Induced nanoparticle aggregation for short nucleic acid quantification by depletion isotachophoresis

A multiplexed ion-exchange membrane-based miRNA (MIX·miR) detection platform for rapid diagnosis of myocardial infarction

Micro RNAs (miRNAs) have shown great potential as rapid and discriminating biomarkers for acute myocardial infarction (AMI) diagnosis. We have developed a multiplexed ion-exchange membrane-based miRNA (MIX·miR) preconcentration/sensing amplification-free platform for quantifying in parallel a panel of miRNAs, including miR-1, miR-208b, and miR-499, from the same plasma samples from: 1) reference subjects with no evident coronary artery disease (NCAD); 2) subjects with stable coronary artery disease (CAD); and 3) subjects experiencing ST-elevation myocardial infarction (STEMI) prior to (STEMI-pre) and following (STEMI-PCI) percutaneous coronary intervention. The picomolar limit of detection from raw plasma and 3-decade dynamic range of MIX·miR permits detection of the miRNA panel in untreated samples from disease patients and its precise standard curve, provided by large 0.1 to 1 V signals and eliminates individual sensor calibration. The use of molecular concentration feature reduces the assay time to less than 30 minutes and increases the detection sensitivity by bringing all targets close to the sensors. miR-1 was low for NCAD patients but more than one order of magnitude above the normal value for all samples from three categories (CAD, STEMI-pre, and STEMI-PCI) of patients with CAD. In fact, miR-1 expression levels of stable CAD, STEMI-pre and STEMI-PCI are each more than 10-fold higher than the previous class, in that order, well above the 95% confidence level of MIX·miR. Its overexpression estimate is significantly higher than the PCR benchmark. This suggests that, in contrast to protein biomarkers of myocardial injury, miR-1 appears to differentiate ischemia from both reperfusion injury and non-AMI CAD patients. The battery-operated MIX·miR can be a portable and low-cost AMI diagnostic device, particularly useful in settings where cardiac catheterization is not readily available to determine the status of coronary reperfusion.

Hydrogels in Electrophoresis: Applications and Advances

A hydrogel is a solid form of polymer network absorbed in a substantial amount of aqueous solution. In electrophoresis, hydrogels play versatile roles including as support media, sieving matrixes, affinity scaffolds, and compositions of molecularly imprinting polymers. Recently, the study of hydrogels has been advancing with unprecedented speed, and the application of hydrogels in separation science has brought new opportunities and possible breakthroughs. A good understanding about the roles and effects of the material is essential for hydrogel applications. This review summarizes the hydrogels that has been described in various modes of electrophoretic separations, including isoelectric focusing gel electrophoresis (IEFGE), isotachophoresis (ITP), gel electrophoresis and affinity gel electrophoresis (AGE). As microchip electrophoresis (ME) is one of the future trends in electrophoresis, thought provoking studies related to hydrogels in ME are also introduced. Novel hydrogels and methods that improve separation performance, facilitate the experimental operation process, allow for rapid analysis, and promote the integration to microfluidic devices are highlighted.

Liquid biopsy technologies based on membrane microfluidics: High-yield purification and selective quantification of biomarkers in nanocarriers

Liquid biopsy, screening cancer non-invasively and frequently by detecting and quantifying molecular markers in physiological fluids, would significantly improve cancer survival rate but it remains a distant goal. The key obstacles presented by the highly heterogeneous samples are rapid/high-yield purification and precise/selective marker capture by their antibody and oligo probes. As irregular expressions of these molecular biomarkers are the key signals, quantifying only those from the cancer cells would greatly enhance the performance of the screening tests. The recent discovery that the biomarkers are carried by nanocarriers, such as exosomes, with cell-specific membrane proteins suggests that such selection may be possible, although a new suite of fractionation and quantification technologies would need to be developed. Although under-appreciated, membrane microfluidics has made considerable contributions to resolving these issues. We review the progress made so far, based on ion-selective, track-etched, and gel membranes and advanced electrophoretic and nano-filtration designs, in this perspective and suggest future directions.

Transitions and Instabilities in Imperfect Ion-Selective Membranes

Numerical investigation of the underlimiting, limiting, and overlimiting current modes and their transitions in imperfect ion-selective membranes with fluid flow through permitted through the membrane is presented. The system is treated as a three layer composite system of electrolyte-porous membrane-electrolyte where the Nernst–Planck–Poisson–Stokes system of equations is used in the electrolyte, and the Darcy–Brinkman approach is employed in the nanoporous membrane. In order to resolve thin Debye and Darcy layers, quasi-spectral methods are applied using Chebyshev polynomials for their accumulation of zeros and, hence, best resolution in the layers. The boundary between underlimiting and overlimiting current regimes is subject of linear stability analysis, where the transition to overlimiting current is assumed due to the electrokinetic instability of the one-dimensional quiescent state. However, the well-developed overlimiting current is inherently a problem of nonlinear stability and is subject of the direct numerical simulation of the full system of equations. Both high and low fixed charge density membranes (low- and high concentration electrolyte solutions), acting respectively as (nearly) perfect or imperfect membranes, are considered. The perfect membrane is adequately described by a one-layer model while the imperfect membrane has a more sophisticated response. In particular, the direct transition from underlimiting to overlimiting currents, bypassing the limiting currents, is found to be possible for imperfect membranes (high-concentration electrolyte). The transition to the overlimiting currents for the low-concentration electrolyte solutions is monotonic, while for the high-concentration solutions it is oscillatory. Despite the fact that velocities in the porous membrane are much smaller than in the electrolyte region, it is further demonstrated that they can dramatically influence the nature and transition to the overlimiting regimes. A map of the bifurcations, transitions, and regimes is constructed in coordinates of the fixed membrane charge and the Darcy number.

Tutorial review: Enrichment and separation of neutral and charged species by ion concentration polarization focusing

Ion concentration polarization focusing (ICPF) is an electrokinetic technique, in which analytes are enriched and separated along a localized electric field gradient in the presence of a counter flow. This field gradient is generated by depletion of ions of the background electrolyte at an ion permselective junction. In this tutorial review, we summarize the fundamental principles and experimental parameters that govern selective ion transport and the stability of the enriched analyte plug. We also examine faradaic ICP (fICP), in which local ion concentration is modulated via electrochemical reactions as an attractive alternative to ICP that achieves similar performance with a decrease in both power consumption and Joule heating. The tutorial covers important challenges to the broad application of ICPF including undesired pH gradients, low volumetric throughput, samples that induce biofouling or are highly conductive, and limited approaches to on- or off-chip analysis. Recent developments in the field that seek to address these challenges are reviewed along with new approaches to maximize enrichment, focus uncharged analytes, and achieve enrichment and separation in water-in-oil droplets. For new practitioners, we discuss practical aspects of ICPF, such as strategies for device design and fabrication and the relative advantages of several types of ion selective junctions and electrodes. Lastly, we summarize tips and tricks for tackling common experimental challenges in ICPF.

A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification

We report a bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput (20 min) extraction of nucleic acids from physiological samples. The design uses a membrane ionic transistor to sustain low-ionic strength in a localized region at a junction, such that the resulting high field can selectively isolate high-charge density nucleic acids from the main flow channel and insert them into a standardized buffer in a side channel that bifurcates from the junction. The high local electric field and the bifurcated field-flow design facilitate concentration reduction of both divalent cation (Ca2+) and molecular PCR inhibitors by more than two orders of magnitude, even with high-throughput continuous loading. The unique design with a large (>20 mM mm-1) on-chip ionic-strength gradient allows miniaturization into a high-throughput field-flow fractionation chip that can be integrated with upstream lysing and downstream PCR/sensor modules for various nucleic acid detection/quantification applications. A concentration-independent 85% yield for extraction and an overall post-PCR yield exceeding 60% are demonstrated for a 111 bp dsDNA in 10 μL of human plasma, compared to no amplification with the raw sample. A net yield four times larger than a commercial extraction kit is demonstrated for miR-39 in human plasma.

Effect of channel geometry on ion-concentration polarization-based preconcentration and desalination

Polarization of the ion-selective systems results in the formation of ion-depleted and ion-concentrated zones in the electrolyte layers adjacent to the system. One can employ ion-concentration polarization for the removal of charged large molecules and small ions from the flowing liquid. Removal of large molecules from the flowing solution and their local accumulation is often referred to as preconcentration, removal of small ions as desalination. Here, we study the effect of the channel geometry on the removal of charged species from their water solutions experimentally. Straight, converging, and diverging channels equipped with a pair of heterogeneous cation-exchange membranes are compared in terms of their effect on preconcentration of an observable fluorescein dye and on desalination of water solution of potassium chloride. Our results show that preconcentration of the dye is not significantly affected by the channel geometry. The distance of the preconcentration band from one of the membranes was approximately the same in all tested channel geometries. The major difference was in the location of the band within the channel, when the conical channels localized the band at one of the channel walls. The straight channel showed a slightly broader range of applicable flow rates. The semibatch desalination of 0.01M KCl solution turned out to be more efficient in conical channels, which was associated with a larger volume of the channel available for the accumulation of the concentrated solution. Our results suggest that conical channels can be advantageously used in transforming the ion-concentration-polarization-based semibatch desalination into a fully continuous one.

Rapid and multi-cycle smFISH enabled by microfluidic ion concentration polarization for in-situ profiling of tissue-specific gene expression in whole C. elegans

Understanding gene regulation networks in multicellular organisms is crucial to decipher many complex physiological processes ranging from development to aging. One technique to characterize gene expression with tissue-specificity in whole organisms is single-molecule fluorescence in situ hybridization (smFISH). However, this protocol requires lengthy incubation times, and it is challenging to achieve multiplexed smFISH in a whole organism. Multiplexing techniques can yield transcriptome-level information, but they require sequential probing of different genes. The inefficient macromolecule exchange through diffusion-dominant transport across dense tissues is the major bottleneck. In this work, we address this challenge by developing a microfluidic/electrokinetic hybrid platform to enable multicycle smFISH in an intact model organism, Caenorhabditis elegans. We integrate an ion concentration polarization based ion pump with a microfluidic array to rapidly deliver and remove gene-specific probes and stripping reagents on demand in individual animals. Using our platform, we can achieve rapid smFISH, an order of magnitude faster than traditional smFISH protocols. We also demonstrate the capability to perform multicycle smFISH on the same individual samples, which is impossible to do off-chip. Our method hence provides a powerful tool to study individual-specific, spatially resolvable, and large-scale gene expression in whole organisms.

Polyvalent Nanoobjects for Precision Diagnostics

As our ability to synthesize and modify nanoobjects has improved, efforts to explore nanotechnology for diagnostic purposes have gained momentum. The variety of nanoobjects, especially those with polyvalent properties, displays a wide range of practical and unique properties well suited for applications in various diagnostics. This review briefly covers the broad scope of multivalent nanoobjects and their use in diagnostics, ranging from ex vivo assays and biosensors to in vivo imaging. The nanoobjects discussed here include silica nanoparticles, gold nanoparticles, quantum dots, carbon dots, fullerenes, polymers, dendrimers, liposomes, nanowires, and nanotubes. In this review, we describe recent reports of novel applications of these various nanoobjects, particularly as polyvalent entities designed for diagnostics.

Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2016-2018)

One of the most cited limitations of capillary and microchip electrophoresis is the poor sensitivity. This review continues to update this series of biannual reviews, first published in Electrophoresis in 2007, on developments in the field of online/in-line concentration methods in capillaries and microchips, covering the period July 2016-June 2018. It includes developments in the field of stacking, covering all methods from field-amplified sample stacking and large-volume sample stacking, through to isotachophoresis, dynamic pH junction, and sweeping. Attention is also given to online or in-line extraction methods that have been used for electrophoresis.

Amplification-free detection of DNA in a paper-based microfluidic device using electroosmotically balanced isotachophoresis

We present a novel microfluidic paper-based analytical device (μPAD) which utilizes the native high electroosmotic flow (EOF) in nitrocellulose to achieve stationary isotachophoresis (ITP) focusing. This approach decouples sample accumulation from the length of the channel, resulting in significant focusing over short channel lengths. We provide a brief theory for EOF-balanced ITP focusing under continuous injection from a depleting reservoir and present the design of a short (7 mm) paper-based microfluidic channel, which allows a 200 μL sample to be processed in approximately 6 min, resulting in a 20 000-fold increase in concentration - a full order of magnitude improvement compared to previous paper-based ITP devices. We show the stability of the assay over longer (40 min) durations of time, and using Morpholino probes, we present the applicability of the device for amplification-free detection of nucleic acids, with a limit-of-detection (LoD) of 5 pM in 10 min. Finally, we utilize the small footprint of the channel and show a multiplexed platform in which 12 assays operate in parallel in a 24-well plate format.

Simultaneous isolation and preconcentration of exosomes by ion concentration polarization

Exosomes carry microRNA biomarkers, occur in higher abundance in cancerous patients than in healthy ones, and because they are present in most biofluids, including blood and urine, these can be obtained noninvasively. Standard laboratory techniques to isolate exosomes are expensive, time consuming, provide poor purity, and recover on the order of 25% of the available exosomes. We present a new microfluidic technique to simultaneously isolate exosomes and preconcentrate them by electrophoresis using a high transverse local electric field generated by ion-depleting ion-selective membrane. We use pressure-driven flow to deliver an exosome sample to a microfluidic chip such that the transverse electric field forces them out of the cross flow and into an agarose gel which filters out unwanted cellular debris while the ion-selective membrane concentrates the exosomes through an enrichment effect. We efficiently isolated exosomes from 1× PBS buffer, cell culture media, and blood serum. Using flow rates from 150 to 200 μL/h and field strengths of 100 V/cm, we consistently captured between 60 and 80% of exosomes from buffer, cell culture media, and blood serum as confirmed by both fluorescence spectroscopy and nanoparticle tracking analysis. Our microfluidic chip maintained this recovery rate for more than 20 min with a concentration factor of 15 for 10 min of isolation.

Kinetic theory for DNA melting with vibrational entropy

By treating DNA as a vibrating nonlinear lattice, an activated kinetic theory for DNA melting is developed to capture the breakage of the hydrogen bonds and subsequent softening of torsional and bending vibration modes. With a coarse-grained lattice model, we identify a key bending mode with GHz frequency that replaces the hydrogen vibration modes as the dominant out-of-phase phonon vibration at the transition state. By associating its bending modulus to a universal in-phase bending vibration modulus at equilibrium, we can hence estimate the entropic change in the out-of-phase vibration from near-equilibrium all-atom simulations. This and estimates of torsional and bending entropy changes lead to the first predictive and sequence-dependent theory with good quantitative agreement with experimental data for the activation energy of melting of short DNA molecules without intermediate hairpin structures.

A compact microfluidic chip with integrated impedance biosensor for protein preconcentration and detection

In this study, a low-cost, compact biochip is designed and fabricated for protein detection. Nanofractures formed by self-assembled gold nanoparticles at junction gaps are applied for ion enrichment and depletion to create a trapping zone when electroosmotic flow occurs in microchannels. An impedance measurement module is implemented based on the lock-in amplifier technique to measure the impedance change during antibody growth on the gold electrodes which is caused by trapped proteins in the detection region. The impedance measurement results confirm the presence of trapped proteins. Distinguishable impedance profiles, measured at frequencies in the range of 10-100 kHz, for the detection area taken before and after the presence of proteins validate the performance of the proposed system.

Selectivity enhancements in gel-based DNA-nanoparticle assays by membrane-induced isotachophoresis: thermodynamics versus kinetics

Selectivity against mutant nontargets with a few mismatches remains challenging in nucleic acid sensing. Sensitivity enhancement by analyte concentration does not improve selectivity because it affects targets and nontargets equally. Hydrodynamic or electrical shear enhanced selectivity is often accompanied by substantial losses in target signals, thereby leading to poor limits of detection. We introduce a platform based on depletion isotachophoresis in agarose gel generated by an ion-selective membrane that allows both selectivity and sensitivity enhancement with a two-step assay involving concentration polarization at an ion-selective membrane. By concentrating both the targets and probe-functionalized nanoparticles by ion enrichment at the membrane, the effective thermodynamic dissociation constant is lowered from 40 nM to below 500 pM, and the detection limit is 10 pM as reported previously. A dynamically optimized ion depletion front is then generated from the membrane with a high electrical shear force to selectively and irreversibly dehybridize nontargets. The optimized selectivity against a two-mismatch nontarget (in a 35-base pairing sequence) is shown to be better than the thermodynamic equilibrium selectivity by more than a hundred-fold, such that there is no detectable signal from the two-mismatch nontarget. We offer empirical evidence that irreversible cooperative dehybridization plays an important role in this kinetic selectivity enhancement and that mismatch location controls the optimum selectivity even when there is little change in the corresponding thermodynamic dissociation constant.

Surface acoustic wave devices for chemical sensing and microfluidics: A review and perspective

Surface acoustic waves (SAWs), are electro-mechanical waves that form on the surface of piezoelectric crystals. Because they are easy to construct and operate, SAW devices have proven to be versatile and powerful platforms for either direct chemical sensing or for upstream microfluidic processing and sample preparation. This review summarizes recent advances in the development of SAW devices for chemical sensing and analysis. The use of SAW techniques for chemical detection in both gaseous and liquid media is discussed, as well as recent fabrication advances that are pointing the way for the next generation of SAW sensors. Similarly, applications and progress in using SAW devices as microfluidic platforms are covered, ranging from atomization and mixing to new approaches to lysing and cell adhesion studies. Finally, potential new directions and perspectives on the field as it moves forward are offered, with a specific focus on potential strategies for making SAW technologies for bioanalytical applications.

Concentration-Gradient Stabilization with Segregated Counter- and Co-Ion Paths: A Quasistationary Depletion Front for Robust Molecular Isolation or Concentration

We study the spatiotemporal dynamics of a microfluidic system with a nonselective microfluidic channel gated by an ion-selective membrane which separates the ion flux paths of cations and anions. To preserve electroneutrality, the ionic concentration in the system is shown to converge to a specific inhomogeneous distribution with robust constant current fluxes. A circuit scaling theory that collapses measured asymptotic currents verifies that this is a generic and robust mechanism insensitive to channel geometry, ion selectivity, and electrolyte ionic strength. This first temporally stationary but spatially inhomogeneous depletion front can be used for modulating ionic current and for isotachophoretic isolation of low-mobility molecules and exosomes on small diagnostic chips for various medical applications that require robust high-throughput and integrated platforms.