay accessory (ASMAA) was used in continuous mapping mode to scan perpendicular to the ATR ridges, revealing complex but repeatable oscillations in the spectral intensities. To understand this behavior, the light path through the optical components was simulated with consideration of the aperture position, ridge-to-channel alignment, and excitation beam profile. With this approach, the simulation reproduced the experimental mapping results and provided evidence that the measurement position and area changed with the aperture position. To demonstrate the assay mode, we obtained spectra along the centerline of individual microchannels and determined noise baselines and limits of detection.

The Present and Future Role of Microfluidics for Protein and Peptide-Based Therapeutics and Diagnostics

The implementation of peptide-based molecules within the medical field has vast potential, owing to their unique nature and predictable physicochemical profiles. However, peptide therapeutic usage is hindered by delivery-related challenges, meaning that their formulations must be altered to overcome these limitations. This process could be propelled by applying microfluidics (MFs) due to its highly controllable and adaptable attributes; however, therapeutic research within this field is extremely limited. Peptides possess multifunctional roles within therapeutic formulations, ranging from enhancing target specificity to acting as the active component of the medicine. Diagnostically, MFs are well explored in the field of peptides, as MFs provide an unsullied platform to provide fast yet accurate examinations. The capacity to add attributes, such as integrated sensors and microwells, to the MF chip, only enhances the attractiveness of MFs as a diagnostic platform. The structural individuality of peptides makes them prime candidates for diagnostic purposes, for example, antigen detection and isolation. Therefore, this review provides a useful insight into the current applications of MFs for peptide-based therapy and diagnostics and highlights potential gaps in the field that are yet to be explored or optimized.

Paper-thin multilayer microfluidic devices with integrated valves

Integrated valve microfluidics has an unparalleled capability to automate rapid delivery of fluids at the nanoliter scale for high-throughput biological experimentation. However, multilayer soft lithography, which is used to fabricate valve-microfluidics, produces devices with a minimum thickness of around five millimeters. This form-factor limitation prevents the use of such devices in experiments with limited sample thickness tolerance such as 4-pi microscopy, stimulated Raman scattering microscopy, and many forms of optical or magnetic tweezer applications. We present a new generation of integrated valve microfluidic devices that are less than 300 μm thick, including the cover-glass substrate, that resolves the thickness limitation. This "thin-chip" was fabricated through a novel soft-lithography technique that produces on-chip micro-valves with the same functionality and reliability of traditional thick valve-microfluidic devices despite the orders of magnitude reduction in thickness. We demonstrated the advantage of using our thin-chip over traditional thick devices to automate fluid control while imaging on a high-resolution inverted microscope. First, we demonstrate that the thin-chip provides an improved signal to noise when imaging single cells with two-color stimulated Raman scattering (SRS). We then demonstrated how the thin-chip can be used to simultaneously perform on-chip magnetic manipulation of beads and fluorescent imaging. This study reveals the potential of our thin-chip in high-resolution imaging, sorting, and bead capture-based single-cell multi-omics applications.

Site-Specific Biofunctionalization of Cellulose and Poly(dimethylsiloxane): A Chemoenzymatic Approach for Surface Engineering

Site-specific, covalent immobilization of protein is of great importance in the design of bioanalytical devices. User-defined covalent coupling of protein onto the surface has been primarily limited to a noncanonical amino acid or cysteine residues. It is desirable to develop a new approach for site-specific biofunctionalization. Herein, we demonstrate a robust and modular chemoenzymatic approach for site-specific, covalent grafting of proteins onto a surface. The synthetic strategy relies on the combination of surface amine functionalization, followed by sortase-mediated coupling. The developed method was validated by site-specific immobilization of two model proteins (glutathione S-transferase and green fluorescent protein) on cellulose and polydimethylsiloxane surfaces via a short recognition motif (LPETG). The covalent coupling of immobilized proteins at the interface was characterized by Fourier Transform Infrared Spectroscopy in attenuated total reflectance mode, X-ray photoelectron spectroscopy, atomic force microscope, and fluorescent microscopy. This enzymatic surface functionalization approach could permit an oriented, homogeneous, and site-specific covalent tethering of LPETG-tag proteins to other materials under mild conditions.

Nanocellulose Films to Improve the Performance of Distance-based Glucose Detection in Paper-based Microfluidic Devices

We report on a simple, cost-effective, instrument-free, and portable distance-based paper device coupled with NFs for the determination of glucose. The analysis reaction is based upon the oxidative etching reaction of silver nanoparticles (AgNPs) in the presence of H₂O₂ that is produced from glucose after a glucose oxidase (GOx) catalytic reaction leading to a morphological transformation of AgNPs. A color band length of AgNPs is coated on to a detection channel and then etched by H₂O₂, and these were changed from a purple color to colorless as a correlate of the glucose concentration. To improve the performance of the enzyme immobilization, NFs, which are biocompatible without compromising their structure and biological activity, were then placed onto the sample zone. The naked-eye detection limit was 0.1 mM for 40 min of analysis time. The recoveries of glucose spiked in the artificial urine samples and control urine samples were then verified by our device and were in the acceptable range of 96 - 100%.

Design of novel, simple, and inexpensive 3D printing-based miniaturized electrochemical platform containing embedded disposable detector for analytical applications

This paper describes the development of a novel, simple, and inexpensive electrochemical device containing an integrated and disposable three-electrode system for detection. The base of this platform consists on a PDMS structure containing microchannels which were prototyped using 3D-printed molds. Pencil graphite leads were inserted into these microchannels and utilized as working, counter and reference electrodes in a novel design. Morphological analysis and electrochemical experiments with benchmark redox probes were carried out in order to evaluate the performance and characterize the miniaturized device proposed. Even using inexpensive materials and a simple fabrication protocol, the electrochemical platform developed provided good repeatability and reproducibility over a low cost (ca. $2 per device), acceptable lifetime (ca. 250 voltammetric runs) and extremely reduced consumption of samples and reagents (order of µL). As proof of concept, the analytical feasibility of the platform was investigated through the simultaneous determination of dopamine (DOPA) and acetaminophen (AC). The two analytes showed linear dependence on the concentration range from 1 to 15 µM and the LODs achieved were 0.21 µM for DOPA and 0.29 µM for AC. Moreover, the platform was successfully applied on the determination of DOPA and AC in spiked blood serum and urine samples. The results obtained with the device described here were better than some reports in literature that use more costly electrodic materials and complex modification steps for the detection of the same analytes.

Measuring proteins in H2O with 2D-IR spectroscopy

The amide I infrared band of proteins is highly sensitive to secondary structure, but studies under physiological conditions are prevented by strong, overlapping water absorptions, motivating the widespread use of deuterated solutions. H/D exchange raises fundamental questions regarding the impact of increased mass on protein dynamics, while deuteration is impractical for biomedical or commercial applications of protein IR spectroscopy. We show that 2D-IR spectroscopy can avoid this problem because the 2D-IR amide I signature of proteins dominates that of water even at sub-millimolar protein concentrations. Using equine blood serum as a test system, we investigate the significant implications of being able to measure the spectroscopy and dynamics of proteins in water, demonstrating relevance in areas ranging from fundamental science to the clinic. Measurements of vibrational relaxation dynamics of serum proteins reveals that deuteration slows down the rate of amide I vibrational relaxation by >10%, indicating a dynamic impact of isotopic exchange in some proteins. The unique link between protein secondary structure and 2D-IR amide I lineshape allows differentiation of signals due to albumin and globulin protein fractions in serum leading to measurements of the biomedically-important albumin to globulin ratio (AGR) with an accuracy of ±4% across a clinically-relevant range. Furthermore, we demonstrate that 2D-IR spectroscopy enables differentiation of the structurally similar globulin proteins IgG, IgA and IgM, opening up a straightforward spectroscopic approach to measuring levels of serum proteins that are currently only accessible via biomedical laboratory testing.

Structural and Thermoanalytical Characterization of 3D Porous PDMS Foam Materials: The Effect of Impurities Derived from a Sugar Templating Process

Polydimethylsiloxane (PDMS) polymers are extensively used in a wide range of research and industrial fields, due to their highly versatile chemical, physical, and biological properties. Besides the different two-dimensional PDMS formulations available, three-dimensional PDMS foams have attracted increased attention. However, as-prepared PDMS foams contain residual unreacted low molecular weight species that need to be removed in order to obtain a standard and chemically stable material for use as a scaffold for different decorating agents. We propose a cleaning procedure for PDMS foams obtained using a sugar templating process, based on the use of two different solvents (hexane and ethanol) as cleaning agents. Thermogravimetry coupled with Fourier Transform Infrared Spectroscopy (TG-FTIR) for the analysis of the evolved gasses was used to characterize the thermal stability and decomposition pathway of the PDMS foams, before and after the cleaning procedure. The results were compared with those obtained on non-porous PDMS bulk as a reference. Micro-CT microtomography and scanning electron microscopy (SEM) analyses were employed to study the morphology of the PDMS foam. The thermogravimetric analysis (TGA) revealed a different thermal behaviour and crosslinking pathway between bulk PDMS and porous PDMS foam, which was also influenced by the washing process. This information was not apparent from spectroscopic or morphological studies and it would be very useful for planning the use of such complex and very reactive systems.