A rapid microfluidic mixer for high-viscosity fluids to track ultrafast early folding kinetics of G-quadruplex under molecular crowding conditions

A TeZla micromixer for interrogating the early and broad folding landscape of G-quadruplex via multistage velocity descending

Biomacromolecular folding kinetics involves fast folding events and broad timescales. Current techniques face limitations in either the required time resolution or the observation window. In this study, we developed the TeZla micromixer, integrating Tesla and Zigzag microstructures with a multistage velocity descending strategy. TeZla achieves a significant short mixing dead time (40 µs) and a wide time window covering four orders of magnitude (up to 300 ms). Using this unique micromixer, we explored the folding landscape of c-Myc G4 and its noncanonical-G4 derivatives with different loop lengths or G-vacancy sites. Our findings revealed that c-Myc can bypass folding intermediates and directly adopt a G4 structure in the cation-deficient buffer. Moreover, we found that the loop length and specific G-vacancy site could affect the folding pathway and significantly slow down the folding rates. These results were also cross-validated with real-time NMR and circular dichroism. In conclusion, TeZla represents a versatile tool for studying biomolecular folding kinetics, and our findings may ultimately contribute to the design of drugs targeting G4 structures.

Recent advances in microfluidics-based bioNMR analysis

Nuclear magnetic resonance (NMR) has been used in a variety of fields due to its powerful analytical capability. To facilitate biochemical NMR (bioNMR) analysis for samples with a limited mass, a number of integrated systems have been developed by coupling microfluidics and NMR. However, there are few review papers that summarize the recent advances in the development of microfluidics-based NMR (μNMR) systems. Herein, we review the advancements in μNMR systems built on high-field commercial instruments and low-field compact platforms. Specifically, μNMR platforms with three types of typical microcoils settled in the high-field NMR instruments will be discussed, followed by summarizing compact NMR systems and their applications in biomedical point-of-care testing. Finally, a conclusion and future prospects in the field of μNMR were given.

A low-cost and high-performance 3D micromixer over a wide working range and its application for high-sensitivity biomarker detection

Homogenous mixing in microfluidic devices is often required for efficient chemical and biological reactions.Passive micromixing without external energy input has attracted much research interest. We have developed a high-performance 3D...

Effect of Molecular Crowding on Complexation of Metal Ions and 8-Quinolinol-5-Sulfonic Acid

The effect of molecular crowding on macromolecular reactions has been revealed by many researchers. In this study, we investigate the complexation of metal ions (Zn, Co, and Cd) with 8-quinolinol-5-sulfonic acid as a model of small-molecular reactions in molecular crowding. The complexation constants for 1:1, 1:2, and total complexation in the presence of polyethylene glycol (PEG, a molecular crowding reagent) are evaluated based on the increase in the reactant activity by volume exclusion and the decrease in the water activity due to the change in osmotic pressure. All complexation constants are enhanced by increasing the concentration of PEG. Its mechanisms differ for 1:1, 1:2, and total complexation. The 1:1 complexation is promoted only by the influence of the water activity, while the reactant and water activities influence the increase in the 1:2 complexation constant. Increasing the molecular weight of PEG further increases the complexation constants, as dehydration of the complex is promoted by a higher hydration number of PEG. Because this study gives the fundamental knowledge for the protein-metal interaction, in which solvation is an important factor, in molecular crowding, it provides new insights into molecular crowding studies and should attract the attention of a broad spectrum of biochemistry researchers.

G-triplex: A new type of CRISPR-Cas12a reporter enabling highly sensitive nucleic acid detection

CRISPR-Cas12a (Cpf1) trans-cleaves ssDNA and this feature has been widely harnessed for nucleic acid detection. Herein, we introduce a new type of Cas12a reporter, G-triplex (G3), and a highly sensitive biosensor termed G-CRISPR. We proved that Cas12a trans-cleaves G3 structures in about 10 min and G3 can serve as an excellent reporter based on the cleavage-induced high-order structure disruption. G3 reporter improves the analytical sensitivity up to 20 folds, enabling the detection of unamplified and amplified DNA as low as 50 pmol and 0.1 amol (one copy/reaction), respectively. G-CRISPR has been utilized for the analysis of 27 PCR-amplified patient samples with HPV infection risk based on both fluorescence and lateral flow assays, resulting in 100% concordance between the two. In comparison with the clinical results, it achieved overall specificity and sensitivity of 100% and 94.7%, respectively. These results suggest that G-CRISPR can serve as a rapid, sensitive, and reliable biosensor, and could further expand the CRISPR toolbox in biomedical diagnostics.

An Investigation of Flow Patterns and Mixing Characteristics in a Cross-Shaped Micromixer within the Laminar Regime

A fast mixing is critical for subsequent practical development of microfluidic devices, which are often used for assays in the detection of reagents and samples. The present work sets up computational fluid dynamics simulations to explore the flow characteristic and mixing mechanism of fluids in cross-shaped mixers within the laminar regime. First, the effects of increasing an operating parameter on local mixing quality along the microchannels are investigated. It is found that sufficient diffusion cannot occur even though the concentration gradient is large at a high Reynolds number. Meanwhile, a method for calculating local mixing efficiency is also characterized. The mixing efficiency varies exponentially with the flow distance. Second, in order to optimize the cross-shaped mixer, the effects of design parameters, namely aspect ratio, mixing angle and blockage, on mixing quality are captured and the visualization of velocity and concentration distribution are demonstrated. The results show that the aspect ratio and the blockage play an important role in accelerating the mixing process. They can improve the mixing efficiency by increasing the mass transfer area and enhancing the chaotic advection, respectively. In contrast, the inflow angle that affects dispersion length is not an effective parameter. Besides, the surface roughness, which makes the disturbance of fluid flow by roughness more obvious, is considered. Three types of rough elements bring benefits for enhancing mixing quality due to the convection induced by the lateral velocity.

Microfluidic Protein Imaging Platform: Study of Tau Protein Aggregation and Alzheimer's Drug Response

Tau protein aggregation is identified as one of the key phenomena associated with the onset and progression of Alzheimer’s disease. In the present study, we performed on-chip confocal imaging of tau protein aggregation and tau–drug interactions using a spiral-shaped passive micromixing platform. Numerical simulations and experiments were performed in order to validate the performance of the micromixer design. We performed molecular modeling of adenosine triphosphate (ATP)-induced tau aggregation in order to successfully validate the concept of helical tau filament formation. Tau aggregation and native tau restoration were realized using an immunofluorescence antibody assay. The dose–response behavior of an Alzheimer’s drug, methylthioninium chloride (MTC), was monitored on-chip for defining the optimum concentration of the drug. The proposed device was tested for reliability and repeatability of on-chip tau imaging. The amount of the tau protein sample used in our experiments was significantly less than the usage for conventional techniques, and the whole protein–drug assay was realized in less than two hours. We identified that intensity-based tau imaging could be used to study Alzheimer’s drug response. In addition, it was demonstrated that cell-free, microfluidic tau protein assays could be used as potential on-chip drug evaluation tools for Alzheimer’s disease.

Versatile Microfluidic Mixing Platform for High- and Low-Viscosity Liquids via Acoustic and Chemical Microbubbles

Microfluidic mixers have been extensively studied due to their wide application in various fields, including clinical diagnosis and chemical research. In this paper, we demonstrate a mixing platform that can be used for low- and high-viscosity liquid mixing by integrating passive (utilizing the special circulating crossflow characteristics of a zigzag microstructure and cavitation surfaces at the zigzag corners) and active (adding an acoustic field to produce oscillating microbubbles) mixing methods. By exploring the relationship between the active and passive mixing methods, it was found that the microbubbles were more likely generated at the corners of the zigzag microchannel and achieved the best mixing efficiency with the acoustically generated microbubbles (compared with the straight channel). In addition, a higher mixing effect was achieved when the microchannel corner angle and frequency were 60° and 75 kHz, respectively. Meanwhile, the device also achieved an excellent mixing effect for high-viscosity fluids, such as glycerol (its viscosity was approximately 1000 times that of deionized (DI) water at 25 °C). The mixing time was less than 1 s, and the mixing efficiency was 0.95 in the experiment. Furthermore, a new microbubble generation method was demonstrated based on chemical reactions. A higher mixing efficiency (0.97) was achieved by combining the chemical and acoustic microbubble methods, which provides a new direction for future applications and is suitable for the needs of lab-on-a-chip (LOC) systems and point-of-care testing (POCT).

Acoustic Actuation of in situ Fabricated Artificial Cilia

We present on-chip acoustic actuation of in situ fabricated artificial cilia. Arrays of cilia structures are UV polymerized inside a microfluidic channel using a photocurable polyethylene glycol (PEG) polymer solution and photomasks. During polymerization, cilia structures are attached to a silane treated glass surface inside the microchannel. Then, the cilia structures are actuated using acoustic vibrations at 4.6 kHz generated by piezo transducers. As a demonstration of a practical application, DI water and fluorescein dye solutions are mixed inside a microfluidic channel. Using pulses of acoustic excitations, and locally fabricated cilia structures within a certain region of the microchannel, a waveform of mixing behavior is obtained. This result illustrates one potential application wherein researchers can achieve spatiotemporal control of biological microenvironments in cell stimulation studies. These acoustically actuated, in situ fabricated, cilia structures can be used in many on-chip applications in biological, chemical and engineering studies.

Effects of molecular confinement and crowding on horseradish peroxidase kinetics using a nanofluidic gradient mixer

The effects of molecular confinement and crowding on enzyme kinetics were studied at length scales and under conditions similar to those found in biological cells. These experiments were carried out using a nanofluidic network of channels constituting a nanofluidic gradient mixer, providing the basis for measuring multiple experimental conditions simultaneously. The 100 nm × 40 μm nanochannels were wet etched directly into borosilicate glass, then annealed and characterized with fluorescein emission prior to kinetic measurements. The nanofluidic gradient mixer was then used to measure the kinetics of the conversion of the horseradish peroxidase (HRP)-catalyzed conversion of non-fluorescent Amplex Red (AR) to the fluorescent product resorufin in the presence of hydrogen peroxide (H2O2). The design of the gradient mixer allows reaction kinetics to be studied under multiple (five) unique solution compositions in a single experiment. To characterize the efficiency of the device the effects of confinement on HRP-catalyzed AR conversion kinetics were studied by varying the starting ratio of AR : H2O2. Equimolar concentrations of Amplex Red and H2O2 yielded the highest reaction rates followed by 2 : 1, 1 : 2, 5 : 1, and finally 1 : 5 [AR] : [H2O2]. Under all conditions, initial reaction velocities were decreased by excess H2O2. Crowding effects on kinetics were studied by increasing solution viscosity in the nanochannels in the range 1.0-1.6 cP with sucrose. Increasing the solution viscosities in these confined geometries decreases the initial reaction velocity at the highest concentration from 3.79 μM min(-1) at 1.00 cP to 0.192 μM min(-1) at 1.59 cP. Variations in reaction velocity are interpreted in the context of models for HRP catalysis and for molecular crowding.

PDMS-based turbulent microfluidic mixer

Over the past decade, homogeneous mixing in microfluidic devices has been a critical challenge, because of the inherently low flow rates in microfluidic channels. Although several mixer designs have been suggested to achieve efficient mixing, most of them involve intricate structures requiring a series of laborious fabrication processes. Operation at high flow rates can greatly enhance mixing by induction of turbulence, but devices that can resist such a high pressure drop to induce turbulence in microfluidic channels are difficult to fabricate, especially for commonly used poly(dimethylsiloxane) (PDMS)-based microfluidic devices. We have developed a Y-shaped, turbulent microfluidic mixer made of PDMS and a glass substrate by strong bonding of the substrates to a nanoadhesive layer deposited via initiated chemical vapor deposition. The high bonding strength of the nanoadhesive layer enables safe operation of the PDMS/glass turbulent microfluidic mixer at a total water flow rate of 40 mL min(-1), corresponding to a Reynolds number, Re, of ~4423, one of the highest values achieved in a microfluidic channel. The turbulence generated as a result of the high Re allows rapid mixing of the input fluids on contact. Image analysis showed that mixing started as soon as the fluids were introduced into the mixer. The experimental results matched the numerical predictions well, demonstrating that convective mixing was dominant as a result of turbulence induced in the microfluidic channel. Using the turbulent microfluidic mixer, we have demonstrated high throughput formation of emulsions with narrower size distribution. It was shown that as the flow rate increases inside the microfluidic channel, the size distribution of resulting emulsions decreases owing to the increase in the turbulent energy dissipation. The turbulent microfluidic mixer developed in this work not only enables rapid mixing of streams, but also increases throughputs of microfluidic reactors.

A microfluidic digital single-cell assay for the evaluation of anticancer drugs

Digital single-cell assays hold high potentials for the analysis of cell apoptosis and the evaluation of chemotherapeutic reagents for cancer therapy. In this paper, a microfluidic hydrodynamic trapping system was developed for digital single-cell assays with the capability of monitoring cellular dynamics over time. The microfluidic chip was designed with arrays of bypass structures for trapping individual cells without the need for surface modification, external electric force, or robotic equipment. After optimization of the bypass structure by both numerical simulations and experiments, a single-cell trapping efficiency of ∼90 % was achieved. We demonstrated the method as a digital single-cell assay for the evaluation of five clinically established chemotherapeutic reagents. As a result, the half maximal inhibitory concentration (IC50) values of these compounds could be conveniently determined. We further modeled the gradual decrease of active drugs over time which was often observed in vivo after an injection to investigate cell apoptosis against chemotherapeutic reagents. The developed method provided a valuable means for cell apoptotic analysis and evaluation of anticancer drugs.

An acoustofluidic micromixer via bubble inception and cavitation from microchannel sidewalls

During the deep reactive ion etching process, the sidewalls of a silicon mold feature rough wavy structures, which can be transferred onto a polydimethylsiloxane (PDMS) microchannel through the soft lithography technique. In this article, we utilized the wavy structures of PDMS microchannel sidewalls to initiate and cavitate bubbles in the presence of acoustic waves. Through bubble cavitation, this acoustofluidic approach demonstrates fast, effective mixing in microfluidics. We characterized its performance by using viscous fluids such as poly(ethylene glycol) (PEG). When two PEG solutions with a resultant viscosity 54.9 times higher than that of water were used, the mixing efficiency was found to be 0.92, indicating excellent, homogeneous mixing. The acoustofluidic micromixer presented here has the advantages of simple fabrication, easy integration, and capability to mix high-viscosity fluids (Reynolds number: ~0.01) in less than 100 ms.

Effect of the crossing-structure sequence on mixing performance within three-dimensional micromixers

The geometry of crossing structure formed by two-layer microchannels determines the axial and transverse movements of contact interface between two liquid streams, which gives us a new method for promoting the micromixers. Hence, we designed four different three-dimensional micromixers by selecting two different crossing structures as basic units (one unit is a crossing structure called "X" and the other is a reversed crossing structure called "rX"). In order to find out how the crossing-structure sequence affects the mixing performance within three-dimensional micromixers, we organized these four mixers in different ways, i.e., the first combination is X-rX-X-rX-…, the second is X-rX-rX-X-…, the third is X-X-rX-X-…, and the last one is X-X-X-X…. Consequently, quite distinct mixing phenomena are engendered. Furthermore, experiments were also conducted using the first and the last models to verify the simulation results. We infer that the last mixer is more likely to trigger chaos and convection by rotating the contact surface than the first one that merely swings the surface even when the flow rates and viscosities of the two liquid streams are increased.

Conformational Dynamics of DNA G-Quadruplex in Solution Studied by Kinetic Capillary Electrophoresis Coupled On-line with Mass Spectrometry

G-quadruplex-forming DNA/RNA sequences play an important role in the regulation of biological functions and development of new anticancer and anti-aging drugs. In this work, we couple on-line kinetic capillary electrophoresis with mass spectrometry (KCE-MS) to study conformational dynamics of DNA G-quadruplexes in solution. We show that peaks shift and its widening in KCE can be used for measuring rate and equilibrium constants for DNA–metal affinity interactions and G-quadruplex formation; and ion mobility mass spectrometry (IM-MS) provides information about relative sizes, absolute molecular masses and stoichiometry of DNA complexes. KCE-MS separates a thrombin-binding aptamer d[GGTTGGTGTGGTTGG] from mutated sequences based on affinity to potassium, and reveals the apparent equilibrium folding constant (K_F≈150 μm), folding rate constant (k_on≈1.70×10³ s⁻¹ m⁻¹), unfolding rate constant (k_off≈0.25 s⁻¹), half-life time of the G-quadruplex (t_1/2≈2.8 s), and relaxation time (τ≈3.9 ms at physiological 150 mm [K⁺]). In addition, KCE-MS screens for a GQ-stabilizing/-destabilizing effect of DNA binding dyes and an anticancer drug, cisplatin.

A novel microfluidic mixer based on dual-hydrodynamic focusing for interrogating the kinetics of DNA-protein interaction

Kinetic measurement of biomacromolecular interaction plays a significant role in revealing the underlying mechanisms of cellular activities. Due to the small diffusion coefficient of biomacromolecules, it is difficult to resolve the rapid kinetic process with traditional analytical methods such as stopped-flow or laminar mixers. Here, we demonstrated a unique continuous-flow laminar mixer based on microfluidic dual-hydrodynamic focusing to characterize the kinetics of DNA-protein interactions. The time window of this mixer for kinetics observation could cover from sub-milliseconds to seconds, which made it possible to capture the folding process with a wide dynamic range. Moreover, the sample consumption was remarkably reduced to <0.55 μL min⁻¹, over 1000-fold saving in comparison to those reported previously. We further interrogated the interaction kinetics of G-quadruplex and the single-stranded DNA binding protein, indicating that this novel micromixer would be a useful approach for analyzing the interaction kinetics of biomacromolecules.

Aeroelasticity-based fluid agitation for lab-on-chips

In this study, we report a robust agitation method for small-volume liquids. It utilizes an elastic diaphragm as the bottom of a liquid chamber, upon which an initial tension is also applied to enhance the aeroelasticity effects at small/micro scales. As a result, spontaneous vibration of the diaphragm can be induced by an external air flow, which further provides fluid agitations. The device structure is simple and can be easily fabricated at low cost. More importantly, the vibration amplitude is controllable and varies widely from several tens to several hundred micrometers depending on the applied air pressure. The resulting agitation is effective and applicable at high viscosities of up to 900 cSt. The influences of air pressure and liquid viscosity on the vibration frequency are discussed. Potential applications of this technique for solid particle agitation, focusing and fluid mixing are also demonstrated.