Effect of buffer flow on DNA separation in a microfabricated electrophoresis system

An adequate buffer reservoir is one essential component of an electrophoresis system, providing current carrying ions and maintaining constant pH. In a microfabricated DNA separation system with on-chip electrodes, the amount of buffer used is limited by the design of the device; the buffer continuity can be easily disturbed by the production of bubbles. Continuously flowing 1 x Tris-borate-EDTA (TBE) buffer over the electrodes at the cathodic end solves both problems. This flow increases the resolution for ssDNA primer separations (21 and 25 bases) to a maximum value of 1.4 within a distance of 1.2 cm, about four times higher than that without flow. Similar improvement has been achieved for dsDNA separation (20 bp ladder; BioRad) at a distance of only 0.4 cm, giving baseline resolution for bands from 20 to 240 bp. We have also investigated the effect of buffer concentration on resolution, and no similar improvement can be obtained by merely increasing the buffer concentration without flow.     

High sample throughput flow immunoassay utilising restricted access columns for the separation of bound and free label

A flow immunodetection system with high sample throughput capacity is described for the screening of various analytes. The immunochemical detection principle is based on the chromatographic separation of the formed immunocomplex (AbAg or AbAg*) and the free antigen (Ag) by a restricted access (RA) column, utilising size-exclusion and reversed-phase mechanism. A fluorescein labelled analyte (Ag*) was used in the competitive assay format with fluorescence detection. The speed and simplicity of the assay were the greatest advantages, allowing measurement of the analyte to be carried out in less than 1 min. The biocompatibility and capacity of the restricted access material allowed multiple injections of up to 5000, without any breakthrough of the fluorescent tracer molecule and thus need for regeneration. The flow immunoassay was developed using the well-known atrazine herbicide and some transformation products as model compounds, due to their human toxicity and widespread use. The sample throughput was 80 samples per hour and the detection limits were 1.4 nM (300 pg/ml) for atrazine (Ab I) and 2.3 nM (500 pg/ml) for the sum of triazines (Ab II–III). Different sample matrices, PBS buffer, creek water, and urine were successfully applied in the flow system without the need for any sample handling step. For plasma samples an additional clean-up step using solid-phase extraction had to be included. The resulting detection limits for atrazine in plasma and water samples using this clean-up and trace enrichment procedure were found to be 2 ng/ml and 20 pg/ml, respectively. The analysis could be performed at a sample throughput rate of 400 per 6-h working shift.     

Dielectrophoretic separation of micron and submicron particles: A review

This paper provides an overview on separation of micron and submicron sized biological (cells, yeast, virus, bacteria, etc.) and nonbiological particles (latex, polystyrene, CNTs, metals, etc.) by dielectrophoresis (DEP), which finds wide applications in the field of medical and environmental science. Mathematical models to predict the electric field, flow profile, and concentration profiles of the particles under the influence of DEP force have also been covered in this review. In addition, advancements made primarily in the last decade, in the area of electrode design (shape and arrangement), new materials for electrode (carbon, silicon, polymers), and geometry of the microdevice, for efficient DEP separation of particles have been highlighted.     

Development of a microfabricated cytometry platform for characterization and sorting of individual leukocytes

Organizing leukocytes into high-density arrays makes these cells amenable to rapid optical characterization and subsequent sorting, pointing to clinical and basic science applications. The present paper describes development of a cytometry platform for creating high-density leukocyte arrays and demonstrates retrieval of single cells from the array. Poly(ethylene glycol)(PEG) photolithography was employed to fabricate arrays of microwells composed of PEG hydrogel walls and glass attachment pads 20 microm x 20 microm and 15 microm x 15 microm in size. PEG micropatterned glass surfaces were further modified with cell-adhesive ligands, poly-L-lysine, anti-CD5 and anti-CD19 antibodies, in order to engineer specific cell-surface interactions within the individual wells. Localization of the fluorescently-labeled proteins in the glass attachment pads of PEG microwells was visualized by fluorescence microscopy. Glass slides micropatterned with PEG and cell-adhesive ligands were exposed to T-lymphocytes for 30 min. These anchorage-independent cells became selectively captured in the ligand-modified microwells forming high-density cell arrays. Cell occupancy in the microwells was found to be antibody-dependent, reaching 94.6 +/- 2.3% for microwells decorated with T-cell specific anti-CD5 antibodies. Laser capture microdissection (LCM) was investigated as a method for sorting cells from the array and retrieval of single selected cells was demonstrated.     

Dielectrophoretic separation of microalgae cells in ballast water in a microfluidic chip

The composition of the ship's ballast water is complex and contains a large number of microalgae cells, bacteria, microplastics, and other microparticles. To increase the accuracy and efficiency of detection of the microalgae cells in ballast water, a new microfluidic chip for continuous separation of microalgae cells based on alternating current dielectrophoresis was proposed. In this microfluidic chip, one piece of 3‐dimensional electrode is embedded on one side and eight discrete electrodes are arranged on the other side of the microchannel. An insulated triangular structure between electrodes is designed for increasing the inhomogeneity of the electric field distribution and enhancing the dielectrophoresis (DEP) force. A sheath flow is designed to focus the microparticles near the electrode, so as to increase the suffered DEP force and improve separation efficiency. To demonstrate the performance of the microfluidic separation chip, we developed two species of microalgae cells (Platymonas and Closterium) and a kind of microplastics to be used as test samples. Analyses of the related parameters and separation experiments by our designed microfluidic chip were then conducted. The results show that the presented method can separate the microalgae cells from the mixture efficiently, and this is the first time to separate two or more species of microalgae cells in a microfluidic chip by using negative and positive DEP force simultaneously, and moreover it has some advantages including simple operation, high efficiency, low cost, and small size and has great potential in on‐site pretreatment of ballast water.     

Dielectric spectroscopy in a micromachined flow cytometer: theoretical and practical considerations

We propose a model to determine the influence of different cell properties, such as size, membrane capacitance and cytoplasm conductivity, on the impedance spectrum as measured in a microfabricated cytometer. A dielectric sphere of equivalent complex permittivity is used as a simplified model to describe a biological cell. The measurement takes place between a pair of facing microelectrodes in a microchannel filled with a saline solution. The model incorporates various cell parameters, such as dielectric properties, size and position in the channel. A 3D finite element model is used to evaluate the magnitude of the electric field in the channel and the resultant changes in charge densities at the measurement electrode boundaries as a cell flows past. The charge density is integrated on the electrode surface to determine the displacement current and the channel impedance for the computed frequency range. The complete impedance model combines the finite element model, the electrode-electrolyte interface impedance and stray impedance, which are measured from a real device. The modeled dielectric complex spectra for various cell parameters are discussed and a measurement strategy for cell discrimination with such a system is proposed. We finally discuss the amount of noise and measurement fluctuations of the sensor.     

The effect of photomask resolution on separation efficiency on microfabricated devices

Separation quality on glass microfluidic devices fabricated from photomasks of different optical resolutions was compared by measuring the dispersion (apparent diffusion) coefficients of a set of standard compounds separated on these devices. Currently, the channel manifolds of most microfluidic devices are patterned using chrome photomasks. A much cheaper, more robust alternative to chrome photomasks are laser photoplotted masks. The primary disadvantage to using laser photoplots is that the optical resolution of these masks is not as high as that of chrome masks, and this feature increases the side-wall roughness of etched channel manifolds patterned using such masks. The increased wall roughness may affect the fluid flow within the channels and, therefore, the separation quality. To determine the effect of increased sidewall channel roughness, microchip channel manifolds were patterned in soda lime glass using a chrome photomask and laser photoplots printed at resolutions of 620, 1240, 3100 and 6200 dots per centimetre (dpc). Separations were performed on these devices using dilute solutions of fluorescently labeled amino acids. The peak variances of the amino acids were calculated at increasing distances down the separation channel and plotted as a function of migration time. From this plot, dispersion coefficients of the analytes were measured. This allowed for a reliable, relatively easy, direct separation analysis among microchips fabricated from the various photomasks. After multiple separations using microchips fabricated from each resolution mask, we found that the change in sidewall surface roughness did not significantly affect the dispersion coefficients measured, and thus the separation quality. The lower mask resolution limit, rather, was governed by the fidelity to which the mask could capture the original CAD design.     

Dielectrophoretic ultra-high-frequency characterization and in silico sorting on uptake of rare earth elements by Cupriavidus necator

Rare earth elements (REEs) are widely used across different industries due to their exceptional magnetic and electrical properties. In this work, Cupriavidus necator is characterized using dielectrophoretic ultra-high-frequency measurements, typically in MHz range to quantify the properties of cytoplasm in C. necator for its metal uptake/bioaccumulation capacity. Cupriavidus necator, a Gram-negative bacteria strain is exposed to REEs like europium, samarium, and neodymium in this study. Dielectrophoretic crossover frequency experiments were performed on the native C. necator species pre- and post-exposure to the REEs at MHz frequency range. The net conductivity of native C. necator, Cupriavidus europium, Cupriavidus samarium, and Cupriavidus neodymium are 15.95 ± 0.029 μS/cm, 16.15 ± 0.028 μS/cm, 16.05 ± 0.029 μS/cm, 15.61 ± 0.005 μS/cm respectively. The estimated properties of the membrane published by our group are used to develop a microfluidic sorter by modeling and simulation to separate REE absorbed C. necator from the unabsorbed native C. necator species using COMSOL Multiphysics commercial software package v5.5.     

Effects of flow and diffusion on chemotaxis studies in a microfabricated gradient generator

An understanding of chemotaxis at the level of cell-molecule interactions is important because of its relevance in cancer, immunology, and microbiology, just to name a few. This study quantifies the effects of flow on cell migration during chemotaxis in a microfluidic device. The chemotaxis gradient within the device was modeled and compared to experimental results. Chemotaxis experiments were performed using the chemokine CXCL8 under different flow rates with human HL60 promyelocytic leukemia cells expressing a transfected CXCR2 chemokine receptor. Cell trajectories were separated into x and y axis components. When the microchannel flow rates were increased, cell trajectories along the x axis were found to be significantly affected (p < 0.05). Total migration distances were not affected. These results should be considered when using similar microfluidic devices for chemotaxis studies so that flow bias can be minimized. It may be possible to use this effect to estimate the total tractile force exerted by a cell during chemotaxis, which would be particularly valuable for cells whose tractile forces are below the level of detection with standard techniques of traction-force microscopy.     

Sequencing of real-world samples using a microfabricated hybrid device having unconstrained straight separation channels

We describe a microfabricated hybrid device that consists of a microfabricated chip containing multiple twin-T injectors attached to an array of capillaries that serve as the separation channels. A new fabrication process was employed to create two differently sized round channels in a chip. Twin-T injectors were formed by the smaller round channels that match the bore of the separation capillaries and separation capillaries were incorporated to the injectors through the larger round channels that match the outer diameter of the capillaries. This allows for a minimum dead volume and provides a robust chip/capillary interface. This hybrid design takes full advantage, such as sample stacking and purification and uniform signal intensity profile, of the unique chip injection scheme for DNA sequencing while employing long straight capillaries for the separations. In essence, the separation channel length is optimized for both speed and resolution since it is unconstrained by chip size. To demonstrate the reliability and practicality of this hybrid device, we sequenced over 1000 real-world samples from Human Chromosome 5 and Ciona intestinalis, prepared at Joint Genome Institute. We achieved average Phred20 read of 675 bases in about 70 min with a success rate of 91%. For the similar type of samples on MegaBACE 1000, the average Phred20 read is about 550-600 bases in 120 min separation time with a success rate of about 80-90%.     

Free-flow electrophoresis in a microfabricated chamber with a micromodule fraction separator. Continuous separation of proteins

Continuous free flow electrophoresis of proteins was carried out in a microfabricated free flow electrophoresis (mFFE) module with the 30-μm thick slit of the separation. The newly developed micromodule fraction separator (MFS) was attached to the down-stream end site of the separation chamber of mFFE. By using the MFS, electrolyte solution from the separation chamber was introduced to the peristaltic pump without disturbing the electrolyte solution flow at the bottom side of the chamber. The separation of protein mixture samples was achieved by a hydroxypropylmethylcellulose pretreatment coating of the separation chamber. The pretreatment of the sample chamber effectively suppressed electroosmotic flow. All fractionated samples were collected using the MFS after continuous elecrophoresis and analyzed by reversed-phase HPLC. From the results of HPLC analyses none of the cytochrome c fractions at the other ports revealed cross talk phenomena at adjacent ports. A similar result occurred for the myoglobin. This means that these proteins were completely separated from each other by continuous mFFE, and the MFS functioned efficiently during continuous electrophoresis.     

Fast separation of oligonucleotide and triplet repeat DNA on a microfabricated capillary electrophoresis device and capillary electrophoresis

A laser-induced fluorescence detection system coupled with a highly sensitive silicon-intensified target (SIT) camera is successfully applied to the imaging of a band for DNA fragment labeling by fluorescence dye in a microchannel, and to the visualizing of the separation process on a microfabricated chip. We demonstrated that an only 6 mm separation channel is sufficient for the separation of triplet repeat DNA fragment and DNA molecular marker within only 12 s. The separation using the microfabricated capillary electrophoresis device is confirmed to be at least 18 times faster than the same separation carried out by conventional capillary electrophoresis with 24.5 cm effective length. The use of a short capillary with 8.5 cm effective length is also efficient for fast separation of DNA; however, the microchip technology is even faster than capillary electrophoresis using a short capillary.     

Measurements of scattered light on a microchip flow cytometer with integrated polymer based optical elements

Flow cytometry is widely used for analyzing microparticles, such as cells and bacteria. In this paper, we report an innovative microsystem, in which several different optical elements (waveguides, lens and fiber-to-waveguide couplers) are integrated with microfluidic channels to form a complete microchip flow cytometer. All the optical elements, the microfluidic system, and the fiber-to-waveguide couplers were defined in one layer of polymer (SU-8, negative photoresist) by standard photolithography. With only a single mask procedure required, all the fabrication and packaging processes can be finished in one day. Polystyrene beads were measured in the microchip flow cytometer, and three signals (forward scattering, large angle scattering and extinction) were measured simultaneously for each bead. To our knowledge this is the first time forward scattered light and incident light extinction were measured in a microsystem using integrated optics. The microsystem can be applied for analyzing different kinds of particles and cells, and can easily be integrated with other microfluidic components.     

Microfluidic array cytometer based on refractive optical tweezers for parallel trapping, imaging and sorting of individual cells

Analysis of genetic and functional variability in populations of living cells requires experimental techniques capable of monitoring cellular processes such as cell signaling of many single cells in parallel while offering the possibility to sort interesting cell phenotypes for further investigations. Although flow cytometry is able to sequentially probe and sort thousands of cells per second, dynamic processes cannot be experimentally accessed on single cells due to the sub-second sampling time. Cellular dynamics can be measured by image cytometry of surface-immobilized cells, however, cell sorting is complicated under these conditions due to cell attachment. We here developed a cytometric tool based on refractive multiple optical tweezers combined with microfluidics and optical microscopy. We demonstrate contact-free immobilization of more than 200 yeast cells into a high-density array of optical traps in a microfluidic chip. The cell array could be moved to specific locations of the chip enabling us to expose in a controlled manner the cells to reagents and to analyze the responses of individual cells in a highly parallel format using fluorescence microscopy. We further established a method to sort single cells within the microfluidic device using an additional steerable optical trap. Ratiometric fluorescence imaging of intracellular pH of trapped yeast cells allowed us on the one hand to measure the effect of the trapping laser on the cells' viability and on the other hand to probe the dynamic response of the cells upon glucose sensing.     

Influence of flow and diffusion on protein separation in a continuous flow electrophoresis cell: computation procedure

Continuous flow zone electrophoresis is an efficient method for the non-destructive separation of biological materials in a flowing film of buffer solution in which the constituents of a sample are separated according to their electrophoretic mobilities, under the influence of an electric field. This paper deals with modeling of flow structure of the buffer solution taking into account the effect of electroosmosis, Joule heating and thermal free convection and the forced convection of axial flow. Modeling of diffusion is examined in a second part. The modeling equations and the corresponding boundary conditions are solved by finite difference methods. The various parameters affecting the quality of the fractionation are analyzed.     

Dielectrophoretic levitation in the presence of shear flow: implications for colloidal fouling of filtration membranes

The ability of dielectrophoretic (DEP) forces created using a microelectrode array to levitate particles in a colloidal suspension is studied experimentally and theoretically. The experimental system employs microfabricated electrode arrays on a glass substrate to apply repulsive DEP forces on polystyrene latex particles suspended in an aqueous medium. A numerical model based on the convection-diffusion-migration equation is presented to calculate the concentration distribution of colloidal particles in shear flow under the influence of a repulsive DEP force field. The results obtained from the numerical simulations are compared against trajectory analysis results and experimental data. The results indicate that by incorporating ac electric field-induced DEP forces in a shear flow, particle accumulation and deposition on the flow channel surfaces can be significantly reduced or even completely averted. The mathematical model is then used to indicate how the deposition behavior is modified in the presence of a permeable substrate, representative of tangential flow membrane filtration operations. The results indicate that the repulsive dielectrophoretic (DEP) forces imparted to the particles suspended in the feed can be employed to mitigate membrane fouling in a cross-flow filtration process.     

Continuous separation of lipid particles from erythrocytes by means of laminar flow and acoustic standing wave forces

Improved continuous acoustic particle separation (separation efficiency close to 100%) and separation of erythrocytes (red blood cells) from lipid microemboli in whole blood is reported.     

Carrier ampholyte‐free free‐flow isoelectric focusing for separation of protein

Free‐flow isoelectric focusing (FFIEF) has the merits of mild separation conditions, high recovery and resolution, but suffers from the issues of ampholytes interference and high cost due to expensive carrier ampholytes. In this paper, a home‐made carrier ampholyte‐free FFIEF system was constructed via orientated migration of H⁺ and OH^? provided by electrode solutions. When applying an electric field, a linear pH gradient from pH 4 to 9 (R² = 0.994) was automatically formed by the electromigration of protons and hydroxyl ions in the separation chamber. The carrier ampholyte‐free FFIEF system not only avoids interference of ampholyte to detection but also guarantees high separation resolution by establishing stable pH gradient. The separation selectivity was conveniently adjusted by controlling operating voltage and optimizing the composition, concentration and flow rate of the carrier buffer. The constructed system was applied to separation of proteins in egg white, followed by MADLI‐TOF‐MS identification. Three major proteins, ovomucoid, ovalbumin and ovotransferrin, were successfully separated according to their pI values with 15 mmol/L Tris‐acetic acid (pH = 6.5) as carrier buffer at a flow rate of 12.9 mL/min.     

Rapid and sensitive separation of trace level protein digests using microfabricated devices coupled to a quadrupole--time-of-flight mass spectrometer

The application of microfabricated devices coupled to a quadrupole time-of-flight mass spectrometer (Qq-TOF-MS) is presented for the analysis of trace level digests of gel-isolated proteins. In order to enhance the sample loading for proteomics analyses, two different on-chip sample preconcentration techniques were evaluated. First, a sample stacking procedure that used polarity switching to remove the sample buffer prior to zone electrophoresis was easily integrated on the microfabricated devices. With the present chip design, this preconcentration technique provided up to 70 nL sample injection with sub-nM detection limits for most peptide standards. For applications requiring larger sample loading, a disposable adsorption preconcentrator using a C18 membrane is incorporated outside the chip. This preconcentration method yielded lower peptide recoveries than that obtainable with sample stacking, and provided a convenient means of injecting several microL of sample with detection limits of typically 2.5 nM for hydrophobic peptides. The analytical merits of both sample enrichment approaches are described for the identification of bands isolated from two-dimensional (2-D) gel separation of protein extracts from Haemophilus influenzae. Accurate molecular mass measurements (< 5 ppm) in peptide mapping experiments is obtained by introducing an internal standard via a post-separation channel. Rapid identification of trace level peptides is also demonstrated using on-line tandem mass spectrometry and database searching with peptide sequence tags.