Real-time PCR array chip with capillary-driven sample loading and reactor sealing for point-of-care applications

A major challenge for the lab-on-a-chip (LOC) community is to develop point-of-care diagnostic chips that do not use instruments. Such instruments include pumping or liquid handling devices for distribution of patient’s nucleic-acid test sample among an array of reactors and microvalves or mechanical parts to seal these reactors. In this paper, we report the development of a primer pair pre-loaded PCR array chip, in which the loading of the PCR mixture into an array of reactors and subsequent sealing of the reactors were realized by a novel capillary-based microfluidics with a manual two-step pipetting operations. The chip is capable of performing simultaneous (parallel) analyses of multiple gene targets and its performance was tested by amplifying twelve different gene targets against cDNA template from human hepatocellular carcinoma using SYBR Green I fluorescent dye. The versatility and reproducibility of the PCR-array chip are demonstrated by real-time PCR amplification of the BNI-1 fragment of SARS cDNA cloned in a plasmid vector. The reactor-to-reactor diffusion of the pre-loaded primer pairs in the chip is investigated to eliminate the possibility of primer cross-contamination. Key technical issues such as PCR mixture loss in gas-permeable PDMS chip layer and bubble generation due to different PDMS-glass bonding methods are investigated.     

DNA Analysis in Microfabricated Formats

The use of microfabricated DNA analysis tools utilizing microfluidics will provide the next generation of inexpensive DNA diagnostics. It will also provide methodologies to measure gene expression in a massively parallel manner, eventually providing the methodologies to measure most or all the human genes of significance on a single chip. These technologies, including PCR analysis, electrophoresis and gene chips are described using examples from the archival literature. This revised version was published online in July 2006 with corrections to the Cover Date.     

DNA chips: a new tool for genetic analysis and diagnostics.

DNA chips are miniaturized microsystems based on the ability of DNA to spontaneously find and bind its complementary sequence in a highly specific and reversible manner, known as hybridization. Labeled DNA molecules in a sample are analyzed by DNA probes tethered at distinct sites on a solid support. The composition of the DNA sample is then deduced by analyzing the signal generated by labels present at each probe site. Applications are widespread: fundamental research, cancer or microbiology diagnostics, genotyping, gene expression, pharmacogenomics, and environmental control. Medical application consists, for example, in the identification and detection of mutations in genes responsible for cancers, or DNA chip analysis of individual polymorphisms which may provide a guide towards the most efficient treatment. In the environmental and agro-industrial fields, DNA chips show great promise in rapidly testing microorganism content, contamination or pathogenicity. DNA chip dimensions offer hybridization sites in the 50-200 micron range, producing arrays ranging from 100 to 1,000,000 different probes per cm2.     

Molecular genotyping: development and limits]

Kits dedicated to molecular genotyping are now commercially available and are routinely used for diagnosis purpose. In the future these kits that use the classical reverse dot-blot approach will be replaced by micro-arrays, DNA chips and Labs on a chip. Some systems and DNA chips designed for medical diagnosis are already available. The present main problem is their very high cost.     

Integrated polymerase chain reaction chips utilizing digital microfluidics

This study reports an integrated microfluidic chip for polymerase chain reaction (PCR) applications utilizing digital microfluidic chip (DMC) technology. Several crucial procedures including sample transportation, mixing, and DNA amplification were performed on the integrated chip using electro-wetting-on-dielectric (EWOD) effect. An innovative concept of hydrophobic/hydrophilic structure has been successfully demonstrated to integrate the DMC chip with the on-chip PCR device. Sample droplets were generated, transported and mixed by the EWOD-actuation. Then the mixture droplets were transported to a PCR chamber by utilizing the hydrophilic/hydrophobic interface to generate required surface tension gradient. A micro temperature sensor and two micro heaters inside the PCR chamber along with a controller were used to form a micro temperature control module, which could perform precise PCR thermal cycling for DNA amplification. In order to demonstrate the performance of the integrated DMC/PCR chips, a detection gene for Dengue II virus was successfully amplified and detected. The new integrated DMC/PCR chips only required an operation voltage of 12V_RMS at a frequency of 3 KHz for digital microfluidic actuation and 9V_DC for thermal cycling. When compared to its large-scale counterparts for DNA amplification, the developed system consumed less sample and reagent and could reduce the detection time. The developed chips successfully demonstrated the feasibility of Lab-On-a-Chip (LOC) by utilizing EWOD-based digital microfluidics.     

A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification

Inexpensive, portable, and easy-to-use devices for rapid detection of microbial pathogens are needed to ensure safety of water and food. In this study, a disposable polymer microfluidic chip for quantitative detection of multiple pathogens using isothermal nucleic acid amplification was developed. The chip contains an array of 15 interconnected reaction wells with dehydrated primers for loop-mediated isothermal amplification (LAMP), and requires only a single pipetting step for dispensing of sample. To improve robustness of loading and amplification, hydrophobic air vents and microvalves were monolithically integrated in the multi-layered structure of the chip using an inexpensive knife plotter. For quantification, LAMP was performed with a highly fluorescent DNA binding dye (SYTO-82) and the reactions monitored in real-time using a low-cost fluorescence imaging system previously developed by our group (Ahmad et al., Biomed. Microdevices 13(5), 929-937). Starting from genomic DNA mixtures, the chip was successfully evaluated for rapid analysis of multiple virulence and marker genes of Salmonella, Campylobacter jejuni, Shigella, and Vibrio cholerae, enabling detection and quantification of 10-100 genomes per μl in less than 20 min. It is anticipated that the microfluidic chip, along with the real-time imaging system, may be a key enabling technology for developing inexpensive and portable systems for on-site screening of multiple pathogens relevant to food and water safety.     

Securing interoperability between chip card based medical information systems and health networks.

Health information systems supporting shared care are going to be distributed and interoperable. Dealing with sensitive personal medical information, such information systems have to provide appropriate security services, allowing only authorised users restricted access rights to the patients' data according to the 'need to know' principle. Especially in healthcare, chip card based information systems occur in the shape of patient data cards providing informational self determination and mobility of the users as well as quality, integrity, accountability, and availability of the data stored on the card, thus improving the shared care of patients. The DIABCARD project aims at the implementation and evaluation of a chip card based medical information system (CCMIS) for facilitating communication and co-operation between health professionals in different organisations or departments caring the same patient with diabetes as an example. In co-operation with the EC-funded TrustHealth(2) project, communication and application security services needed are provided like strong authentication as well as the derived services such as authorisation, access control, accountability, confidentiality, etc. The solution is based on Health Professional Cards and Trusted Third Party services. In addition to the secure handling of the patient's chip card and data in DIABCARD workstations, the secure communication between these workstations and related departmental systems has been implemented. Based on the results of this feasibility study, an enhanced security services specification for the DIABCARD example of a CCMIS is provided which will be implemented in the framework of a health network being established in the German federal state Bavaria. Beside the preferred solution of a combination of Patient Identification Card and Patient Data Card, lower level alternatives using card-verifiable certificates are explained in some details. Finally, a few legal issues, future trends like the XML standard set and their implications for the solution presented as well as for distributed health information systems in general are shortly discussed.     

A Rapid Processing Technology of Water Quality Microfluidic Chip

In this study,a unique rapid processing technology for microfluidic chips made of polymethylmethacrylate(PMMA) was realized.The common laser engraving machine is used to etch the chip reaction unit and microchannel,and the printing chip is what you see is what you get;the pressurized heat sealing technology is used to quickly complete the chip sealing and packaging;the metal electrodes and lines that need to be laid are embedded into the chip by hot melting;the contact points on the fixed base of the contact chip card are used to connect with the external equipment,so as to make the bearing sample react,detect and complex lines and chips.It is self-contained and isolated from the external equipment circuit.The chip becomes disposable and can be replaced quickly and conveniently.The chip processed by this technology has rapid,cheap and convenient improvement and innovation,which makes the production of microfluidic chip easier and more practical,and even makes the chip a disposable consumable with general interface,which will greatly promote the industrialization of microfluidic chip,and has market-oriented promotion value in the field of water quality and food detection.     

Development and Characterization of Microfluidic Devices and Systems for Magnetic Bead-Based Biochemical Detection

This paper presents the development and characterization of a generic microfluidic system for magnetic bead-based biochemical detection. Microfluidic and electrochemical detection devices such as microvalves, flow sensors, biofilters, and immunosensors have been successfully developed and individually characterized in this work. Magnetically driven microvalves, pulsed-mode microflow sensors, magnetic particle separators as biofilters, and electrochemical immunosensors have been sep-arately fabricated and tested. The fabricated microfluidic components have been surface-mounted on the microfluidic motherboard for fully integrated microfluidic biochemical detection system. A magnetic bio-bead approach has been adopted for both sampling and manipulating target biological molecules. Magnetic beads were used as both substrate of antibodies and carriers of target antigens for magnetic bead-based immunoassay, which was chosen as a proof-of-concept for the generic microfluidic bio-chemical detection system. The microfluidic and electrochemical immunosensing experiment results obtained from this work have shown that the biochemical sensing capability of the complete microfluidic subsystem is suitable for portable biochemical detection of bio-molecules. The methodology and system, which has been developed in this work, can be extended to generic bio-molecule detection and analysis systems by replacing antibody/antigen with appropriate bio receptors/reagents such as DNA fragments or oligonucleotides for application towards DNA analysis and/or high throughput protein analysis.     

A multilevel Lab on chip platform for DNA analysis

Lab-on-chips (LOCs) are critical systems that have been introduced to speed up and reduce the cost of traditional, laborious and extensive analyses in biological and biomedical fields. These ambitious and challenging issues ask for multi-disciplinary competences that range from engineering to biology. Starting from the aim to integrate microarray technology and microfluidic devices, a complex multilevel analysis platform has been designed, fabricated and tested (All rights reserved—IT Patent number TO2009A000915). This LOC successfully manages to interface microfluidic channels with standard DNA microarray glass slides, in order to implement a complete biological protocol. Typical Micro Electro Mechanical Systems (MEMS) materials and process technologies were employed. A silicon/glass microfluidic chip and a Polydimethylsiloxane (PDMS) reaction chamber were fabricated and interfaced with a standard microarray glass slide. In order to have a high disposable system all micro-elements were passive and an external apparatus provided fluidic driving and thermal control. The major microfluidic and handling problems were investigated and innovative solutions were found. Finally, an entirely automated DNA hybridization protocol was successfully tested with a significant reduction in analysis time and reagent consumption with respect to a conventional protocol.     

Automatic microfluidic platform for cell separation and nucleus collection

This study reports a new biochip capable of cell separation and nucleus collection utilizing dielectrophoresis (DEP) forces in a microfluidic system comprising of micropumps and microvalves, operating in an automatic format. DEP forces operated at a low voltage (15 V_p–p) and at a specific frequency (16 MHz) can be used to separate cells in a continuous flow, which can be subsequently collected. In order to transport the cell samples continuously, a serpentine-shape (S-shape) pneumatic micropump device was constructed onto the chip device to drive the samples flow through the microchannel, which was activated by the pressurized air injection. The mixed cell samples were first injected into an inlet reservoir and driven through the DEP electrodes to separate specific samples. Finally, separated cell samples were collected individually in two outlet reservoirs controlled by microvalves. With the same operation principle, the nucleus of the specific cells can be collected after the cell lysis procedure. The pumping rate of the micropump was measured to be 39.8 μl/min at a pressure of 25 psi and a driving frequency of 28 Hz. For the cell separation process, the initial flow rate was 3 μl/min provided by the micropump. A throughput of 240 cells/min can be obtained by using the developed device. The DEP electrode array, microchannels, micropumps and microvalves are integrated on a microfluidic chip using micro-electro-mechanical-systems (MEMS) technology to perform several crucial procedures including cell transportation, separation and collection. The dimensions of the integrated chip device were measured to be 6 × 7 cm. By integrating an S-shape pump and pneumatic microvalves, different cells are automatically transported in the microchannel, separated by the DEP forces, and finally sorted to specific chambers. Experimental data show that viable and non-viable cells (human lung cancer cell, A549-luc-C8) can be successfully separated and collected using the developed microfluidic platform. The separation accuracy, depending on the DEP operating mode used, of the viable and non-viable cells are measured to be 84 and 81%, respectively. In addition, after cell lysis, the nucleus can be also collected using a similar scheme. The developed automatic microfluidic platform is useful for extracting nuclear proteins from living cells. The extracted nuclear proteins are ready for nuclear binding assays or the study of nuclear proteins.     

Microfabrication Technology for the Production of Capillary Array Electrophoresis Chips

Improvements in the fabrication, sample handling and electrical addressing of capillary array electrophoresis (CAE) chips have permitted the development of high density, high-throughput devices capable of analyzing 48 samples in about 20 minutes. The fabrication of high density capillary arrays on 10 cm diameter substrates required the characterization of glasses that yield high quality etches and the development of improved sacrificial etch masks. Using these improved fabrication techniques, high-quality, deep channel etches are routinely obtained. Methods for bonding large area substrates and for drilling arrays of 100 or more access holes have also been developed. For easier sample introduction, we use an array of sample wells fabricated from an elastomeric sheet. The practicality of these technologies is demonstrated through the analysis of 12 DNA samples in parallel on a microfabricated CAE chip, the development of methods for injecting multiple samples onto a single capillary without cross contamination, and the operation of a microfabricated array of 12 capillaries with 4 sample injections per capillary that can analyze 48 samples.     

氧化还原电解脱保护DNA在片合成新方法的探讨

DNA芯片是一种新的高通量DNA分析检测技术。DNA芯片把大量已知序列探针集成在基片上 ,通过与标记的若干靶核苷酸序列杂交 ,可以对生物细胞或组织中大量的基因信息进行检测和分析。DNA芯片的制备方法大致可以分为点样法和在片合成法。本文初步探索了以氧化还原电解脱保护法为特征的电助基因芯片制备方法 ,获得了一些有意义的结果     

32P-Post-labelling method improvements for aromatic compound-related molecular epidemiology studies

The (32)P-post-labelling assay has emerged as a major tool for detecting bulky DNA adducts in subjects exposed to carcinogens, especially aromatic compounds. However, the (32)P-post-labelling protocol still requires the use of high amounts of radioactivity, i.e. 25-50 muCi per sample, an obstacle that limits its use in large studies. The characterization of the DNA adducts measured is also limited. Methodological improvements and increased DNA adduct characterization are necessary to make this assay capable of achieving higher throughput. A new protocol was tested to ensure efficient hydrolysis to reduce the use of radioactive material and to obtain higher chromatography resolution. Different chromatography systems based on high-urea or ammonium hydroxide systems were also employed to characterize the adducts being measured. Improvements were tested by re-analysing DNA adducts in a group of police officers and urban residents in Genoa, Italy. The analysis of carcinogen-modified DNA standards was also included in the study for qualitative and quantitative comparison. An efficient DNA digestion was obtained using a method involving hydrolysis by micrococcal nuclease and a mixture of two spleen phosphodiesterases at fixed concentrations. A 72% reduction of the amount of radioactivity used for labelling was achieved in respect to the non-modified protocol without loss of DNA adduct sensitivity. An improved chromatography resolution was obtained by reducing the volume of sample to be spotted on the chromatogram. Lower volume of spotting sample can decrease sample diffusion and the formation of unresolved spots on the thin-layer chromatography plate. The amount of output produced using a single batch of carrier-free [gamma-(32)P]ATP was increased by about 3.5-fold. A complex pattern of DNA adducts was observed in leukocytes using both high-urea or isopropanol-ammonium hydroxide systems, two techniques effective in the detection of aromatic DNA adducts. The above observations indicate that DNA adducts being measured are likely to have been induced by aromatic compounds.     

基因芯片核心技术及其进展

基因芯片是最近发展起来的一项高通量的基因表达分析技术.就基因芯片核心技术的关键环节及其最新进展作一综述,主要包括:载体(或基片)表面化学修饰,核酸片段制备,基因芯片制备,标记,杂交和芯片扫描分析.全面介绍了目前各个技术环节的工艺要点及其优缺点.指明了需要进一步改进的技术方向,旨在推进这一技术的推广应用.     

A micro circulating PCR chip using a suction-type membrane for fluidic transport

A new micromachined circulating polymerase chain reaction (PCR) chip is reported in this study. A novel liquid transportation mechanism utilizing a suction-type membrane and three microvalves were used to create a new microfluidic control module to rapidly transport the DNA samples and PCR reagents around three bio-reactors operating at three different temperatures. When operating at a membrane actuation frequency of 14.29 Hz and a pressure of 5 psi, the sample flow rate in the microfluidic control module can be as high as 18 μL/s. In addition, an array-type microheater was adopted to improve the temperature uniformity in the reaction chambers. Open-type reaction chambers were designed to facilitate temperature calibration. Experimental data from infrared images showed that the percentage of area inside the reaction chamber with a thermal variation of less than 1°C was over 90% for a denaturing temperature of 94°C. Three array-type heaters and temperature sensors were integrated into this new circulating PCR chip to modulate three specific operating temperatures for the denaturing, annealing, and extension steps of a PCR process. With this approach, the cycle numbers and reaction times of the three separate reaction steps can be individually adjusted. To verify the performance of this circulating PCR chip, a PCR process to amplify a detection gene (150 base pairs) associated with the hepatitis C virus was performed. Experimental results showed that DNA samples with concentrations ranging from 10⁵ to 10²copies/μL can be successfully amplified. Therefore, this new circulating PCR chip may provide a useful platform for genetic identification and molecular diagnosis.     

Polymer-Based Packaging Platform for Hybrid Microfluidic Systems

A polymer-based packaging platform for creating hybrid microfluidic systems is presented. Polydimethylsiloxane (PDMS) is cast into an acrylic mold frame with suspended elements that are removed after curing to form chip cavities, inlet and outlet ports, microchannels, and reservoirs. The packaging approach enables the integration of off-the-shelf components such as pumps and valves with glass microfluidic devices, electronic chips, sample reservoirs, and flow channels. A particle pre-concentration module with a glass capture chip and integrated micropump is shown as an example. A pneumatically driven microfluidic pumping module is also shown. Custom microfluidic interconnects for interfacing to micro-scale fluidic systems are presented. The connectors are capable of withstanding more than 1000 psi and allow microdevices to be rapidly connected to macroscopic devices and systems, without the use of tools.     

An automatic temperature-control system for solutions in free flow

 We describe a temperature-control system for solutions in free flow, suitable for electrophysiological or optical studies of isolated cells, natural epithelia or cell culture monolayers. The system is small enough to be located close to the preparation and was designed specifically to be coupled to the inlets of a modified, continuous-flow Ussing chamber, allowing rapid change of the solutions bathing tissue surfaces. The system consists of a highly compact monoblock heating unit and a control circuit. Solutions from different reservoirs, kept at room temperature or lower (from an ice bath), can be rapidly switched at the inlet of the heating unit by manually or electrically actuated microvalves without affecting the temperature of the fluid leaving the heating unit. The control unit consists of a bead thermistor firmly placed close to the heating unit outlet and an electronic circuit which is basically a proportional controller. This unit continuously regulates the electric current through the Ni-Cr heater, keeping the temperature of the fluid leaving the heating unit constant at a preset value. The system allows control of fluid temperature (normally 37°C) for flow rates in the range of 1.0 ml/min to 12 ml/min. However, the temperature can be set at any value above that of the incoming fluid. Received: 26 May 1998 / Received after revision: 1 September 1998 / Accepted: 14 September 1998