Silicon-glass Chip Research Articles

Convenient two-step method constructed silicon-based microfluidic chip for fast CYP2C19 SNPs detection.

The rapid detection of single nucleotide polymorphisms (SNPs) in the CYP2C19 gene is crucial for precise clopidogrel usage. Quantitative real-time polymerase chain reaction (qPCR), as a powerful amplification tool, has been widely employed for CYP2C19 SNPs detection. However, traditional qPCR suffers from long amplification times and high reagent consumption. To address these challenges, this work presents a microfluidic SNPs detection device based on on-chip qPCR. The device includes a rapid thermal cycling system, an optical detection system, a control system, and a complementary silicon-glass chip for CYP2C19 SNPs detection. Compared to commercial qPCR instruments that take 1 hour for testing, this device completes the test in just 15 minutes (40 PCR cycles). The resulting linearity is similar to that found using commercial qPCR instruments but with higher amplification efficiency. Additionally, compared with other silicon-based qPCR chips, this chip is constructed by using a convenient two-step method and offers low manufacturing costs, which potentially reduces single-test costs to an acceptable level. This makes our chip promising for point-of-care testing (POCT).

Optimization of Structure and Control Technology of Tunnel Magnetoresistive Accelerometer

In this work, an optimized tunnel magnetoresistive (TMR) accelerometer with a closed-loop control system was developed and evaluated. The device first introduces a silicon spring–mass sensing structure lower than 50 Hz into TMR-based accelerometry for enhancing the mechanical sensitivity and subsequent readout sensitivity. Simultaneously, in order to realize the in-plane electrostatic feedback control, the comb structure is designed along with the sensing mechanism, owning combined benefits of integrated processing and large feedback force. The whole sensing structure is a silicon-glass chip, fabricated by the standard micro-electromechanical system (MEMS) process—deep dry silicon on glass (DDSOG) process. A permanent rubber magnet is assembled on the proof mass for conversion from the displacement to variation of the magnetic field intensity, which is further detected by a pair of symmetrically arranged TMR sensors. The voltage signals output from TMR sensors are then sent into an analog circuit via an interface module for force-feedback control. The simulation analysis indicates that the proposed MEMS sensing structure has a low natural frequency of 44.55 Hz, corresponding to a compliant mechanical sensitivity of 125.5 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> /g. Meanwhile, a maximum magnetic sensitivity of about 0.1 mT/mm is available in a height of 6 mm above the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$3\times 3\times0.3$ </tex-math></inline-formula> mm magnet. Finally, the experiments on the assembled prototype demonstrated that a scale factor of 1.79 V/g and a bias stability of 228 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{g}$ </tex-math></inline-formula> have been achieved in the closed-loop modality, which verifies the effectiveness of the proposed TMR MEMS accelerometer.

Creation of micro-and nanochannels on the surface of silicon chips by lithography methods and investigation of ion transport in channel

We developed a technique for fabrication microfluidic silicon-glass chips with a system of nanochannels connecting two microchannel using traditional optical lithography and a focused ion beam. To investigate the transport phenomena in the nanochannels we experimentally studied their ion conductivity and using optical microscopy confirmed the existence of the diffusion flow through them. The developed method allows us to create systems of nanochannels with on-purpose geometry and controlled sizes. Devices with such nanochannels can be applied in the creation of biosensor devices and for genetic studies.

Numerical study of the coupling layer between transducer and chip in acoustofluidic devices.

By numerical simulation in two and three dimensions, the coupling layer between the transducer and microfluidic chip in ultrasound acoustofluidic devices is studied. The model includes the transducer with electrodes, microfluidic chip with a liquid-filled microchannel, and coupling layer between the transducer and chip. Two commonly used coupling materials, solid epoxy glue and viscous glycerol, as well as two commonly used device types, glass capillary tubes and silicon-glass chips, are considered. It is studied how acoustic resonances in ideal devices without a coupling layer are either sustained or attenuated as a coupling layer of increasing thickness is inserted. A simple criterion based on the phase of the acoustic wave for whether a given zero-layer resonance is sustained or attenuated by the addition of a coupling layer is established. Finally, by controlling the thickness and the material, it is shown that the coupling layer can be used as a design component for optimal and robust acoustofluidic resonances.

Multichamber hybrid microfluidic chips for nucleic acids detection by qPCR assay

The efficiency of silicon-glass chips for the nucleic acids analysis with a concentration of 106-102 copies/µl using various algorithms of searching threshold cycles is shown. Hypotheses that explain the observed PCR efficiency decrease for microfluidic chips compared to polymer test tubes are discussed.

Visualization of fracturing fluid dynamics in a nanofluidic chip

Hydraulic fracturing is responsible for remarkable production from shale and tight formations, albeit at the cost of significant water usage. The flow dynamics of oil and fracturing fluid in nanopores remains largely uncharacterized, in part due to the challenge of conducting experiments at nanoscales. In this paper, we demonstrate a nanofluidic-based approach to visualize the fluid displacement during hydraulic fracturing. Nanoporous silicon-glass chips with circular and square grain shapes and identical depth of 175 nm were fabricated using reactive-ion etching (RIE) and anodic bonding. Leveraging the inherent fluorescence property of the oil, the fluorescence microscopy was used to record the dynamics of the fluid displacement inside the chip. Performance of three different fracturing fluids - deionized water, potassium chloride (KCl) solution, and slick water - were evaluated based on the volumetric infiltration in the nanoporous network, entrapment of fracturing fluid in the porous media, and total production during drawdown. The KCl solution had the highest infiltration rate (fill factor of 0.68) and the lowest entrapment factor (0.39), resulting in the highest fracturing fluid recovery representing 43% in the square grain geometry with similar results for circular grains. With the fast quantification and ease of operation here, the nanofluidic approach enables a rapid screening of different fracturing fluids to inform shale oil operators.

A Microfabricated Propofol Trap for Breath-Based Anesthesia Depth Monitoring

This paper reports a golden microtrap chip for anesthetic depth monitoring. The chip selectively captures the propofol (2,6-diisopropylphenol) compound, which is a widely used substance for anesthesia, by filtering out the other species found in human breath. The fabricated silicon-glass chip is 12 mm on each side and consists of an array of high aspect ratio parabolic reflectors inside its 7 mm × 7 mm × 0.24 mm cavity. The interior surfaces of the chip are coated with an electroplated gold layer having a surface roughness of around 6.82 nm, which is an order of magnitude higher than a gold layer deposited by electron (e)-beam evaporation. Uncoated and e-beam gold-coated chips are unable to trap propofol and other compounds found in human breath. In contrast, silicon-glass chips coated with Tenax TA (2,6 diphenylene oxide), a gas adsorbing polymer, captures propofol among other volatiles present in human breath. Only devices coated with an electroplated gold layer demonstrate selective affinity for the target compound propofol. For the same propofol concentration, these golden microtraps show consistent capture efficiency with less than 8% variation in the trapped propofol amount while tested with different human breath samples. These microfabricated chips have the potential to accurately quantify the amount of propofol present in human breath samples without incorporating the gas chromatography column into the testing setup, resulting in faster analysis and reduced cost and complexity.

Parallel Real-Time PCR on a Chip for Genetic Tug-of-War (gTOW) Method

A microchip-based real-time polymerase chain reaction (PCR) device has been developed for the genetic tug-of-war (gTOW) method that provides quantitative data for research on biorobustness and systems biology. The device was constructed of a silicon glass chip, a temperature controlling Peltier element, and a microscope. A parallel real-time amplification process of target genes on the plasmids and the housekeeping genes in a model eukaryote Saccharomyces cerevisiae were detected simultaneously, and the copy number of the target genes were estimated. The device provides unique quantitative data that can be used to augment understanding of the system-level properties of living cells.

Design of a silicon-based plasmonic biosensor chip for human blood-group identification

Surface plasmon resonance based silicon-chip biosensor is proposed for the detection of different human blood groups in near infrared region. The plasmonic structure based on silicon glass chip is suitable for simple and accurate low volume blood-group detection. Experimental results describing the wavelength-dependent refractive index variation of different blood groups are considered for theoretical calculations. The results are explained in terms of light coupling and plasmon resonance condition. The sensor's performance is closely analyzed in terms of its angular shift and curve width in order to predict the design considerations enabling precise blood-group identification. The proposed low-volume blood-group biosensor chip can be very useful in medical application.

Apoptotic cell death dynamics of HL60 cells studied using a microfluidic cell trap device

This paper presents the design, fabrication and first results of a microfluidic cell trap device for analysis of apoptosis. The microfluidic silicon-glass chip enables the immobilization of cells and real-time monitoring of the apoptotic process. Induction of apoptosis, either electric field mediated or chemically induced with tumour necrosis factor (TNF-alpha), in combination with cycloheximide (CHX), was addressed. Exposure of cells to the appropriate fluorescent dyes, FLICA and PI, allows one to discriminate between viable, apoptotic and necrotic cells. The results showed that the onset of apoptosis and the transitions during the course of the cell death cascade were followed in chemically induced apoptotic HL60 cells. For the case of electric field mediated cell death, the distinction between apoptotic and necrotic stage was not clear. This paper presents the first results to analyse programmed cell death dynamics using this apoptosis chip and a first step towards an integrated apoptosis chip for high-throughput drug screening on a single cellular level.

Increased amplification efficiency of microchip-based PCR by dynamic surface passivation.

Surface passivation is critical for effective PCR using silicon-glass chips. We tested a dynamic polymer-based surface passivation method. Polyethylene glycol 8000 (PEG 8000) or polyvinylpyrrolidone 40 (PVP-40) applied at 0.75% (w/v) in the reaction mixture produced significant surface passivation effects using either native or SiO2-precoated silicon-glass chips. PCR amplification was achieved from human genomic DNA as a template as well as from human lymphocytes. The dynamic surface passivation effect of PEG 8000 remained similar under both conditions. Dynamic surface passivation offers a simple and cost-effective method to make microfabricated silicon-glass chips PCR friendly. It can also be used in combination with static passivation (silicon oxide surface layer) to further improve PCR performance using silicon-glass PCR chips.

Degenerate Oligonucleotide Primed–Polymerase Chain Reaction and Capillary Electrophoretic Analysis of Human DNA on Microchip-Based Devices

Random amplification of the human genome using the degenerate oligonucleotide primed–polymerase chain reaction (DOP-PCR) was performed in a silicon–glass chip. An aliquot of the DOP-PCR amplified genomic DNA was then introduced into another silicon–glass chip for a locus-specific, multiplex PCR of the dystrophin gene exons in order to detect deletions causing Duchenne/Becker muscular dystrophy. Amplicons were analyzed by both conventional capillary electrophoresis and microchip electrophoresis and results were compared to those obtained using standard non-chip-based PCR assays. Results from microchip electrophoresis were consistent with those from conventional capillary electrophoresis. Whole genome amplification products obtained by DOP-PCR proved to be a suitable template for multiplex PCR as long as amplicon size was <250 bp. Successful detection and resolution of all PCR products from the multiplex PCR clearly shows the feasibility of performing complex PCR assays using microfabricated devices.

Analysis of ligase chain reaction products amplified in a silicon-glass chip using capillary electrophoresis

Ligase chain reaction (LCR) is a useful molecular technique for detecting known point mutations. We report the first example of the use of a disposable silicon-glass micro-chip for LCR and thefirst application capillary electrophoresis (CE) to analyze samples amplified by LCR in a chip. Silicon-glass chips were manufactured using conventional photolithography and anodic bonding. The chips provide three distinct advantages for LCR: excellent thermal conductivity, a micro reaction volume (<10 μl), and reproducible,, low-cost manufacturing. Investigation and quantitation of amplification efficiency of LCR in a chip or in a tube requires an analytical technique that is faster and more convenient than the conventional slab gel methods. Slab gel electrophoresis uses relatively large amounts of sample and is labor-intensive and time-consuming, and thus is unsuitable for the separation and detection of LCR products. In contrast CE requires sample volumes (original LCR products) of less than 1 μl and is therefore well-suited to analysis of the micro-volume reaction mixture from chips. We combined CE with a sensitive laser induced fluorescence (LIF) detection system for the rapid separation and quantitative detection of LCR products amplified from the lacI gene in a silicon-glass chip. Comparative studies were made with LCR between tubes and silicon-glass chips. CE-LIF analysis is ideally suited to examination of micro-LCR amplification with high thoughput. The technologies may find medical uses in disease diagnosis and research.

Chip PCR. II. Investigation of different PCR amplification systems in microbabricated silicon-glass chips

We examined PCR in silicon dioxide-coated silicon-glass chips (12 microl in volume with a surface to volume ratio of approximately 17.5 mm(2)/microl) using two PCR reagent systems: (i) the conventional reagent system using Taq DNA polymerase; (ii) the hot-start reagent system based on a mixture of TaqStart antibody and Taq DNA polymerase. Quantitative results obtained from capillary electrophoresis for the expected amplification products showed that amplification in microchips was reproducible (between batch coefficient of variation 7.71%) and provided excellent yields. We also used the chip for PCR directly from isolated intact human lymphocytes. The amplification results were comparable with those obtained using extracted human genomic DNA. This investigation is fundamental to the integration of sample preparation, polynucleotide amplification and amplicate detection on a microchip.

Chip PCR. I. Surface passivation of microfabricated silicon-glass chips for PCR

The microreaction volumes of PCR chips (a microfabricated silicon chip bonded to a piece of flat glass to form a PCR reaction chamber) create a relatively high surface to volume ratio that increases the significance of the surface chemistry in the polymerase chain reaction (PCR). We investigated several surface passivations in an attempt to identify 'PCR friendly' surfaces and used those surfaces to obtain amplifications comparable with those obtained in conventional PCR amplification systems using polyethylene tubes. Surface passivations by a silanization procedure followed by a coating of a selected protein or polynucleotide and the deposition of a nitride or oxide layer onto the silicon surface were investigated. Native silicon was found to be an inhibitor of PCR and amplification in an untreated PCR chip (i.e. native slicon) had a high failure rate. A silicon nitride (Si(3)N(4) reaction surface also resulted in consistent inhibition of PCR. Passivating the PCR chip using a silanizing agent followed by a polymer treatment resulted in good amplification. However, amplification yields were inconsistent and were not always comparable with PCR in a conventional tube. An oxidized silicon (SiO(2) surface gave consistent amplifications comparable with reactions performed in a conventional PCR tube.

Micromachining: A new direction for clinical analyzers

Abstract