Molecular rheotaxis directs DNA migration and concentration against a pressure-driven flow

Surface chemistry-based continuous separation of colloidal particles via diffusiophoresis and diffusioosmosis

The separation of colloidal particles is of great importance in many fields, such as purification, sensing, and bioanalysis. However, separating particles based on their surface physico-chemical properties remains challenging. This study demonstrates through experimental and theoretical analyses that diffusiophoresis and diffusioosmosis enable the continuous separation of carboxylate polystyrene particles with similar sizes and zeta potentials but distinct surface concentrations of carboxyl groups. In the proposed approach, the particles are exposed to salt concentration gradients generated in a double-junction microfluidic device, fed with low and high electrolyte concentration streams. As the particles move across environments with varying salinity levels, their dynamics are affected by the sensitivity of their electrophoretic mobility - and consequently, their apparent zeta potential, which is proportional to it - to the local salt concentration. The apparent zeta potential, measured via electrophoretic light scattering, and its sensitivity to salt concentration are influenced by the ionic conduction occurring near the particle surface whose intensity depends, in turn, on the concentration of surface carboxyl groups. By harnessing these effects, colloids with comparable apparent zeta potentials but different surface concentrations of carboxyl groups are separated with high efficiency when they exhibit opposite apparent zeta potential sensitivities to salt. This simple approach, which relies on an easy-to-operate device with no external energy source, has discipline-spanning potential for the continuous separation of colloids distinguished solely by surface properties like roughness, permeability, heterogeneity, and chemical composition that influence the sensitivities of their electrophoretic mobility and, thus apparent zeta potential, to the salt concentration.

Capillary-based, multifunctional manipulation of particles and fluids via focused surface acoustic waves

Surface acoustic wave (SAW)-enabled acoustofluidic technologies have recently atttracted increasing attention for applications in biology, chemistry, biophysics, and medicine. Most SAW acoustofluidic devices generate acoustic energy which is then transmitted into custom microfabricated polymer-based channels. There are limited studies on delivering this acoustic energy into convenient commercially-available glass tubes for manipulating particles and fluids. Herein, we have constructed a capillary-based SAW acoustofluidic device for multifunctional fluidic and particle manipulation. This device integrates a converging interdigitated transducer to generate focused SAWs on a piezoelectric chip, as well as a glass capillary that transports particles and fluids. To understand the actuation mechanisms underlying this device, we performed finite element simulations by considering piezoelectric, solid mechanic, and pressure acoustic physics. This experimental study shows that the capillary-based SAW acoustofluidic device can perform multiple functions including enriching particles, patterning particles, transporting particles and fluids, as well as generating droplets with controlled sizes. Given the usefulness of these functions, we expect that this acoustofluidic device can be useful in applications such as pharmaceutical manufacturing, biofabrication, and bioanalysis.

Reversible Self-Assembly of Nucleic Acids in a Diffusiophoretic Trap

The formation and dissociation of duplexes or higher order structures from nucleic acid strands is a fundamental process with widespread applications in biochemistry and nanotechnology. Here, we introduce a simple experimental system-a diffusiophoretic trap-for the non-equilibrium self-assembly of nucleic acid structures that uses an electrolyte gradient as the driving force. DNA strands can be concentrated up to hundredfold by a diffusiophoretic trapping force that is caused by the electric field generated by the electrolyte gradient. We present a simple equation for the field to guide selection of appropriate trapping electrolytes. Experiments with carboxylated silica particles demonstrate that the diffusiophoretic force is long-ranged, extending over hundreds of micrometers. As an application, we explore the reversible self-assembly of branched DNA nanostructures in the trap into a macroscopic gel. The structures assemble in the presence of an electrolyte gradient, and disassemble upon its removal, representing a prototypical adaptive response to a macroscopic non-equilibrium state.

Isotachophoresis with Oscillating Sample Zones to Control the Spatial Overlap of Co-focused Species

Microfluidic isotachophoresis (ITP) is a powerful technique that can significantly increase the reaction rate of homogeneous chemical reactions by cofocusing reactants in a narrow sample zone. Correspondingly, ITP has been utilized to reduce the reaction time in various bioanalytical assays. However, in conventional ITP, it is hardly possible to control the reaction rate in real time, i.e., speeding up or slowing down a reaction on demand. Here, we experimentally demonstrate a new mode of ITP that allows the spatial overlap of two ITP zones to be precisely controlled over time, which is a crucial first step toward controlling reaction rates. Two nonreactive samples are initially focused and separated by a spacer using a DC electric field. By superimposing an oscillating field component with sufficiently high amplitude on the DC field, the spatial overlap of their concentration profiles is temporarily increased due to electromigration dispersion. The time-average of this overlap can be precisely controlled by varying the frequency and amplitude of the oscillation. We suggest that this scheme can be transferred to chemical reactions between ionic species with sufficiently different electrophoretic mobilities. Tuning the parameters of the oscillatory electric field should allow direct control of the corresponding reaction rate.

Voltage and concentration gradients across membraneless interface generated next to hydrogels: relation to glycocalyx

Next to many hydrophilic surfaces, including those of biological cells and tissues, a layer of water that effectively excludes solutes and particles can be generated. This interfacial water is the subject of research aiming for practical applications such as removal of salts, pathogens or manipulation of biomolecules. However, the exact mechanism of its creation is still elusive because its persistence and extension contradict hydrogen-bond dynamics and electric double layer predictions. The experimentally recorded negative voltage of this interfacial water remains to be properly explained. Even less is known about the nature of such water layers in biological systems. We present experimental evidence for ion and particle exclusion as a result of separation of ionic charges with distinct diffusion rates across a liquid junction at the gel/water interface and the subsequent repulsion of ions of a given sign by a like-charged gel surface. Gels represent features of biological interfaces (in terms of functional groups and porosity) and are subject to biologically relevant chemical triggers. Our results show that gels with -OSO3- and -COO- groups can effectively generate ion- and particle-depleted regions of water reaching over 100 μm and having negative voltage up to -30 mV. Exclusion distance and electric potential depend on the liquid junction potential at the gel/water interface and on the concentration gradient at the depleted region/bulk interface, respectively. The voltage and extension of these ion- and particle-depleted water layers can be effectively modified by CO2 (respiratory gas) or KH2PO4 (cell metabolite). Possible implications pertain to biologically unstirred water layers and a cell's bioenergetics.

Diffusiophoresis of Weakly Charged Fluid Droplets in a General Electrolyte Solution: An Analytical Theory

Owing to the importance of analytical results for electrokinetics of colloidal entities, we performed a mathematical analysis to determine the closed form analytical results for the diffusiophoretic velocity of a hydrophobic and polarizable fluid droplet. A comprehensive mathematical model is developed for diffusiophoresis, considering the background aqueous medium as general electrolytes (e.g., binary valence-symmetric/asymmetric electrolytes and a mixed solution of binary electrolytes). We performed our analysis under a weak concentration gradient, and the analytical results for diffusiophoretic velocity are calculated within the Debye-Hückel electrostatic framework. The exact form of the diffusiophoretic velocity is further approximated with negligible error, and the approximate form is found to be free from any of the cumbersome exponential integrals and thus very convenient for practical use. The present theory also covers the diffusiophoresis of perfectly dielectric as well as perfectly conducting droplets as its limiting case. In addition, we have further derived a number of closed form expressions for diffusiophoretic velocity pertaining to several particular cases, and we observed that the derived limit correctly recovers the available existing analytical results for diffusiophoretic velocity. Thus, the present analytical theory for diffusiophoresis can be applied to a wide class of fluidic droplets, e.g., hydrophobic and dielectric oil/conducting mercury droplets, air bubbles, nanoemulsions, as well as any polarizable and hydrophobic fluidic droplet suspended in a solution of general electrolytes.

Detecting Isotachophoresis Zones Hidden in Noise Using Signal Processing

Lowering the limit of detection in chemical or biochemical analysis is key to extending the application scope of sensing schemes. Usually, this is related to an increased instrumentation effort, which in turn precludes many commercial applications. We demonstrate that the signal-to-noise ratio of isotachophoresis-based microfluidic sensing schemes can be substantially increased merely by postprocessing of recorded signals. This becomes possible by exploiting knowledge about the physics of the underlying measurement process. The implementation of our method is based on microfluidic isotachophoresis and fluorescence detection, for which we take advantage of the physics of electrophoretic sample transport and the structure of noise in the imaging process. We demonstrate that by processing only 200 images, the detectable concentration, compared to the detection from a single image, is already lowered by 2 orders of magnitude without any additional instrumentation effort. Furthermore, we show that the signal-to-noise ratio is proportional to the square root of the number of fluorescence images, which leaves room for further lowering of the detection limit. In the future, our results could be relevant for various applications where the detection of minute sample amounts plays a role.

Shape- and orientation-dependent diffusiophoresis of colloidal ellipsoids

We present the diffusiophoresis of ellipsoidal particles induced by ionic solute gradients. Contrary to the common expectation that diffusiophoresis is shape independent, here we show experimentally that this assumption breaks down when the thin Debye layer approximation is relaxed. By tracking the translation and rotation of various ellipsoids, we find that the phoretic mobility of ellipsoids is sensitive to the eccentricity and the orientation of the ellipsoid relative to the imposed solute gradient, and can further lead to nonmonotonic behavior under strong confinement. We show that such a shape- and orientation-dependent diffusiophoresis of colloidal ellipsoids can be easily captured by modifying theories for spheres.

Directed colloidal assembly and banding via DC electrokinetics

Manipulating the transport and assembly of colloidal particles to form segregated bands or ordered supracolloidal structures plays an important role in many aspects of science and technology, from understanding the origin of life to synthesizing new materials for next-generation manufacturing, electronics, and therapeutics. One commonly used method to direct colloidal transport and assembly is the application of electric fields, either AC or DC, due to its feasibility. However, as colloidal segregation and assembly both require active redistribution of colloidal particles across multiple length scales, it is not apparent at first sight how a DC electric field, either externally applied or internally induced, can lead to colloidal structuring. In this Perspective, we briefly review and highlight recent advances and standing challenges in colloidal transport and assembly enabled by DC electrokinetics.

Unidirectional drying of a suspension of diffusiophoretic colloids under gravity

Recent experiments (K. Inoue and S. Inasawa, RSC Adv., 2020, 10, 15763-15768) and simulations (J.-B. Salmon and F. Doumenc, Phys. Rev. Fluids, 2020, 5, 024201) demonstrated the significant impact of gravity on unidirectional drying of a colloidal suspension. However, under gravity, the role of colloid transport induced by an electrolyte concentration gradient, a mechanism known as diffusiophoresis, is unexplored to date. In this work, we employ direct numerical simulations and develop a macrotransport theory to analyze the advective-diffusive transport of an electrolyte-colloid suspension in a unidirectional drying cell under the influence of gravity and diffusiophoresis. We report three key findings. First, drying a suspension of solute-attracted diffusiophoretic colloids causes the strongest phase separation and generates the thinnest colloidal layer compared to non-diffusiophoretic or solute-repelled colloids. Second, when colloids are strongly solute-repelled, diffusiophoresis prevents the formation of colloid concentration gradient and hence gravity has a negligible effect on colloidal layer formation. Third, our macrotransport theory predicts new scalings for the growth of the colloidal layer. The scalings match with direct numerical simulations and indicate that the colloidal layer produced by solute-repelled diffusiophoretic colloids could be an order of magnitude thicker compared to non-diffusiophoretic or solute-attracted colloids. Our results enable tailoring the separation of colloid-electrolyte suspensions by tuning the interactions between the solvent, electrolyte, and colloids under Earth's or microgravity, which is central to ground-based and in-space applications.

Diffusiophoresis and Diffusio-osmosis into a Dead-End Channel: Role of the Concentration-Dependence of Zeta Potential

Chemically induced transport methods open up new opportunities for colloidal transport in dead-end channel geometries. Diffusiophoresis, which describes particle movement under an electrolyte concentration gradient, has previously been demonstrated in dead-end channels. The presence of solute concentration gradients in such channels induces particle motion (phoresis) and fluid flow along solid walls (osmosis). The particle velocity inside a dead-end channel is thus influenced by particle diffusiophoresis and wall diffusio-osmosis. The magnitude of phoresis and osmosis depends on the solute's relative concentration gradient, the electrokinetic parameters of the particle and the wall, and the diffusivity contrast of cations and anions. Although it is known that some of those parameters are affected by electrolyte concentration, e.g., zeta potential, research to date often interprets results using averaged and constant zeta potential values. In this work, we demonstrate that concentration-dependent zeta potentials are essential when the zeta potential strongly depends on electrolyte concentration for correctly describing the particle transport inside dead-end channels. Simulations including concentration-dependent zeta potentials for the particle and wall matched with experimental observations, whereas simulations using constant, averaged zeta potentials failed to capture particle dynamics. These results contribute to the fundamental understanding of diffusiophoresis and the diffusio-osmosis process.

Diffusiophoresis of a spherical particle in porous media

Recent experiments by Doan et al. (Nano Lett., 2021, 21, 7625-7630) demonstrated and measured colloid diffusiophoresis in porous media but existing theories cannot predict the observed colloid motion. Here, using regular perturbation method, we develop a mathematical model that can predict the diffusiophoretic motion of a charged colloidal particle driven by a binary monovalent electrolyte concentration gradient in a porous medium. The porous medium is modeled as a Brinkman medium with a constant Darcy permeability. The linearized Poisson-Boltzmann equation is employed to model the equilibrium electric potential distribution that is driven out-of-equilibrium under diffusiophoresis. We report three key findings. First, we demonstrate that colloid diffusiophoresis could be drastically hindered in a porous medium due to the additional hydrodynamic drag compared to diffusiophoresis in a free electrolyte solution. Second, we show that the variation of the diffusiophoretic motion with respect to a change in the electrolyte concentration in a porous medium could be qualitatively different from that in a free electrolyte solution. Third, our results match quantitatively with experimental measurements, highlighting the predictive power of the present model. The mathematical model developed here could be employed to design diffusiophoretic colloid transport in porous media, which are central to applications such as nanoparticle drug delivery and enhanced oil recovery.

Collective Behaviors of Active Matter Learning from Natural Taxes Across Scales

Taxis orientation is common in microorganisms, and it provides feasible strategies to operate active colloids as small-scale robots. Collective taxes involve numerous units that collectively perform taxis motion, whereby the collective cooperation between individuals enables the group to perform efficiently, adaptively, and robustly. Hence, analyzing and designing collectives is crucial for developing and advancing microswarm toward practical or clinical applications. In this review, natural taxis behaviors are categorized and synthetic microrobotic collectives are discussed as bio-inspired realizations, aiming at closing the gap between taxis strategies of living creatures and those of functional active microswarms. As collective behaviors emerge within a group, the global taxis to external stimuli guides the group to conduct overall tasks, whereas the local taxis between individuals induces synchronization and global patterns. By encoding the local orientations and programming the global stimuli, various paradigms can be introduced for coordinating and controlling such collective microrobots, from the viewpoints of fundamental science and practical applications. Therefore, by discussing the key points and difficulties associated with collective taxes of different paradigms, this review potentially offers insights into mimicking natural collective behaviors and constructing intelligent microrobotic systems for on-demand control and preassigned tasks.

Enhanced Accumulation of Colloidal Particles in Microgrooved Channels via Diffusiophoresis and Steady-State Electrolyte Flows

The delivery of colloidal particles in dead-end microstructures is very challenging, since these geometries do not allow net flows of particle-laden fluids; meanwhile, diffusive transport is slow and inefficient. Recently, we introduced a novel particle manipulation strategy, based on diffusiophoresis, whereby the salt concentration gradient between parallel electrolyte streams in a microgrooved channel induces the rapid (i.e., within minutes) and reversible accumulation, retention, and removal of colloidal particles in the microgrooves. In this study, we investigated the effects of salt contrast and groove depth on the accumulation process in silicon microgrooves and determined the experimental conditions that lead to a particle concentration peak of more than four times the concentration in the channel bulk. Also, we achieved an average particle concentration in the grooves of more than twice the concentration in the flowing streams and almost 2 orders of magnitude larger than the average concentration in the grooves in the absence of a salt concentration gradient. Analytical sufficient and necessary conditions for particle accumulation are also derived. Finally, we successfully tested the accumulation process in polydimethylsiloxane microgrooved channels, as they are less expensive to fabricate than silicon microgrooved substrates. The controlled and enhanced accumulation of colloidal particles in dead-end structures by solute concentration gradients has potential applications in soft matter and living systems, such as drug delivery, synthetic biology, and on-chip diagnostics.

Microscale Diffusiophoresis of Proteins

Living systems are characterized by their spatially highly inhomogeneous nature which is susceptible to modify fundamentally the behavior of biomolecular species, including the proteins that underpin biological functionality in cells. Spatial gradients in chemical potential are known to lead to strong transport effects for colloidal particles, but their effect on molecular scale species such as proteins has remained largely unexplored. Here, we improve on existing diffusiophoresis microfluidic technique to measure protein diffusiophoresis in real space. The measurement of proteins is made possible by two ameliorations. First, a label-free microscope is used to suppress label interference. Second, improvements in numerical methods are developed to meet the particular challenges posed by small molecules. We demonstrate that individual proteins can undergo strong diffusiophoretic motion in salt gradients in a manner which is sufficient to overcome diffusion and which leads to dramatic changes in their spatial organization on the scale of a cell. Moreover, we demonstrate that this phenomenon can be used to control the motion of proteins in microfluidic devices. These results open up a path towards a physical understanding of the role of gradients in living systems in the spatial organization of macromolecules and highlight novel routes towards protein sorting applications on device.

Diffusiophoresis, Diffusioosmosis, and Microfluidics: Surface-Flow-Driven Phenomena in the Presence of Flow

Diffusiophoresis is the spontaneous motion of particles under a concentration gradient of solutes. Since the first recognition by Derjaguin and colleagues in 1947 in the form of capillary osmosis, the phenomenon has been broadly investigated theoretically and experimentally. Early studies were mostly theoretical and were largely interested in surface coating applications, which considered the directional transport of coating particles. In the past decade, advances in microfluidics enabled controlled demonstrations of diffusiophoresis of micro- and nanoparticles. The electrokinetic nature and the typical scales of interest of the phenomenon motivated various experimental studies using simple microfluidic configurations. In this review, I will discuss studies that report diffusiophoresis in microfluidic systems, with the focus on the fundamental aspects of the reported results. In particular, parameters and influences of diffusiophoresis and diffusioosmosis in microfluidic systems and their combinations are highlighted.

Toward the Development of Rapid, Specific, and Sensitive Microfluidic Sensors: A Comprehensive Device Blueprint

Recent advances in nano/microfluidics have led to the miniaturization of surface-based chemical and biochemical sensors, with applications ranging from environmental monitoring to disease diagnostics. These systems rely on the detection of analytes flowing in a liquid sample, by exploiting their innate nature to react with specific receptors immobilized on the microchannel walls. The efficiency of these systems is defined by the cumulative effect of analyte detection speed, sensitivity, and specificity. In this perspective, we provide a fresh outlook on the use of important parameters obtained from well-characterized analytical models, by connecting the mass transport and reaction limits with the experimentally attainable limits of analyte detection efficiency. Specifically, we breakdown when and how the operational (e.g., flow rates, channel geometries, mode of detection, etc.) and molecular (e.g., receptor affinity and functionality) variables can be tailored to enhance the analyte detection time, analytical specificity, and sensitivity of the system (i.e., limit of detection). Finally, we present a simple yet cohesive blueprint for the development of high-efficiency surface-based microfluidic sensors for rapid, sensitive, and specific detection of chemical and biochemical analytes, pertinent to a variety of applications.

Reversible Trapping of Colloids in Microgrooved Channels via Diffusiophoresis under Steady-State Solute Gradients

The controlled transport of colloids in dead-end structures is a key capability that can enable a wide range of applications, such as biochemical analysis, drug delivery, and underground oil recovery. This Letter presents a new trapping mechanism that allows the fast (i.e., within a few minutes) and reversible accumulation of submicron particles within dead-end microgrooves by means of parallel streams with different salinity level. For the first time, particle focusing in dead-end structures is achieved under steady-state gradients. Confocal microscopy analysis and numerical investigations show that the particles are trapped at a flow recirculation region within the grooves due to a combination of diffusiophoresis transport and hydrodynamic effects. Counterintuitively, the particle velocity at the focusing point is not vanishing and, hence, the particles are continuously transported in and out of the focusing point. The accumulation process is also reversible and one can cyclically trap and release the colloids by controlling the salt concentration of the streams via a flow switching valve.

Zirconia Hybrid Nanoshells for Nutrient and Toxin Detection

Monitoring milk quality is of fundamental importance in food industry, because of the nutritional value and resulting position of milk in daily diet. The detection of small nutrients and toxins in milk is challenging, considering high sample complexity and low analyte abundance. In addition, the slow analysis and tedious sample preparation hinder the large-scale application of conventional detection techniques. Herein, zirconia hybrid nanoshells are constructed to enhance the performance of laser desorption/ionization mass spectrometry (LDI MS). Zirconia nanoshells with the optimized structures and compositions are used as matrices in LDI MS and achieve direct analysis of small molecules from 5 nL of native milk in ≈1 min, without any purification or separation. Accurate quantitation of small nutrient is achieved by introducing isotope into the zirconia nanoshell-assisted LDI MS as the internal standard, offering good consistency to biochemical analysis (BCA) with R²  = 0.94. Further, trace toxin is enriched and identified with limit-of-detection (LOD) down to 4 pm, outperforming the current analytical methods. This work sheds light on the personalized design of material-based tool for real-case bioanalysis and opens up new opportunities for the simple, fast, and cost-effective detection of various small molecules in a broad field.

Acoustofluidic multi-well plates for enrichment of micro/nano particles and cells

Controllable enrichment of micro/nanoscale objects plays a significant role in many biomedical and biochemical applications, such as increasing the detection sensitivity of assays, or improving the structures of bio-engineered tissues. However, few techniques can perform concentrations of micro/nano objects in multi-well plates, a very common laboratory vessel. In this work, we develop an acoustofluidic multi-well plate, which adopts an array of simple, low-cost and commercially available ring-shaped piezoelectric transducers for rapid and robust enrichment of micro/nanoscale particles/cells in each well of the plate. The enrichment mechanism is validated and characterized through both numerical simulations and experiments. We observe that the ring-shaped piezoelectric transducer can generate circular standing flexural waves in the substrate of each well, and that the vibrations can induce acoustic streaming near the interface between the substrate and a fluid droplet placed within the well; this streaming can drive micro/nanoscale objects to the center of the droplet for enrichment. Moreover, the acoustofluidic multi-well plate can realize simultaneous and consistent enrichment of biological cells in each well of the plate. With merits such as simplicity, controllability, low cost, and excellent compatibility with other downstream analysis tools, the developed acoustofluidic multi-well plate could be a versatile tool for many applications such as micro/nano fabrication, self-assembly, biomedical/biochemical sensing, and tissue engineering.

Colloid Separation by CO2-Induced Diffusiophoresis

We present a microfluidic crossflow separation of colloids enabled by the dissolution of CO₂ gas in aqueous suspensions. The dissolved CO₂ dissociates into H⁺ and HCO₃^- ions, which are efficient candidates for electrolytic diffusiophoresis, because of the fast diffusion of protons. By exposing CO₂ gas to one side of a microfluidic flow channel, a crossflow gradient can be created, enabling the crossflow diffusiophoresis of suspended particles. We develop a simple two-dimensional model to describe the coupled transport dynamics that is due to the competition of advection and diffusiophoresis. Furthermore, we show that oil nanoemulsions can be effectively separated by utilizing highly charged particles as a carrier vehicle, which is otherwise difficult to achieve. These results demonstrate a portable, versatile method for separating particles in broad applications including oil extraction, drug delivery, and bioseparation.

Electrode-Free Concentration and Recovery of DNA at Physiologically Relevant Ionic Concentrations

Advances in microanalytical and microfluidic technologies have enabled rapid and amplification-free detection of DNA with a high signal-to-noise ratio. The low sample volume, however, poses a limit in the DNA detection sensitivity, which can be challenging for analyzing rare DNA in physiological samples. One way to improve the sensitivity is to concentrate the DNA in the sample prior to the analysis. The most common DNA concentration techniques are based on electrokinetics, which require an external electric field and generally become ineffective in high ionic concentration conditions. In this work, we present a facile method termed high-salt molecular rheotaxis (HiSMRT) to concentrate and recover DNA from samples with physiologically relevant ionic concentrations without any external electric field. HiSMRT requires only pressure-driven flow and ion concentration gradient to induce a stable local electric field and achieve DNA concentration, making it impervious to high ionic concentrations. We demonstrate that HiSMRT performs robustly at ionic concentrations equivalent to 2%-20% of the ionic concentration in blood serum. HiSMRT can concentrate DNA by up to 960-fold and recover an average of 96.4% of the DNA fragments from 2.0 to 23 kbp uniformly. The concentration process using HiSMRT takes as little as 7.5 min. Moreover, we show that this technique can be easily integrated to perform DNA concentration, size separation, and single-molecule detection all in one platform. We anticipate that this technique will be applicable to a wide range of biological samples and will help to improve the sensitivity of nucleic acid detection for low-abundance DNA biomarkers.

μLAS technology for DNA isolation coupled to Cas9-assisted targeting for sequencing and assembly of a 30 kb region in plant genome

Cas9-assisted targeting of DNA fragments in complex genomes is viewed as an essential strategy to obtain high-quality and continuous sequence data. However, the purity of target loci selected by pulsed-field gel electrophoresis (PFGE) has so far been insufficient to assemble the sequence in one contig. Here, we describe the μLAS technology to capture and purify high molecular weight DNA. First, the technology is optimized to perform high sensitivity DNA profiling with a limit of detection of 20 fg/μl for 50 kb fragments and an analytical time of 50 min. Then, μLAS is operated to isolate a 31.5 kb locus cleaved by Cas9 in the genome of the plant Medicago truncatula. Target purification is validated on a Bacterial Artificial Chromosome plasmid, and subsequently carried out in whole genome with μLAS, PFGE or by combining these techniques. PacBio sequencing shows an enrichment factor of the target sequence of 84 with PFGE alone versus 892 by association of PFGE with μLAS. These performances allow us to sequence and assemble one contig of 29 441 bp with 99% sequence identity to the reference sequence.

Dynamic Transport Control of Colloidal Particles by Repeatable Active Switching of Solute Gradients

Diffusiophoresis (DP) is described as typically being divided into chemiphoresis (CP) and electrophoresis (EP), and the related theory is well-established. However, not only the individual effect of CP and EP but also the size dependency on the resulting DP of colloidal particles has not yet been comprehensively demonstrated in an experimental manner. In this paper, we present a dynamic transport control mechanism for colloidal particles by developing a micro-/nanofluidic DP platform (MNDP). We demonstrate that the MNDP can generate transient and/or steady-state concentration gradients, making it possible to control the direction and rate of transport of colloidal particles through the individual manipulation of CP and EP by simply and rapidly switching solutions. In addition, the MNDP allows the size-dependent separation as well as fractionation of submicron particles through the individual manipulation of CP and EP, thus empirically validating the classic theoretical model for DP under the influence of electrical double layer (EDL) thickness. Furthermore, we provide theoretical analysis and simulation results that will enable the development of a versatile separation and/or fractionation technique for various colloidal particles, including biosamples, according to their size or electrical feature.

Transverse migration and microfluidic concentration of DNA using Newtonian buffers

We present experimental evidence that DNA can be concentrated due to an electrohydrodynamic coupling between a pressure-driven flow and a parallel electric field. The effects of buffer properties on the process were measured in a microfluidic channel. The concentration rates and the efficiency of trapping DNA were quantified as functions of the ion and polymer concentrations of the buffer solution. Buffers with large ion concentrations hindered the ability to trap DNA, reducing the short-time efficiency of the concentration process from nearly 100% to zero. Importantly, DNA was trapped in the microfluidic channel even when the buffer solution lacked any measurable viscoelastic response. These observations indicate that electrohydrodynamic migration drives the concentration of DNA. We found no evidence of viscoelastic migration in these experiments.

Particle entrainment in dead-end pores by diffusiophoresis

The transport of particulate matter to and from dead-end pores is difficult to achieve due to confinement effects. Diffusiophoresis is a phenomenon that results in the controlled motion of colloids along solute concentration gradients. Thus, by establishing an electrolyte concentration gradient within dead-end pores, it is possible to induce the flow of particles into and out of the pores via diffusiophoresis, as has been demonstrated recently. In this paper, we explain the pore-scale mechanism by which individual colloids are entrained in dead-end pores by diffusiophoresis. We flow particles past a series of dead-end pores in the presence of a solute concentration gradient. Our results reveal that particles execute pore-to-pore hops before ultimately being captured. We categorize an event as particle capture when the particle's trajectory terminates within the dead-end pore. Experiments and numerical simulations demonstrate that particle capture only occurs when flowing particles are positioned sufficiently close to the pore entry. Outside this capture region, the particles have insufficient diffusiophoretic velocities to induce capture and their dynamics are largely dominated by their free-stream advective velocities. We observe that the particles move closer to the device wall as they hop, thereby reducing the effect of flow advection and increasing that of diffusiophoresis. These results enhance our understanding of suspension dynamics in a driven system and have implications for the development, design, and optimization of diffusiophoretic platforms for drug delivery, cosmetics, and material recovery.

Spontaneous Selective Preconcentration Leveraged by Ion Exchange and Imbibition through Nanoporous Medium

Manipulating mechanism of particle’s motion has been extensively studied for the sample preparation in microfluidic applications including diagnostics, food industries, biological analyses and environmental monitoring. However, most of conventional methods need additional external forces such as electric field or pressure and complicated channel designs, which demand highly complex fabrication processes and operation strategies. In addition, these methods have inherent limitations of dilution or mixing during separation or preconcentration step, respectively, so that a number of studies have reported an efficient selective preconcentration process, i.e. conducting the separation and preconcentration simultaneously. In this work, a power-free spontaneous selective preconcentration method was suggested based on leveraging convective flow over diffusiophoresis near the water-absorbing nanoporous ion exchange medium, which was verified both by simulation and experiment. Especially, the velocity of the convective flow by an imbibition deviated from the original tendency of t^−1/2 due to non-uniformly patterned nanoporous medium that has multiple cross-sectional areas. As a result, the direction of particle’s motion was controlled at one’s discretion, which led to the spontaneous selective preconcentration of particles having different diffusiophoretic constant. Also, design rule for maximizing the efficiency was recommended. Thus, this selective preconcentration method would play as a key mechanism for power-free lab on a chip applications.

Characterization of surface-solute interactions by diffusioosmosis

The accurate measurement of wall zeta potentials and solute-surface interaction length scales for electrolyte and non-electrolyte solutes, respectively, is critical to the design of many biomedical and microfluidic applications. We present a novel microfluidic approach using diffusioosmosis for measuring either the zeta potentials or the characteristic interaction length scales for surfaces exposed to, respectively, electrolyte or non-electrolyte solutes. When flows containing different solute concentrations merge in a junction, local solute concentration gradients can drive diffusioosmotic flow due to electrokinetic, steric, and other interactions between the solute molecules and solid surfaces. We demonstrate a microfluidic system consisting of a long, narrow pore connecting two large side channels in which solute concentration gradients drive diffusioosmosis within the pore, resulting in predictable fluid velocity/pressure and solute profiles. Furthermore, we present analytical results and a methodology to determine the zeta potential or interaction length scale for the pore surfaces based on the solute concentrations in the main side channels, the flow rate in the pore, and the pressure drop across the pore. We apply this method to the experimental data of Lee et al. to predict the zeta potentials of their system, and we use 3D numerical simulations to validate the theory and show that end effects caused by the junctions are negligible for a wide range of parameters. Because the dynamics in the proposed system are driven by diffusioosmosis, this technique does not suffer from certain disadvantages associated with the use of sensitive electronics in traditional zeta potential measurement approaches such as streaming potential, streaming current, or electroosmosis. To the best of our knowledge this is the first flow-based approach to characterize surface/solute interactions with non-electrolyte solutes.

Versatile Analysis of DNA-Biomolecule Interactions in Solution by Hydrodynamic Separation and Single Molecule Detection

DNA can interact with a wide array of molecules with a range of binding affinities, stoichiometry, and size-scales. We present a sensitive, quantitative, and versatile platform for sensing and evaluating these diverse DNA-biomolecule interactions and DNA conformational changes in free solution. Single molecule free solution hydrodynamic separation utilizes differences in hydrodynamic mobility to separate bound DNA-biomolecule complexes from unbound DNA and determine the associated size change that results from binding. Single molecule detection enables highly quantitative analysis of the fraction of DNA in the bound and unbound state to characterize binding behavior including affinity, stoichiometry, and cooperativity. A stacked injection scheme increases throughput to enable practical analysis of DNA-biomolecule interactions using only picoliters of sample per measurement. To demonstrate analysis of DNA-protein interactions on a local scale, we investigate binding of the E. coli single stranded binding protein to two DNA oligos both individually and in direct competition. We show that stoichiometry and cooperativity is a function of DNA length and verify these differences in binding characteristics through direct competition. To demonstrate analysis of DNA-small molecule interactions and global conformational changes, we also assess DNA condensation with the polyamine spermidine. We use hydrodynamic mobility to evaluate the size of spermidine-condensed DNA and single molecule burst analysis to evaluate DNA packing within the condensed globules relative to free-coiled DNA. This platform thus presents a versatile tool capable of quantitative and sensitive evaluation of diverse biomolecular interactions, complex properties, and binding characteristics.

µLAS: Sizing of expanded trinucleotide repeats with femtomolar sensitivity in less than 5 minutes

We present µLAS, a lab-on-chip system that concentrates, separates, and detects DNA fragments in a single module. µLAS speeds up DNA size analysis in minutes using femtomolar amounts of amplified DNA. Here we tested the relevance of µLAS for sizing expanded trinucleotide repeats, which cause over 20 different neurological and neuromuscular disorders. Because the length of trinucleotide repeats correlates with the severity of the diseases, it is crucial to be able to size repeat tract length accurately and efficiently. Expanded trinucleotide repeats are however genetically unstable and difficult to amplify. Thus, the amount of amplified material to work with is often limited, making its analysis labor-intensive. We report the detection of heterogeneous allele lengths in 8 samples from myotonic dystrophy type 1 and Huntington disease patients with up to 750 CAG/CTG repeats in five minutes or less. The high sensitivity of the method allowed us to minimize the number of amplification cycles and thus reduce amplification artefacts without compromising the detection of the expanded allele. These results suggest that µLAS can speed up routine molecular biology applications of repetitive sequences and may improve the molecular diagnostic of expanded repeat disorders.

Diffusiophoresis in ionic surfactants: effect of micelle formation

We explore the consequences of micelle formation for diffusiophoresis of charged colloidal particles in ionic surfactant concentration gradients, using a quasi-chemical association model for surfactant self assembly. The electrophoretic contribution to diffusiophoresis is determined by re-arranging the Nernst-Planck equations, and the chemiphoretic contribution is estimated by making plausible approximations for the density profiles in the electrical double layer surrounding the particle. For sub-micellar solutions we find that a particle will typically be propelled down the concentration gradient, although electrophoresis and chemiphoresis are finely balanced and the effect is sensitive to the detailed parameter choices and simplifying assumptions in the model. Above the critical micelle concentration (CMC), diffusiophoresis becomes much weaker and may even reverse sign, due to the fact that added surfactant goes into building micelles and not augmenting the monomer or counterion concentrations. We present detailed calculations for sodium dodecyl sulfate (SDS), finding that the typical drift speed for a colloidal particle in a ∼100 μm length scale SDS gradient is ∼1 μm s-1 below the CMC, falling to ⪅0.2 μm s-1 above the CMC. These predictions are broadly in agreement with recent experimental work.

Single Molecule Free Solution Hydrodynamic Separation for Size Profiling of Serum Cell-Free DNA

Circulating cell-free DNA (cfDNA) has accumulated significant interest as a noninvasive biomarker. One important accessible parameter, the cfDNA size distribution, appears to be of significant value. Here, we introduce our single molecule free solution hydrodynamic separation platform (SML-FSHS) for robust characterization of the cfDNA size profile from human serum. The platform utilizes hydrodynamic separation for DNA sizing and cylindrical illumination confocal spectroscopy (CICS) for highly sensitive single molecule detection and quantification of DNA molecules. We first used a custom wide dynamic range DNA ladder (50 bp-23 kbp) stained with an intercalating dye to create a calibration curve relating DNA retention time to DNA size in base pairs. From this, we demonstrate that the system can profile the cfDNA size distributions in a clinical sample with wide sizing dynamic range and high resolution ~5% of fragment length) all in a single run. The method consumes negligible (3pL) volume of precious sample and minimizes sample processing bias that affects other methods such as PCR and sequencing. We also compare the cfDNA size distributions from stage 1V cancer patients with normal patient samples and demonstrate that specific cfDNA size ranges may correlate with disease state. In addition, we can absolutely quantify cfDNA and gate out the contributions of cellular contamination by size. With these properties, we believe that this platform can help to accelerate future circulating DNA research.