Miniaturized platforms for the detection of single-nucleotide polymorphisms

Conventional methods for detecting single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in human beings, are mostly limited by their analysis time and throughputs. In contrast, advances in microfabrication technology have led to the development of miniaturized platforms that can potentially provide rapid high-throughput analysis at small sample volumes. This review highlights some of the recent developments in the miniaturization of SNP detection platforms, including microarray-based, bead-based microfluidic and microelectrophoresis-based platforms. Particular attention is paid to their ease of fabrication, analysis time, and level of throughput.     

Label-free electrical discrimination of cells at normal, apoptotic and necrotic status with a microfluidic device

As a label-free alternative of conventional flow cytometry, chip-based impedance measurement for single cell analysis has attracted increasing attentions in recent years. In this paper, we designed a T-shape microchannel and fabricated a pair of gold electrodes located horizontally on each side of the microchannel using a transfer printing method. Instant electric signals of flowing-through single cells were then detected by connecting the electrodes to a Keithley resistance and capacitance measurement system. Experimental results based on the simultaneous measurement of resistance and capacitance demonstrated that HL-60 and SMMC-7721 cells could be differentiated effectively. Moreover, SMMC-7721 cells at normal, apoptotic and necrotic status can also be discriminated in the flow. We discussed the possible mechanism for the discrimination of cell size and cell status by electrical analysis, and it is believed that the improvement of detection with our design results from more uniform distribution of the electric field. This microfluidic design may potentially become a promising approach for the label-free cell sorting and screening.     

Rapid pre-concentration of Escherichia coli in a microfluidic paper-based device using ion concentration polarization

We report a microfluidic paper based analytical device implementing ion concentration polarization (ICP) for rapid pre-concentration of Escherichia coli in water. The fabricated device consists of a paper channel with a Nafion^® membrane and in-built micro wire electrodes to supply electric voltage to induce the ICP effect. E. coli cells were stained with SYTO 9 and fluorescence was used as a sensing method. The device achieved high concentration factor up to 2 × 10⁵ within minutes. The effect of total ion concentration, on ICP and fluorescence intensity was studied. The reported device and method are suitable and effective for detection of E. coli during ballast water quality monitoring, coastal water quality monitoring where high salinity water is present.     

Hierarchical porous polymer beads prepared by polymerization-induced phase separation and emulsion-template in a microfluidic device

Porous polymer beads（PPBs） containing hierarchical bimodal pore structure with gigapores and meso-macropores were prepared by polymerization-induced phase separation（PIPS） and emulsion-template technique in a glass capillary microfluidic device（GCMD）. Fabrication procedure involved the preparation of water-in-oil emulsion by emulsifying aqueous solution into the monomer solution that contains porogen. The emulsion was added into the GCMD to fabricate the（water-in-oil）-in-water double emulsion droplets. The flow rate of the carrier continuous phase strongly influenced the formation mechanism and size of droplets. Formation mechanism transformed from dripping to jetting and size of droplets decreased from 550 μm to 250 μm with the increase in flow rate of the carrier continuous phase. The prepared droplets were initiated for polymerization by on-line UV-irradiation to form PPBs. The meso-macropores in these beads were generated by PIPS because of the presence of porogen and gigapores obtained from the emulsion-template. The pore morphology and pore size distribution of the PPBs were investigated extensively by scanning electron microscopy and mercury intrusion porosimetry（MIP）. New pore morphology was formed at the edge of the beads different from traditional theory because of different osmolarities between the water phase of the emulsion and the carrier continuous phase. The morphology and proportion of bimodal pore structure can be tuned by changing the kind and amount of porogen.     

Development of a microfluidic paper-based analytical device for the determination of salivary aldehydes

A low cost, disposable and easy to use microfluidic paper-based analytical device (μPAD) was developed for simple and non-invasive determination of total aldehydes in saliva with a potential to be used in epidemiological studies to assess oral cancer risk. The μPAD is based on the colour reaction between aldehydes (e.g. acetaldehyde, formaldehyde), 3-methyl-2-benzothiazolinone hydrazone (MBTH) and iron(III) to form an intense blue coloured formazan dye. The newly developed μPAD has a 3D design with two overlapping paper layers. The first layer comprises 15 circular detection zones (8 mm in diameter), each impregnated with 8 μL of MBTH, while the second layer contains 15 reagent zones (4 mm in diameter). Two μL of iron(III) chloride are added to each one of the second layer zones after the addition of sample to the detection zones in the first layer. All hydrophilic zones of the μPAD are defined by wax printing using a commercial wax printer.     

Quantitative analysis of Caenorhabditis elegans chemotaxis using a microfluidic device

Caenorhabditis elegans, one of the widely studied model organisms, sense external chemical cues and perform relative chemotaxis behaviors through its simple chemosensory neuronal system. To study the mechanism underlying chemosensory behavior, a rapid and reliable method for quantitatively analyzing the worms' behaviors is essential. In this work, we demonstrated a microfluidic approach for investigating chemotaxis responses of worms to chemical gradients. The flow-based microfluidic chip was consisted of circular tree-like microchannels, which was able to generate eight flow streams containing stepwise chemical concentrations without the difference in flow velocity. Worms' upstream swimming into microchannels with various concentrations was monitored for quantitative analysis of the chemotaxis behavior. By using this microfluidic chip, the attractive and repellent responses of C. elegans to NaCl were successfully quantified within several minutes. The results demonstrated the wild type-like repellent responses and severely impaired attractive responses in grk-2 mutant animals with defects in calcium influx. In addition, the chemotaxis analysis of the third stage larvae revealed that its gustatory response was different from that in the adult stage. Thus, our microfluidic method provided a useful platform for studying the chemosensory behaviors of C. elegans and screening of chemosensation-related chemical drugs.     

Detection of polymerase chain reaction fragments using a conducting polymer-modified screen-printed electrode in a microfluidic device

A simple and fast method for electrochemical detection of amplified fragments by PCR was successfully developed using CE in a microfluidic device with a modified screen-printed carbon electrode (SPCE). The surfaces of the SPCE were modified with poly-5,2'-5',2'-terthiophene-3'-carboxylic acid, which improves the analysis performance by lowering the detection potential, enhancing the S/N characteristics, and avoiding electrode poisoning. DNA fragments amplified by PCR were separated within 210 s in a 75.5 mm-long coated-separation channel at a separation field strength of -200 V/cm. To minimize the sample adsorption into the inner surface of the capillary wall, which disturbs the separation, a dynamically coated capillary with an acrylamide solution was used. Furthermore, the analysis procedure was simplified and rendered reproducible by using 0.50% w/v hydroxyethylcellulose as a separation matrix in a coated channel. The reproducibility of the analysis employing the coated channel yielded RSD of 4.3% for the peak areas and 1.4% for the migration times in eight repetitive measurements at a modified electrode, compared with 21.3 and 9.4% for a bare electrode. The sensitivity of the assay was 18.74 pAs/(pg/microL) with a detection limit of 584.31 +/- 1.3 fg/microL.     

Separation of model mixtures of epsilon-globin positive fetal nucleated red blood cells and anucleate erythrocytes using a microfluidic device

Microfluidic devices are capable of separating microparticles and cells. We developed and tested the efficiency of silicon cross-flow microfilters for the separation of primitive fetal nucleated red blood cells (FNRBCs) and adult anucleate red blood cell (AARBCs) from model mixtures. Stepwise improvements over three generations of device design resulted in an increasing trend in the recovery of FNRBCs. We obtained a recovery of FNRBCs (74.0 ± 6.3%, p < 0.05, n = 5) using the third generation device, with a depletion of 46.5 ± 3.2% AARBCs from the cell mixture. The purity of FNRBCs in the enriched fraction was enhanced by a factor of 1.7-fold.     

A comprehensive in Silico analysis of the functional and structural impact of single nucleotide polymorphisms (SNPs) in the human IL-33 gene

Interleukin 33 (IL-33) is the latest member of the IL-1 cytokine family, which plays both pro - and anti-inflammatory functions. Numerous Single-nucleotide polymorphisms (SNPs) in the IL-33 gene have been recognized to be associated with a vast variety of inflammatory disorders. SNPs associated studies have become a crucial approach in uncovering the genetic background of human diseases. However, distinguishing the functional SNPs in a disease-related gene from a pool of both functional and neutral SNPs is a major challenge and needs multiple experiments of hundreds or thousands of SNPs in candidate genes. This study aimed to identify the possible deleterious SNPs in the IL-33 gene using bioinformatics predictive tools. The nonsynonymous SNPs (nsSNPs) were analyzed by SIFT, PolyPhen, PROVEAN, SNP&GO, MutPred, SNAP, PhD SNP, and I-Mutant tools. The Non-coding SNPs (ncSNPs) were also analyzed by SNPinfo and RegulomeDB tools. In conclusion, our in-silico analysis predicted 5 nsSNPs and 22 ncSNPs as potential candidates in the IL-33 gene for future genetic association studies.     

Construction of microscale structures in enclosed microfluidic networks by using a magnetic beads based method

A large number of microscale structures have been used to elaborate flowing control or complex biological and chemical reaction on microfluidic chips. However, it is still inconvenient to fabricate microstructures with different heights (or depths) on the same substrate. These kinds of microstructures can be fabricated by using the photolithography and wet-etching method step by step, but involves time-consuming design and fabrication process, as well as complicated alignment of different masters. In addition, few existing methods can be used to perform fabrication within enclosed microfluidic networks. It is also difficult to change or remove existing microstructures within these networks. In this study, a magnetic-beads-based approach is presented to build microstructures in enclosed microfluidic networks. Electromagnetic field generated by microfabricated conducting wires (coils) is used to manipulate and trap magnetic beads on the bottom surface of a microchannel. These trapped beads are accumulated to form a microscale pile with desired shape, which can adjust liquid flow, dock cells, modify surface, and do some other things as those fabricated microstructures. Once the electromagnetic field is changed, trapped beads may form new shapes or be removed by a liquid flow. Besides being used in microfabrication, this magnetic-beads-based method can be used for novel microfluidic manipulation. It has been validated by forming microscale dam structure for cell docking and modified surface for cell patterning, as well as guiding the growth of neurons.     

Separation and electrochemical detection of paracetamol and 4-aminophenol in a paper-based microfluidic device

The present work describes the construction and application of a simple, low cost and sensitive microfluidic paper-based device with electrochemical detection for the detection of paracetamol and 4-aminophenol. The separation channels of a width of 2.0 mm were created on paper using a wax printing process to define the regions of the device. A baseline separation level of the analytes can be obtained in 0.1 mol L⁻¹ acetate buffer solution at pH 4.5 and by injecting 500 nL of the standard solutions at 12 mm from the working electrode. The electrochemical detection system was created at the end of the channels through a process known as sputtering. The previously separated analytes were detected at the end of the hydrophilic separation channel by applying a potential of 400 mV vs. pseudo Au on the working electrode. Experimental variables such as type of paper (cation exchanger and n1), pH, sample volume, applied potential and distance of sample injection were evaluated and, under the conditions of higher response, it was possible to obtain detection limits of 25.0 and 10.0 μmol L⁻¹ for paracetamol and 4-aminophenol, respectively.     

Simultaneous analysis of nitrate and nitrite in a microfluidic device with a Cu-complex-modified electrode

A CE microsystem coupled with a microchip and a copper-(3-mercaptopropyl) trimethoxysilane (Cu-MPS) complex-modified carbon paste electrode (CPE) was developed for the simultaneous analysis of nitrite and nitrate. The method is based on the electrocatalytic reduction of both analytes with the modified electrode. The Cu-MPS complex was characterized by voltammetric, XPS, and FT-IR analyses. Experimental parameters affecting the sensitivity of the modified electrode were assessed and optimized. The best separation was achieved in a 60 mm separation channel filled with a 20 mM acetate buffer of pH 5.0 containing 3.0 mM CTAB at separation field strength of -250 V/cm within 90 s. The detection potential for the simultaneous analysis of nitrite and nitrate was found to be -225 mV versus Ag/AgCl. A reproducible response (RSD of 3.2% (nitrite) and 2.8% (nitrate), n = 8) for repetitive sample injections reflected the negligible electrode fouling at the modified CPE. The interference effect was examined for other inorganic ions and biological compounds. A wide hydrodynamic range between 0.25 and 120 microM was observed for analyzing nitrite and nitrate with the sensitivities of 0.069 +/- 0.003 and 0.065 +/- 0.002 nA/microM, and the detection limits, based on S/N = 3, were found to be 0.09 +/- 0.007 and 0.08 +/- 0.009 microM, respectively. The applicability of the method to water and urine samples analyses was demonstrated.     

Analysis of herbicides on a single C30 bead via a microfluidic device combined with electrospray ionization quadrupole time-of-flight mass spectrometer

An integrated system combining microfluidic device with electrospray ionization quadrupole time-of-flight mass spectrometer (ESI-Q-TOF-MS) was developed for detecting a series of herbicides on a single C₃₀ bead. We presented single C₃₀ beads manipulation which had absorbed sequential herbicides, based on the precise control of the concentration and absorption time. The simple microchip consisting of a straight channel and a hole in the middle enabled single C₃₀ bead introduction, transformation and location. ESI-Q-TOF-MS was employed to realize highly sensitive qualitative analysis and implement semi-quantitative analysis. Once the C₃₀ bead contacted with eluting solution, the solute transferred into eluting and would be detected by ESI-Q-TOF-MS. Depending on desorption curves obtained, accurate and clear characteristic peaks for each analysts were carried out. Our investigations on single-particle analysis showed that the combination of microfluidic device and mass spectrum could reduce the analysis time to 5 min and the solvent consumption to 2.5 μL, realize high sensitivity detection, and avoid the complex sample pretreatment. The significant potential on analysis of environmental samples on this combination system by single particle was demonstrated.     

A simplified PDMS microfluidic device with a built-in suction actuator for rapid production of monodisperse water-in-oil droplets

We previously established an automatic droplet-creation technique that only required air evacuation of a PDMS microfluidic device prior to use. Although the rate of droplet production with this technique was originally slow (∼10 droplets per second), this was greatly improved (∼470 droplets per second) in our recent study by remodeling the original device configuration. This improvement was realized by the addition of a degassed PDMS layer with a large surface area-to-volume ratio that served as a powerful vacuum generator. However, the incorporation of the additional PDMS layer (which was separate from the microfluidic PDMS layer itself) into the device required reversible bonding of five different layers. In the current study, we aimed to simplify the device architecture by reducing the number of constituent layers for enhancing usability of this microfluidic droplet generator while retaining its rapid production rate. The new device consisted of three layers. This comprised a degassed PDMS slab with microfluidic channels on one surface and tens of thousands of vacuum-generating micropillars on the other surface, which was simply sandwiched by PMMA layers. Despite its simplified configuration, this new device created monodisperse droplets at an even faster rate (>1000 droplets per second).     

Rapid screening of phenylketonuria using a CD microfluidic device

We herein present a compact disc (CD) microfluidic chip based hybridization assay for phenylketonuria (PKU) screening. This CD chip is composed of a polydimethylsiloxane (PDMS) top layer containing 12 DNA hybridization microchannels, and a glass bottom layer with hydrogel pad conjugated DNA oligonucleotides. Reciprocating flow was generated on the CD chip through a simple rotation-pause operation to facilitate rapid DNA hybridization. When rotated the CD chip, the sample solution was driven into the hybridization channel by centrifugal force. When stopped the CD chip, the sample plug was pulled backward through the channel by capillary force. The hybridization assay was firstly validated with control samples and was then used to analyze 30 clinical samples from pregnant women with suspected PKU fetus. The on-chip DNA hybridization was completed in 15 min with a sample consumption as low as 1.5μL, and the limit-of-detection (LOD) of DNA template was 0.7ng/μL. Among the 30 samples tested, V245V mutation was identified in 4 cases while R243Q mutation was detected in one case. Results of the hybridization assay were confirmed by DNA sequencing. This CD-chip based hybridization assay features short analysis time, simple operation and low cost, thus has the potential to serve as the tool for PKU screening.     

Fluorescence detection of single-nucleotide polymorphisms with two simple and low cost methods: a double-DNA-probe method and a bulge form method

Two 10-mer DNA probes, or one 20-mer DNA probe, respectively, hybridize with a 21-mer target DNA to form a vacancy or bulge opposite the target nucleotide. The former double-DNA-probe method and the latter bulge form method are applicable to the detection of single-nucleotide polymorphisms (SNPs). A small fluorescent dye enters into the vacancy or bulge and binds with a target nucleotide via a hydrogen bonding interaction, which causes fluorescence quenching. The interaction between fluorescent dye and the target nucleotide is confirmed by measuring the melting temperature and fluorescence spectra. The fluorescent dye, ADMND (2-amino-5,7-dimethyl-1,8-naphthyridine), is found to selectively bind with C over A or G. The methods proposed here are economic, convenient, and effective for the fluorescence detection of SNPs. Finally, the double-DNA-probe method and bulge form method are successfully applied to the detection of C/G and C/A mutations in the estrogen receptor 2 gene and progesterone receptor gene using ADMND.     

Rapid and quantitative DNA analysis of genetic mutations for polycystic kidney disease (PKD) using magnetic/luminescent nanoparticles

Rapid and accurate detection of genetic mutations based on nanotechnology would provide substantial advances in detection of polycystic kidney disease (PKD), a disease whose current methods of detection are cumbersome due to the large size and duplication of the mutated gene. In this study, a nanotechnology-based DNA assay was developed for detection of SNPs (single nucleotide polymorphisms) in a feline autosomal dominant PKD (ADPKD) model which can readily be adapted to diagnosis of human ADPKD type 1. Europium and terbium phosphors were doped into gadolinium crystal hosts with a magnetic core, providing stable luminescence and the possibility of magnetic manipulations in a solution-based assay. A hybridization-in-solution DNA assay was optimized for feline PKD gene SNP detection using genomic DNA extracted from feline kidney tissue and blood. This assay showed a substantial differentiation between PKD and control specimens. The nanotechnology-based DNA assay is attractive from the viewpoint of rapid availability, simple methodology, and cost reduction for clinical use to detect mutations involved in human ADPKD and other genetic diseases. Figure Schematic diagram of PKD (Polycystic Kidney Disease) SNPs detection assay using feline genomic DNA in magnetic/luminescent nanoparticle-based DNA hybridization     

The influence of electrolyte concentration on nanofractures fabricated in a 3D-printed microfluidic device by controlled dielectric breakdown

A three-dimensional-printed microfluidic device made of a thermoplastic material was used to study the creation of molecular filters by controlled dielectric breakdown. The device was made from acrylonitrile butadiene styrene by a fused deposition modeling three-dimensional printer and consisted of two V-shaped sample compartments separated by 750 µm of extruded plastic gap. Nanofractures were formed in the thin piece of acrylonitrile butadiene styrene by controlled dielectric breakdown by application voltage of 15–20 kV with the voltage terminated when reaching a defined current threshold. Variation of the size of the nanofractures was achieved by both variation of the current threshold and by variation of the ionic strength of the electrolyte used for breakdown. Electrophoretic transport of two proteins, R-phycoerythrin (RPE; <10 nm in size) and fluorescamine-labeled BSA (f-BSA; 2–4 nm), was used to monitor the size and transport properties of the nanofractures. Using 1 mM phosphate buffer, both RPE and f-BSA passed through the nanofractures when the current threshold was set to 25 µA. However, when the threshold was lowered to 10 µA or lower, RPE was restricted from moving through the nanofractures. When we increased the electrolyte concentration during breakdown from 1 to 10 mM phosphate buffer, BSA passed but RPE was blocked when the threshold was equal to, or lower than, 25 µA. This demonstrates that nanofracture size (pore area) is directly related to the breakdown current threshold but inversely related to the concentration of the electrolyte used for the breakdown process.     

Hydrophilic surface modification of cyclic olefin copolymer microfluidic chips using sequential photografting

The plastic material known as cyclic olefin copolymer (COC) is a useful substrate material for fabricating microfluidic devices due to its low cost, ease of fabrication, excellent optical properties, and resistance to many solvents. However, the hydrophobicity of native COC limits its use in bioanalytical applications. To increase surface hydrophilicity and reduce protein adsorption, COC surfaces were photografted with poly(ethylene glycol) methacrylate (PEGMA) using a two-step sequential approach: covalently-bound surface initiators were formed in the first step and graft polymerization of PEGMA was then carried out from these sites in the second step. Contact angle measurements were used to monitor and quantify the changes in surface hydrophilicity as a function of grafting conditions. As water droplet contact angles decreased from 88 degrees for native COC to 45 degrees for PEGMA-grafted surfaces, protein adsorption was also reduced by 78% for the PEGMA-modified COC microchannels as determined by a fluorescence assay. This photografting technique should enable the use of COC microdevices in a variety of bioanalytical applications that require minimal nonspecific adsorption of biomolecules.     

Analysis of amino acids and proteins using a poly(methyl methacrylate) microfluidic system

Plastic microchips are very promising analytical devices for the high-speed analysis of biological compounds. However, due to its hydrophobicity, their surface strongly interacts with nonpolar analytes or species containing hydrophobic domains, resulting in a significant uncontrolled adsorption on the channel walls. This paper describes the migration of fluorescence-labeled amino acids and proteins using the poly(methyl methacrylate) microchip. A cationic starch derivative significantly decreases the adsorption of analytes on the channel walls. The migration time of the analytes was related to their molecular weight and net charge or pI of the analytes. FITC-BSA migrated within 2 min, and the theoretical plate number of the peak reached 480,000 plates/m. Furthermore, proteins with a wide range of pI values and molecular weights migrated within 1 min using the microchip.