Microfluidics for exosome isolation and analysis: enabling liquid biopsy for personalized medicine

Exosomes, the smallest sized extracellular vesicles (∽30-150 nm) packaged with lipids, proteins, functional messenger RNAs and microRNAs, and double-stranded DNA from their cells of origin, have emerged as key players in intercellular communication. Their presence in bodily fluids, where they protect their cargo from degradation, makes them attractive candidates for clinical application as innovative diagnostic and therapeutic tools. But routine isolation and analysis of high purity exosomes in clinical settings is challenging, with conventional methods facing a number of drawbacks including low yield and/or purity, long processing times, high cost, and difficulties in standardization. Here we review a promising solution, microfluidic-based technologies that have incorporated a host of separation and sensing capabilities for exosome isolation, detection, and analysis, with emphasis on point-of-care and clinical applications. These new capabilities promise to advance fundamental research while paving the way toward routine exosome-based liquid biopsy for personalized medicine.

Smartphone-Enabled Detection Strategies for Portable PCR-Based Diagnostics

Incredible progress continues to be made toward development of low-cost nucleic acid-based diagnostic solutions suitable for deployment in resource-limited settings. Detection components play a vitally important role in these systems, but have proven challenging to adapt for operation in a portable format. Here we describe efforts aimed at leveraging the capabilities of consumer-class smartphones as a convenient platform to enable detection of nucleic acid products associated with DNA amplification via the polymerase chain reaction (PCR). First, we show how fluorescence-based detection can be incorporated into a portable convective thermocycling system controlled by a smartphone app. Raw images captured by the phone's camera are processed to yield real-time amplification data comparable to benchtop instruments. Next, we leverage smartphone imaging to achieve label-free detection of PCR products by monitoring changes in electrochemical reactivity of embedded metal electrodes as the target DNA concentration increases during replication. These advancements make it possible to construct rugged inexpensive nucleic acid detection components that can be readily embedded in a variety of portable bioanalysis instruments.

A Buoyancy-Driven Compact Thermocycler for Rapid PCR

We have designed a novel convective flow-based thermocycling system capable of performing high-speed DNA amplification via the polymerase chain reaction in a simplified and inexpensive format. Successful amplification of a 191 bp influenza-A target is demonstrated within 25 min using a 10 μL reaction volume with no modification to standard laboratory protocols. The system is simple to assemble and can be readily integrated with existing laboratory instrumentation for automated operation. (JALA 2006;11:217–21)

Novel Convective Flow Based Approaches for High-Throughput PCR Thermocycling

A critical need exists for the development of next-generation genomic analysis instrumentation capable of offering significantly higher throughput at a lower cost than current technology. In this paper, we explore the potential of natural convection-based systems to address these issues by providing a thermocycling hardware platform capable of performing rapid polymerase chain reaction (PCR) amplification of DNA. These systems can be arrayed in a multi-well format that is simple to operate, is suitable for integration with high-throughput automated liquid handling systems, and can be easily and inexpensively mass-produced.

Lab-on-a-Drone: Toward Pinpoint Deployment of Smartphone-Enabled Nucleic Acid-Based Diagnostics for Mobile Health Care

We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. Standard sample preparation is enabled by leveraging the drone's motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging.

Tunable in-situ electro-polymerization of hydrogel films for microchip-based bioanalysis

Electro-polymerization phenomena have been previously investigated at the macroscale in the context of producing polymeric coatings over extended surface areas. But electrical actuation also offers exquisite local control of the polymerized films' position, morphology, and thickness, suggesting compelling advantages in microfluidic-based analysis systems. Here, we introduce a microfabricated platform incorporating arrays of individually addressable on-chip electrodes capable of generating discretely positioned electro-polymerized hydrogel films inside microchannels in timescales of ∼5 min. Sequential actuation of specific electrode pairs initiates localized propagation of anchored polyacrylamide gel films and permits directed control of their size, shape, and growth rate. In addition to precise positioning of hydrogel films, obstacles, and barriers within microchannel networks, our approach makes it possible to encapsulate macromolecules within the films during polymerization, suggesting utility in a host of areas including separations, sample purification, and immunoassays.

Characterization of enzymatic micromachining for construction of variable cross-section microchannel topologies

The ability to harness enzymatic activity as an etchant to precisely machine biodegradable substrates introduces new possibilities for microfabrication. This flow-based etching is straightforward to implement, enabling patterning of microchannels with topologies that incorporate variable depth along the cross-sectional dimension. Additionally, unlike conventional small-molecule formulations, the macromolecular nature of enzymatic etchants enables features to be precisely positioned. Here, we introduce a kinetic model to characterize the enzymatic machining process and its localization by co-injection of a macromolecular inhibitor species. Our model captures the interaction between enzyme, inhibitor, and substrate under laminar flow, enabling rational prediction of etched microchannel profiles so that cross-sectional topologies incorporating complex lateral variations in depth can be constructed. We also apply this approach to achieve simultaneous widening of an entire network of microchannels produced in the biodegradable polymeric substrate poly(lactic acid), laying a foundation to construct systems incorporating a broad range of internal cross-sectional dimensions by manipulating the process conditions.

Noise-enhanced gel electrophoresis

Macromolecules confined within a nanoporous matrix experience entropic trapping when their dimensions approach the average pore size, leading to emergence of anomalous transport behavior that can be beneficial in separation applications. But the ability to exploit these effects in practical settings (e.g., electrophoretic separation of DNA) has been hindered by additional dispersion introduced as a consequence of the uncorrelated process by which the embedded macromolecules discretely hop from pore to pore. Here, we show how both the source and solution to these difficulties are intimately linked to the inherent dynamics of the underlying activated transport mechanism. By modulating the applied electric field at a frequency tuned to the characteristic activation timescale, a resonance condition can be established that synergistically combines accelerated mobility and reduced diffusion. This resonance effect can be precisely manipulated by adjusting the magnitude and period of the driving electric field, enabling enhanced separation performance and bi-directional transport of different-sized species to be achieved. Notably, these phenomena are readily accessible in ordinary hydrogels (as opposed to idealized nanomachined topologies) suggesting broad potential to apply them in a host of useful settings.

DNA mutation detection and analysis using miniaturized microfluidic systems

Identification of genetic sequence variations occurring on a population-wide scale is key to unraveling the complex interactions that are the underlying cause of many medical disorders and diseases. A critical need exists, however, for advanced technology to enable DNA mutation analysis to be performed with significantly higher throughput and at significantly lower cost than is currently attainable. Microfluidic systems offer an attractive platform to address these needs by combining the ability to perform rapid analysis with a simplified device format that can be inexpensively mass-produced. This paper will review recent progress toward developing these next-generation systems and discuss challenges associated with adapting these technologies for routine laboratory use.

Using microchip gel electrophoresis to probe DNA-drug binding interactions

Binding of small molecules with DNA plays an important role in many biological functions such as DNA replication, repair, and transcription. These interactions also offer enormous potential as targets for diagnostics and therapeutics, leading to intense interest in development of methods to probe the underlying binding events. In this chapter, we present a new approach to investigate the structural changes that accompany binding of DNA and small molecules. Instead of relying on conventional yet delicate single-molecule imaging methods, we show how a single microchip gel electrophoresis experiment incorporating both constant electric field and on-off actuation over a specific frequency range enables fundamental structural parameters (e.g., contour and persistence lengths) to be simultaneously determined. The microchip format offers an attractive combination of simplicity and scale-up potential that makes it amenable for high-throughput screening.

Entropic stochastic resonance enables trapping under periodic confinement: a Brownian-dynamics study

Entropically mediated phenomena are of emerging interest as a driving force for microscale and nanoscale transport, but their underlying stochastic nature makes them challenging to rationally manipulate and control. Stochastic resonance offers an intriguing avenue to overcome these difficulties by establishing a clear connection between the system response (the output) and an externally imposed driving force (the input). Previous studies have generally adopted a signal-processing viewpoint to classify the output in terms of a signal-to-noise ratio, but this link does not convey information that is immediately useful to infer parameters relevant to transport. Here we address this issue by applying Brownian-dynamics simulations to elucidate the residence time distribution encountered by a particle as it travels through a channel incorporating periodic constrictions. A sinusoidal longitudinal driving force is applied with a superimposed continuous orthogonal component, making it possible to identify frequency and amplitude conditions where temporal coherence with the particle's motion can be achieved. This resonant state reflects a synergistic combination of geometry and driving force that can be exploited to confine species at discrete locations, offering possibilities for directed manipulation.

Smartphone-based detection of unlabeled DNA via electrochemical dissolution

We describe a novel approach that enables unlabeled biomolecules and chemical analytes to be detected using ordinary smartphone optics. Electrochemical reactivity of chromium, ordinarily considered detrimental, is harnessed here to generate a signature that can be easily seen by monitoring electrode dissolution under ordinary white-light illumination. The simplicity and robustness of this approach eliminates the need for labeling and/or pre-programming with specific receptors (e.g., oligonucleotide probes), making it feasible to greatly expand availability of a host of assays where detection complexity is a limiting constraint.

Graphene-enhanced nanorefrigerants

Recent reports that a host liquid's thermal properties can be augmented by dispersal of small quantities of nanoparticles have stimulated intense interest as an intriguing avenue to produce advanced heat transfer fluids. But effects are challenging to exploit in practical settings because it is difficult to prepare refrigerant-based dispersions displaying sufficient long-term stability. Moreover, the most dramatic enhancements in thermal conductivity obtained using anisotropic nanomaterials (e.g., carbon nanotubes) are achieved at the expense of a severe viscosity increase. Here we overcome these limitations by introducing a robust surfactant-mediated dispersal method that enables stable suspensions containing a range of nanomaterials to be straightforwardly prepared as additives to ordinary commercial refrigerants. We apply this approach to formulate a new class of nanorefrigerants containing graphene nanosheets that uniquely match the superior thermal conductivity enhancements attained in carbon nanotube suspensions without their accompanying viscosity penalty. These suspensions can be directly substituted for conventional refrigerants to inexpensively achieve increased efficiency in many thermal management applications.

Education: DNA replication using microscale natural convection

There is a need for innovative educational experiences that unify and reinforce fundamental principles at the interface between the physical, chemical, and life sciences. These experiences empower and excite students by helping them recognize how interdisciplinary knowledge can be applied to develop new products and technologies that benefit society. Microfluidics offers an incredibly versatile tool to address this need. Here we describe our efforts to create innovative hands-on activities that introduce chemical engineering students to molecular biology by challenging them to harness microscale natural convection phenomena to perform DNA replication via the polymerase chain reaction (PCR). Experimentally, we have constructed convective PCR stations incorporating a simple design for loading and mounting cylindrical microfluidic reactors between independently controlled thermal plates. A portable motion analysis microscope enables flow patterns inside the convective reactors to be directly visualized using fluorescent bead tracers. We have also developed a hands-on computational fluid dynamics (CFD) exercise based on modeling microscale thermal convection to identify optimal geometries for DNA replication. A cognitive assessment reveals that these activities strongly impact student learning in a positive way.

A simple microfluidic probe of nanoparticle suspension stability

We describe a simple experimental tool that enables stability of multicomponent nanoparticle suspensions to be readily assessed by establishing a confinement-imposed chemical discontinuity at the interface between co-flowing laminar streams in a microchannel. When applied to examine Al(2)O(3) nanoparticle suspensions, this method readily reveals compositions that are susceptible to aggregation even when conventional bulk measurements (zeta potential, dynamic light scattering, bulk viscosity) suggest only subtle differences between formulations. This microfluidic stability test enables simple and rapid assessment of quality and variability in complex multicomponent mixtures for which few, if any, comparable data exist. The paradoxical ease at which localized aggregation can be triggered in suspensions that would otherwise appear stable also serves as a caution to researchers undertaking tracer-based studies of nanomaterial suspensions.

Rapid PCR thermocycling using microscale thermal convection

Many molecular biology assays depend in some way on the polymerase chain reaction (PCR) to amplify an initially dilute target DNA sample to a detectable concentration level. But the design of conventional PCR thermocycling hardware, predominantly based on massive metal heating blocks whose temperature is regulated by thermoelectric heaters, severely limits the achievable reaction speed¹. Considerable electrical power is also required to repeatedly heat and cool the reagent mixture, limiting the ability to deploy these instruments in a portable format.

Thermal convection has emerged as a promising alternative thermocycling approach that has the potential to overcome these limitations^2-9. Convective flows are an everyday occurrence in a diverse array of settings ranging from the Earth's atmosphere, oceans, and interior, to decorative and colorful lava lamps. Fluid motion is initiated in the same way in each case: a buoyancy driven instability arises when a confined volume of fluid is subjected to a spatial temperature gradient. These same phenomena offer an attractive way to perform PCR thermocycling. By applying a static temperature gradient across an appropriately designed reactor geometry, a continuous circulatory flow can be established that will repeatedly transport PCR reagents through temperature zones associated with the denaturing, annealing, and extension stages of the reaction (Figure 1). Thermocycling can therefore be actuated in a pseudo-isothermal manner by simply holding two opposing surfaces at fixed temperatures, completely eliminating the need to repeatedly heat and cool the instrument.

One of the main challenges facing design of convective thermocyclers is the need to precisely control the spatial velocity and temperature distributions within the reactor to ensure that the reagents sequentially occupy the correct temperature zones for a sufficient period of time^10,11. Here we describe results of our efforts to probe the full 3-D velocity and temperature distributions in microscale convective thermocyclers¹². Unexpectedly, we have discovered a subset of complex flow trajectories that are highly favorable for PCR due to a synergistic combination of (1) continuous exchange among flow paths that provides an enhanced opportunity for reagents to sample the full range of optimal temperature profiles, and (2) increased time spent within the extension temperature zone the rate limiting step of PCR. Extremely rapid DNA amplification times (under 10 min) are achievable in reactors designed to generate these flows.

Tailoring the nanoporous architecture of hydrogels to exploit entropic trapping

Macromolecules embedded in a nanoporous matrix display anomalous transport behavior in the entropic trapping regime. But these phenomena have not been widely explored in hydrogel matrices because it has not been clear how to link them to the underlying heterogeneous nanopore morphology. Here we introduce a theoretical model that establishes this connection and describe microchip DNA electrophoresis experiments that demonstrate how entropic trapping effects can be exploited to yield a trend of increasing resolving power with DNA size (the opposite of what is conventionally observed).

Vortex-assisted DNA delivery

Electroporation is one of the most widely used methods to deliver exogenous DNA payloads into cells, but a major limitation is that only a small fraction of the total membrane surface is permeabilized. Here we show how this barrier can be easily overcome by harnessing hydrodynamic effects associated with Dean flows that occur along curved paths. Under these conditions, cells are subjected to a combination of transverse vortex motion and rotation that enables the entire membrane surface to become uniformly permeabilized. Greatly improved transfection efficiencies are achievable with only a simple modification to the design of existing continuous flow electroporation systems.

A direct probe of the interplay between bilayer morphology and surface reactivity in polymersomes

Bilayer vesicles self-assembled from amphiphilic poly(ethylene oxide)-b-polybutadiene (PEO-b-PBd) copolymers are cell-like structures whose high stability and tunable membrane properties make them ideal for use as potential drug carriers and cell mimicry templates. Understanding how the surface interactions (reaction, binding, etc.) are governed by the bilayer structure is critical to enable construction of polymersomes with tailored colloidal behavior. Here, we adapt a previously established chemical labeling method by incorporating coumarin functionalized copolymer into the vesicular structure. This allows us to probe the effect of poly(ethylene glycol) (PEG) brush and surface architecture on the bimolecular quenching reaction occurring at the polymersome surface. Using these measurements, we have tracked quenching in free solution, on bare particles, and on two types of vesicle surfaces: one where the functionalized copolymer groups are longer than the surrounding unfunctionalized copolymer, and one where both functionalized and unfunctionalized groups are the same length. We find that quenching in the presence of the PEG brush proceeds at less than half the free solution rate in both vesicle architectures. However, the quenching rate is further reduced when the functionalized and unfunctionalized groups are the same length. The surface reaction appears to be dominated by quencher diffusion, a conclusion supported by conductivity measurements and ion partition studies indicating that these effects arise as a consequence of retarded ion mobility in the presence of the PEG brush rather than ion exclusion effects. These studies reveal the interplay between the vesicle bilayer architecture (copolymer composition, chain length, local concentration surrounding the active site) and the surface reaction rate, thereby providing useful insights that can help guide the design of polymersomes with desired functional properties.

Reflection interference contrast microscopy of arbitrary convex surfaces

Current accurate applications of reflection interference contrast microscopy (RICM) are limited to known geometries; when the geometry of the object is unknown, an approximated fringe spacing analysis is usually performed. To complete an accurate RICM analysis in more general situations, we review and improve the formulation for intensity calculation based on nonplanar interface image formation theory and develop a method for its practical implementation in wedges and convex surfaces. In addition, a suitable RICM model for an arbitrary convex surface, with or without a uniform layer such as a membrane or ultrathin coating, is presented. Experimental work with polymer vesicles shows that the coupling of the improved RICM image formation theory, the calculation method, and the surface model allow an accurate reconstruction of the convex bottom shape of an object close to the substrate by fitting its experimental intensity pattern.

Interfacial complexation explains anomalous diffusion in nanofluids

A recent report describing dramatic anomalous enhancement in mass transport properties of nanofluids (>1000% increase in tracer dye diffusivity) has excited intense interest, but the findings have yet to be conclusively confirmed or explained. Here we investigate these phenomena using a microfluidic approach to directly probe tracer diffusion so that interactions between the suspension's principle components (nanoparticles, surfactant, and dye) can be clearly identified. Under conditions matching previously reported studies, we unexpectedly observe spontaneous formation of highly focused and intensely fluorescent plumes at the interface between fluid streams, suggesting strong complexation interactions between the dye and nanoparticles. These phenomena, driven by competition between the rates at which free tracer molecules are transported into the interfacial zone subsequently consumed by dye-nanoparticle complexation, have likely been incorrectly interpreted as anomalous diffusion enhancement. These interactions are important to consider when devising tracer-based studies of nanoparticle suspensions and may lay a foundation for new adsorption-based analytical methods.

DNA focusing using microfabricated electrode arrays

Focusing methods are a key component in many miniaturized DNA analysis systems because they enable dilute samples to be concentrated to detectable levels while being simultaneously confined within a specified volume inside the microchannel. In this chapter, we describe a focusing method based on a device design incorporating arrays of addressable on-chip microfabricated electrodes that can locally increase the concentration of DNA in solution by electrophoretically sweeping it along the length of a microchannel. By applying a low voltage (approximately 1-2 V) between successive pairs of neighboring electrodes, the intrinsically negatively charged DNA fragments are induced to migrate toward and collect at each anode, thereby allowing the quantity of accumulated DNA to be precisely metered. We have characterized the kinetics of this process, and found the response to be robust over a range of different sample compositions and buffer environments.

Microchip DNA electrophoresis with automated whole-gel scanning detection

Gel electrophoresis continues to play an important role in miniaturized bioanalytical systems, both as a stand alone technique and as a key component of integrated lab-on-a-chip diagnostics. Most implementations of microchip electrophoresis employ finish-line detection methods whereby fluorescently labeled analytes are observed as they migrate past a fixed detection point near the end of the separation channel. But tradeoffs may exist between the simultaneous goals of maximizing resolution (normally achieved by using longer separation channels) and maximizing the size range of analytes that can be studied (where shorter separation distances reduce the time required for the slowest analytes to reach the detector). Here we show how the miniaturized format can offer new opportunities to employ alternative detection schemes that can help address these issues by introducing an automated whole-gel scanning detection system that enables the progress of microchip-based gel electrophoresis of DNA to be continuously monitored along an entire microchannel. This permits flexibility to selectively observe smaller faster moving fragments during the early stages of the separation before they have experienced significant diffusive broadening, while allowing the larger slower moving fragments to be observed later in the run when they can be better resolved but without the need for them to travel the entire length of the separation channel. Whole-gel scanning also provides a continuous and detailed picture of the electrophoresis process as it unfolds, allowing fundamental physical parameters associated with DNA migration phenomena (e.g., mobility, diffusive broadening) to be rapidly and accurately measured in a single experiment. These capabilities are challenging to implement using finish-line methods, and make it possible to envision a platform capable of enabling separation performance to be rapidly screened in a wide range of gel matrix materials and operating conditions, even allowing separation and matrix characterization steps to be performed simultaneously in a single self-calibrating experiment.

Review of electrophoresis and BioMEMS in 2007: American Electrophoresis Society 24th Annual Meeting

Researchers came together for the 24th Annual Meeting of the American Electrophoresis Society (AES), which was held November 4-9, 2007, at the Salt Palace Convention Center in Salt Lake City, UT, U.S.A. The Annual AES meeting is held in conjunction with the annual meeting of the American Institute of Chemical Engineers (AIChE). This year's meeting had a significant emphasis on theoretical and experimental advances in Biological Micro Electro Mechanical Systems (BioMEMS), electrokinetics, and proteomics technologies. A total of 15 sessions were held, within which 71 presentations and 18 posters were discussed. This review provides a brief sampling of the exciting research presented at the conference.

BioMEMS and Electrophoresis in 2006: Review of the 23rd Annual Meeting of the American Electrophoresis Society

The 23rd Annual Meeting of the American Electrophoresis Society (AES) was held at the San Francisco Hilton in San Francisco, California on 12-17 November 2006. This year's meeting featured a look toward the future, with an emphasis on theoretical and experimental advances in miniaturization of BioMEMS, electrokinetics, and proteomics technologies. A total of 13 sessions accommodating 71 presentations and 18 posters were held in conjunction with the Annual Meeting of the American Institute of Chemical Engineers (AIChE). This review and corresponding special issue of Biomicrofluidics provide a sampling of some of the exciting research presented at the conference.

Preface to Special Topic: Papers from the 2006 Annual Meeting of the American Electrophoresis Society, San Francisco, CA

This Special Topic section of Biomicrofluidics is dedicated to original papers from the 2006 Annual Meeting of the American Electrophoresis Society (AES: http:/www.aesociety.org). This five-day meeting held in San Francisco, California, included five sessions on BioMEMS and Microfluidics and four sessions on Advances in Electrokinetics and Electrophoresis. AES and its corresponding symposia provide the most focused and well-organized meeting forum for diverse biological and engineering researchers working on electrokinetics. The work featured in this Special Topic section is no exception; it ranges from nanochannel electrophoresis to bioparticle sorting.

Development of a miniature calorimeter for identification and detection of explosives and other energetic compounds

The development of versatile systems capable of providing rapid, portable, and inexpensive detection of explosives and energetic compounds are critically needed to offer enhanced levels of protection against current and future threats to homeland security, as well as satisfying a wide range of applications in the fields of forensic analysis, emergency response, and industrial hazards analysis. Calorimetric techniques have been largely overlooked in efforts to develop advanced chemical analysis technology, largely because of limitations associated with the physical size of the instruments and the relatively long timescales (>30 min) required to obtain a result. This miniaturized calorimeter circumvents these limitations, thereby creating a first-of-its-kind system allowing thermal analysis to be performed in a portable format that can be configured for use in a variety of field operations with a significantly reduced response time (approximately 2 min). Unlike current explosives detectors, this system is based on calorimetric techniques that are inherently capable of providing direct measurements of energy release potential and therefore do not depend on prior knowledge of familiar compounds.

Using in situ rheology to characterize the microstructure in photopolymerized polyacrylamide gels for DNA electrophoresis

Photopolymerized cross-linked polyacrylamide hydrogels are attractive sieving matrix formulations for DNA electrophoresis owing to their rapid polymerization times and the potential to locally tailor the gel pore structure through spatial variation of illumination intensity. This capability is especially important in microfluidic systems, where photopolymerization allows gel matrices to be precisely positioned within complex microchannel networks. Separation performance is also directly related to the nanoscale gel pore structure, which is in turn strongly influenced by polymerization kinetics. Unfortunately, detailed studies of the interplay among polymerization kinetics, mechanical properties, and structural morphology are lacking in photopolymerized hydrogel systems. In this paper, we address this issue by performing a series of in situ dynamic small-amplitude oscillatory shear measurements during photopolymerization of cross-linked polyacrylamide electrophoresis gels to investigate the relationship between rheology and parameters associated with the gelation environment including UV intensity, monomer and cross-linker composition, and reaction temperature. In general, we find that the storage modulus G' increases with increasing initial monomer concentration, cross-linker concentration, and polymerization temperature. The steady-state value of G', however, exhibits a more complex dependence on UV intensity that varies with gel concentration. A simple model based on rubber elasticity theory is used to obtain estimates of the average gel pore size that are in surprisingly good agreement with corresponding data obtained from analysis of DNA electrophoretic mobility in gels cast under identical polymerization conditions.

Reactions and fluidics in miniaturized natural convection systems

Buoyancy-driven convection offers a novel and greatly simplified mechanism for generating continuous nonpulsatile flow fields and performing thermally activated biochemical reactions. In this paper, we build on our previous work by constructing a multiwell device incorporating an array of 35-microL cylindrical cavities to perform polymerase chain reaction (PCR) amplification of a 191-base pair fragment associated with membrane channel proteins M1 and M2 of the influenza-A virus in as little as 15 min with performance comparable to conventional thermocyclers. We also describe entirely new adaptations of convective flows by conducting a series of coordinated flow visualization and computational studies to explore the design of closed-loop systems to execute tunable thermocycling, pumping, and mixing operations in a format suitable for integration into miniaturized biochemical analysis systems. Using 15-microL convective flow loops, we are able to perform PCR amplification of the same 191-base pair fragment associated with the influenza-A virus, as well as a 295-base pair segment of the human beta-actin gene in a format offering an enhanced degree of control and tunability. These convective flow devices can be further scaled down to nanoliter volumes and are ideally suited as a platform for a new generation of low-power, portable microfluidic DNA analysis systems.

Multivortex micromixing

The ability to mix liquids in microchannel networks is fundamentally important in the design of nearly every miniaturized chemical and biochemical analysis system. Here, we show that enhanced micromixing can be achieved in topologically simple and easily fabricated planar 2D microchannels by simply introducing curvature and changes in width in a prescribed manner. This goal is accomplished by harnessing a synergistic combination of (i) Dean vortices that arise in the vertical plane of curved channels as a consequence of an interplay between inertial, centrifugal, and viscous effects, and (ii) expansion vortices that arise in the horizontal plane due to an abrupt increase in a conduit's cross-sectional area. We characterize these effects by using confocal microscopy of aqueous fluorescent dye streams and by observing binding interactions between an intercalating dye and double-stranded DNA. These mixing approaches are versatile and scalable and can be straightforwardly integrated as generic components in a variety of lab-on-a-chip systems.

Collection, focusing, and metering of DNA in microchannels using addressable electrode arrays for portable low-power bioanalysis

Although advances in microfluidic technology have enabled increasingly sophisticated biosensing and bioassay operations to be performed at the microscale, many of these applications employ such small amounts of charged biomolecules (DNA, proteins, and peptides) that they must first be preconcentrated to a detectable level. Efficient strategies for precisely handling minute quantities of biomolecules in microchannel geometries are critically needed; however, it has proven challenging to achieve simultaneous concentration, focusing, and metering capabilities with current-generation sample-injection technology. By using microfluidic chips incorporating arrays of individually addressable microfabricated electrodes, we demonstrate that DNA can be sequentially concentrated, focused into a narrow zone, metered, and injected into an analysis channel. This technique transports charged biomolecules between active electrodes upon application of a small potential difference (1 V) and is capable of achieving orders of magnitude concentration increases within a small device footprint. The collected samples are highly focused, with sample zone size and shape defined solely by electrode geometry.

Separation performance of single-stranded DNA electrophoresis in photopolymerized cross-linked polyacrylamide gels

Considerable effort has been directed toward optimizing performance and maximizing throughput in ssDNA electrophoresis because it is a critical analytical step in a variety of genomic assays. Ultimately, it would be desirable to quantitatively determine the achievable level of separation resolution directly from measurements of fundamental physical properties associated with the gel matrix rather than by the trial and error process often employed. Unfortunately, this predictive capability is currently lacking, due in large part to the need for a more detailed understanding of the fundamental parameters governing separation performance (mobility, diffusion, and dispersion). We seek to address this issue by systematically characterizing electrophoretic mobility, diffusion, and dispersion behavior of ssDNA fragments in the 70-1,000 base range in a photopolymerized cross-linked polyacrylamide matrix using a slab gel DNA sequencer. Data are collected for gel concentrations of 6, 9, and 12%T at electric fields ranging from 15 to 40 V/cm, and resolution predictions are compared with corresponding experimentally measured values. The data exhibit a transition from behavior consistent with the Ogston model for small fragments to behavior in agreement with the biased reptation model at larger fragment sizes. Mobility data are also used to estimate the mean gel pore size and compare the predictions of several models.

Polymerase chain reaction in miniaturized systems: big progress in little devices

A critical need exists for advanced technologies that enable genomic-based DNA analysis to be performed with significantly higher throughput and at a significantly lower cost than is attainable with current hardware. Miniaturized polymerase chain reaction systems offer an attractive platform to address these needs, combining the ability to perform rapid thermocycling with a portable device format that can be inexpensively mass produced. We review recent efforts aimed at developing these next-generation systems and discuss some of the practical considerations involved in adapting this technology for routine laboratory use.

Fluid mixing in planar spiral microchannels

Mixing of fluids at the microscale poses a variety of challenges, many of which arise from the fact that molecular diffusion is the dominant transport mechanism in the laminar flow regime. While considerable progress has been made toward developing strategies to achieve improved mixing in microfluidic systems, many of these techniques introduce additional complexity to device fabrication and/or operation processes. In this work, we explore the use of compact spiral-shaped flow geometries designed to achieve efficient mixing in a format that can be constructed using a single planar soft lithography step without the need for multilayer alignment. A series of 150 microm-wide by 29 microm-tall channels were constructed, each of which incorporated a series of spiral shaped sections arrayed along the flow path. Five spiral designs with varying channel lengths were investigated, and mixing studies were carried out at flow rates corresponding to Reynolds numbers ranging from 0.02 to 18.6. Under appropriate conditions, transverse Dean flows are induced that augment diffusive transport and promote enhanced mixing in considerably shorter downstream distances as compared with conventional planar straight channel designs. Mixing efficiency can be further enhanced by incorporating expansion vortex effects via abrupt changes in cross-sectional area along the flow path.

An inexpensive microslab gel DNA electrophoresis system with real-time fluorescence detection

In this paper, we describe the construction of a simple yet powerful gel electrophoresis apparatus that can be used to perform size-selective separations of DNA fragments in virtually any laboratory. This system employs a microslab gel format with a novel gel casting technique that eliminates the need for delicate combs to define sample loading wells. The compact size of the microslab gel format allows rapid separations to be performed at low voltages using submicroliter sample volumes. Real time fluorescence detection of the migrating DNA fragments is accomplished using an inexpensive digital microscope that directly connects to any PC with a USB interface. The microscope is readily adaptable for this application by replacing its white light source with a blue light-emitting diode (LED) and adding an appropriate emission filter. Both polyacrylamide and agarose gels can be used as separation matrices. Separation performance was characterized using standard dsDNA ladders, and correct sizing of a 191 bp PCR product was achieved in 15 min. The low cost and simplicity of this system makes it ideally suited for use in a variety of laboratory and educational settings.

An integrated microfluidic device for influenza and other genetic analyses

An integrated microfluidic device capable of performing a variety of genetic assays has been developed as a step towards building systems for widespread dissemination. The device integrates fluidic and thermal components such as heaters, temperature sensors, and addressable valves to control two nanoliter reactors in series followed by an electrophoretic separation. This combination of components is suitable for a variety of genetic analyses. As an example, we have successfully identified sequence-specific hemagglutinin A subtype for the A/LA/1/87 strain of influenza virus. The device uses a compact design and mass production technologies, making it an attractive platform for a variety of widely disseminated applications.

Thermoplastic Elastomer Gels: An Advanced Substrate for Microfluidic Chemical Analysis Systems

We demonstrate the use of thermoplastic elastomer gels as advanced substrates for construction of complex microfluidic networks suitable for use in miniaturized chemical analysis systems. These gels are synthesized by combining inexpensive polystyrene-(polyethylene/polybutylene)-polystyrene triblock copolymers with a hydrocarbon extender oil for which the ethylene/butylene midblocks are selectively miscible. The insoluble styrene end blocks phase separate into localized nanodomains, resulting in the formation of an optically transparent, viscoelastic, and biocompatible gel network that is melt-processable at temperatures in the vicinity of 100 degrees C. This unique combination of properties allows microfluidic channels to be fabricated in a matter of minutes by simply making impressions of the negative relief structures on heated master molds. Melt processability allows multiple impressions to be made against different masters to construct complex geometries incorporating multi-height features within the same microchannel. Intricate interconnected multilayered structures are also easily fabricated owing to the ability to bond and seal multiple layers by briefly heating the material at the bond interface. Thermal and mechanical properties are tunable over a wide range through proper selection of gel composition.