Fabrication and characterization of a PDMS–glass hybrid continuous-flow PCR chip

Recent advances in smart wearable sensors for continuous human health monitoring

In recent years, the biochemical and biological research areas have shown great interest in a smart wearable sensor because of its increasing prevalence and high potential to monitor human health in a non-invasive manner by continuous screening of biomarkers dispersed throughout the biological analytes, as well as real-time diagnostic tools and time-sensitive information compared to conventional hospital-centered system. These smart wearable sensors offer an innovative option for evaluating and investigating human health by incorporating a portion of recent advances in technology and engineering that can enhance real-time point-of-care-testing capabilities. Smart wearable sensors have emerged progressively with a mixture of multiplexed biosensing, microfluidic sampling, and data acquisition systems incorporated with flexible substrate and bodily attachments for enhanced wearability, portability, and reliability. There is a good chance that smart wearable sensors will be relevant to the early detection and diagnosis of disease management and control. Therefore, pioneering smart wearable sensors into reality seems extremely promising despite possible challenges in this cutting-edge technology for a better future in the healthcare domain. This review presents critical viewpoints on recent developments in wearable sensors in the upcoming smart digital health monitoring in real-time scenarios. In addition, there have been proactive discussions in recent years on materials selection, design optimization, efficient fabrication tools, and data processing units, as well as their continuous monitoring and tracking strategy with system-level integration such as internet-of-things, cyber-physical systems, and machine learning algorithms.

Design and fabrication of microfluidics devices for molecular biology applications

In the past decade, microfluidics has emerged as a rapidly growing area with potential to reduce cost and reagent consumption. It has been used for detection of nucleic acids and high-throughput screening of cells and metabolites. It is extensively used for extraction of DNA, RNA, proteins, biomolecules, as well as for cloning and transformation of plasmid into cells. Microfluidics is made up of polydimethylsiloxane (PDMS) polymer which is transparent and is used for preparation of a wide range of devices and systems. In this chapter, we discuss advances and challenges of using microfluidics in molecular biology and its biomedical applications.

Microfluidics based point-of-care for disease diagnostics

Microfluidics platform is widely used for several basic biological to advanced biotechnological applications. It reduces the expenditure of reagent consumption by readily reducing the volume of the reaction system. It is being used for early diagnosis of diseases, detection of pathogens, cancer markers, high-throughput screening and many such applications. Currently, microfluidics and lab-on-chip is integrated together with sample preparation, extraction, analysis and detection of biomarkers for disease diagnosis. This technology offers low-cost, rapid, sensitive and paper-based lateral flow mode of detection which is user-friendly and scalable. In this chapter, we highlight recent developments in microfluidics platform for disease diagnosis.

Thin flexible lab-on-a-film for impedimetric sensing in biomedical applications

Microfluidic cytometers based on coulter principle have recently shown a great potential for point of care biosensors for medical diagnostics. Here, we explore the design of an impedimetric microfluidic cytometer on flexible substrate. Two coplanar microfluidic geometries are compared to highlight the sensitivity of the device to the microelectrode positions relative to the detection volume. We show that the microelectrodes surface area and the geometry of the sensing volume for the cells strongly influence the output response of the sensor. Reducing the sensing volume decreases the pulse width but increases the overall pulse amplitude with an enhanced signal-to-noise ratio (~ max. SNR = 38.78 dB). For the proposed design, the SNR was adequate to enable good detection and differentiation of 10 µm diameter polystyrene beads and leukemia cells (~ 6–21 µm). Also, a systematic approach for irreversible & strong bond strength between the thin flexible surfaces that make up the biochip is explored in this work. We observed the changes in surface wettability due to various methods of surface treatment can be a valuable metric for determining bond strength. We observed permanent bonding between microelectrode defined polypropylene surface and microchannel carved PDMS due to polar/silanol groups formed by plasma treatment and consequent covalent crosslinking by amine groups. These experimental insights provide valuable design guidelines for enhancing the sensitivity of coulter based flexible lab-on-a-chip devices which have a wide range of applications in point of care diagnostics.

An introduction to microfluidics and their applications

In the past decade, microfluidics and lab-on-chip are rapidly growing area. It has been used for number of biology to biotechnology and medicine applications. It has the potential to reduce cost of reagent and time of experiment. It has been used integrated with automation for extraction and detection of protein, nucleic acids, enzymes, metabolites and delivery of drug to target location. It has been used for drug discovery, high throughput screening of potent drug and used for delivery. Paper based microfluidics was used for point-of-care diagnosis for accurate treatment of diseases. In this chapter, we highlight advances of microfluidics devices for number of biological and translational science applications.

Recent findings and applications of biomedical engineering for COVID-19 diagnosis: a critical review

COVID-19 is one of the most severe global health crises that humanity has ever faced. Researchers have restlessly focused on developing solutions for monitoring and tracing the viral culprit, SARS-CoV-2, as vital steps to break the chain of infection. Even though biomedical engineering (BME) is considered a rising field of medical sciences, it has demonstrated its pivotal role in nurturing the maturation of COVID-19 diagnostic technologies. Within a very short period of time, BME research applied to COVID-19 diagnosis has advanced with ever-increasing knowledge and inventions, especially in adapting available virus detection technologies into clinical practice and exploiting the power of interdisciplinary research to design novel diagnostic tools or improve the detection efficiency. To assist the development of BME in COVID-19 diagnosis, this review highlights the most recent diagnostic approaches and evaluates the potential of each research direction in the context of the pandemic.

A Review of Capillary Pressure Control Valves in Microfluidics

Microfluidics offer microenvironments for reagent delivery, handling, mixing, reaction, and detection, but often demand the affiliated equipment for liquid control for these functions. As a helpful tool, the capillary pressure control valve (CPCV) has become popular to avoid using affiliated equipment. Liquid can be handled in a controlled manner by using the bubble pressure effects. In this paper, we analyze and categorize the CPCVs via three determining parameters: surface tension, contact angle, and microchannel shape. Finally, a few application scenarios and impacts of CPCV are listed, which includes how CPVC simplify automation of microfluidic networks, work with other driving modes; make extensive use of microfluidics by open channel, and sampling and delivery with controlled manners. The authors hope this review will help the development and use of the CPCV in microfluidic fields in both research and industry.

A Microfluidic Approach for Biosensing DNA within Forensics

Reducing the risk of (cross-)contamination, improving the chain of custody, providing fast analysis times and options of direct analysis at crime scenes: these requirements within forensic DNA analysis can be met upon using microfluidic devices. To become generally applied in forensics, the most important requirements for microfluidic devices are: analysis time, method of DNA detection and biocompatibility of used materials. In this work an overview is provided about biosensing of DNA, by DNA profiling via standard short tandem repeat (STR) analysis or by next generation sequencing. The material of which a forensic microfluidic device is made is crucial: it should for example not inhibit DNA amplification and its thermal conductivity and optical transparency should be suitable for achieving fast analysis. The characteristics of three materials frequently used materials, i.e., glass, silicon and PDMS, are given, in addition to a promising alternative, viz. cyclic olefin copolymer (COC). New experimental findings are presented about the biocompatibility of COC and the use of COC chips for multiple displacement amplification and real-time monitoring of DNA amplification.

Design and Fabrication of Low-cost Microfluidic Channel for Biomedical Application

This paper presents the design, simulation and low-cost fabrication of microfluidic channel for biomedical application. Channel is fabricated using soft lithography technique. Printed Circuit Board (PCB) is used to make the master for the channel. Channel pattern is transferred on PCB plate using toner transfer technique followed by ferric chloride etching. Paper also discusses, the issues involved in PCB based master fabrication and their viable solutions. Glass is used as substrate material and the channel is made of Sylgard 184 Polydimethylsiloxane (PDMS). Channel is interfaced with a syringe pump to observe the fluid flow. To predict the behavior of the channel, FEM simulation is performed using COMSOL Multiphysics 5.2a. There is a good match between the theoretical, simulation and test results. Finally, to test the biocompatibility of the channel, genomic DNA is passed through the channel and gel electrophoresis analysis is performed.

CO2 Laser Fabrication of PMMA Microfluidic Double T-Junction Device with Modified Inlet-Angle for Cost-Effective PCR Application

The formation of uniform droplets and the control of their size, shape and monodispersity are of utmost importance in droplet-based microfluidic systems. The size of the droplets is precisely tuned by the channel geometry, the surface interfacial tension, the shear force and fluid velocity. In addition, the fabrication technique and selection of materials are essential to reduce the fabrication cost and time. In this paper, for reducing the fabrication cost Polymethyl methacrylate (PMMA) sheet is used with direct write laser technique by VERSA CO₂ laser VLS3.5. This laser writing technique gives minimum channel width of about 160 μm, which limit miniaturizing the droplet. To overcome this, modification on double T-junction (DTJ) channel geometry has been done by modifying the channel inlets angles. First, a two-dimensional (2D) simulation has been done to study the effect of the new channel geometry modification on droplet size, droplets distribution inside the channel, and its throughput. The fabricated modified DTJ gives the minimum droplet diameter of 39±2 μm, while DTJ channel produced droplet diameter of 48±4 μm at the same conditions. Moreover, the modified double T-junction (MDTJ) decreases the variation in droplets diameter at the same flow rates by 4.5–13% than DTJ. This low variation in the droplet diameter is suitable for repeatability of the DNA detection results. The MDTJ also enhanced the droplet generation frequency by 8–25% more than the DTJ channel. The uniformity of droplet distribution inside the channel was enhanced by 3–20% compared to the DTJ channel geometry. This fabrication technique eliminates the need for a photomask and cleanroom environment in addition shortening the cost and time. It takes only 20 min for fabrication. The minimum generated droplet diameter is within 40 μm with more than 1000 droplets per second (at 10 mL/h. oil flow rate). The device is a high-throughput and low-cost micro-droplet formation aimed to be as a front-end to a dynamic droplet digital PCR (ddPCR) platform for use in resource-limited environment.

Thermoelectric Materials—Strategies for Improving Device Performance and Its Medical Applications

Thermoelectrics, in particular solid-state conversion of heat to electricity and vice versa, is expected to be a key energy harvesting and temperature management solution in coming years. There has been a resurgence in the search for new materials for advanced thermoelectric energy conversion applications and to enhance the properties of existing materials. In this paper, we review recent efforts on improving figure-of-merit (ZT) through alloying and nano structuring. As heatsink characteristics dictate the performance of thermoelectric modules, various types of heatsink designs has been investigated. Several reported strategies for improving ZT are critically assessed. A notable increase in figure-of-merit of thermoelectric materials (TE) has opened up new areas of applications especially in the medical field. Peltier cooling devices are widely employed for patient core temperature control, skin cooling, medical device and laboratory equipment cooling. Application of these devices in the medical field both in temperature control and power generation has been studied in detail. It is envisioned that this study will provide profound knowledge on the thermoelectric based materials and its role in medical applications.

Emerging ultrafast nucleic acid amplification technologies for next-generation molecular diagnostics

Over the last decade, nucleic acid amplification tests (NAATs) including polymerase chain reaction (PCR) were an indispensable methodology for diagnosing cancers, viral and bacterial infections owing to their high sensitivity and specificity. Because the NAATs can recognize and discriminate even a few copies of nucleic acid (NA) and species-specific NA sequences, NAATs have become the gold standard in a wide range of applications. However, limitations of NAAT approaches have recently become more apparent by reason of their lengthy run time, large reaction volume, and complex protocol. To meet the current demands of clinicians and biomedical researchers, new NAATs have developed to achieve ultrafast sample-to-answer protocols for the point-of-care testing (POCT). In this review, ultrafast NA-POCT platforms are discussed, outlining their NA amplification principles as well as delineating recent advances in ultrafast NAAT applications. The main focus is to provide an overview of NA-POCT platforms in regard to sample preparation of NA, NA amplification, NA detection process, interpretation of the analysis, and evaluation of the platform design. Increasing importance will be given to innovative, ultrafast amplification methods and tools which incorporate artificial intelligence (AI)-associated data analysis processes and mobile-healthcare networks. The future prospects of NA POCT platforms are promising as they allow absolute quantitation of NA in individuals which is essential to precision medicine.

Micromachining Microchannels on Cyclic Olefin Copolymer (COC) Substrates with the Taguchi Method

Micromilling is a straightforward approach to the manufacture of polymer microfluidic devices for applications in chemistry and biology. This fabrication process reduces costs, provides a relatively simple user interface, and enables the fabrication of complex structures, which makes it ideal for the development of prototypes. In this study, we investigated the influence of micromilling parameters on the surface roughness of a cyclic olefin copolymer (COC) substrate. We then employed factor analysis to determine the optimal cutting conditions. The parameters used in all experiments were the spindle speed, the feed rate, and the depth of cut. Roughness was measured using a stylus profilometer. The lowest roughness was 0.173 μm at a spindle speed of 20,000 rpm, feed rate of 300 mm/min, and cut depth of 20 μm. Factor analysis revealed that the feed rate has the greatest impact on surface quality, whereas the depth of cut has the least impact.

Laser-induced heating integrated with a microfluidic platform for real-time DNA replication and detection

This study developed a microfluidic platform for replicating and detecting DNA in real time by integrating a laser and a microfluidic device composed of polydimethylsiloxane. The design of the microchannels consisted of a laser-heating area and a detection area. An infrared laser was used as the heating source for DNA replication, and the laser power was adjusted to heat the solutions directly. In addition, strong biotin–avidin binding was used to capture and detect the replicated products. The biotin on one end was bound to avidin and anchored to the surface of the microchannels, whereas the biotin on the other end was bound to the quantum dots (Qdots). The results showed that the fluorescent intensity of the Qdots bound to the replicated products in the detection area increased with the number of thermal cycles created by the laser. When the number of thermal cycles was ≥10, the fluorescent intensity of the Qdots was directly detectable on the surface of the microchannels. The proposed method is more sensitive than detection methods entailing gel electrophoresis.

Restraining non-specific adsorption of protein using Parylene C-caulked polydimethylsiloxane

Non-specific adsorption (NSA) of proteins on surface is a critical issue in polydimethylsiloxane (PDMS)-based microfluidics, which may either considerably decrease the efficiency of a continuous flow reaction or cause a large background noise in a heterogeneous sensing. This work introduced a new method to restrain NSA of protein by caulking PDMS with Parylene C, i.e., forming a Parylene C-caulked PDMS (pcPDMS) surface. The caulking depth of Parylene C inside PDMS matrix was characterized by laser scanning confocal microscopy based on a detectable autofluorescence intensity difference between Parylene C and PDMS after being annealed at 270 °C for 2 h in nitrogen. NSA of bovine serum albumin (BSA) on the inner surfaces of PDMS and pcPDMS microchannels was experimentally compared. The results indicated that the adsorbed BSA on the pcPDMS surface were 35.2% of that on the pristine PDMS surface after the BSA solution flowing through the microchannels at a flow rate of 2000 nL/min, a typical scenario of the continuous flow reaction. In a case mimicking the heterogeneous sensing, after a 60 min washing of phosphate buffered saline flow on a pre-saturated BSA adsorbed surface, the residual BSA on the pcPDMS surface was only 4.5% of that on the pristine PDMS surface. Adsorption/desorption coefficients of BSA on the PDMS and the pcPDMS surfaces were extracted from the experimental results based on the first-order Langmuir model, which indicated that the pcPDMS has a lower adsorption coefficient (Ka ) and a higher desorption coefficient (Kd ), compared to those of the pristine PDMS. A preliminary experiment also indicated that Taq polymerase kept 93.0% activity after flowing through a pcPDMS microchannel, while only 28.9% activity was left after passing a pristine PDMS microchannel under the same operation condition.

Simple and Rapid Immobilization of Coating Polymers on Poly(dimethyl siloxane)-glass Hybrid Microchips by a Vacuum-drying Method

A simple and rapid vacuum-drying modification method was applied to several neutral and charged polymers to obtain coating layers for controlling electroosmotic flow (EOF) and suppressing sample adsorption on poly(dimethyl siloxane) (PDMS)-glass hybrid microchips. In the vacuum-dried poly(vinylpyrrolidone) coating, the electroosmotic mobility (μeo) was suppressed from +2.1 to +0.88 × 10(-4) cm(2)/V·s, and the relative standard deviation (RSD) of μeo was improved from 10.2 to 2.5% relative to the bare microchannel. Among several neutral polymers, poly(vinylalcohol) (PVA) and poly(dimethylacrylamide) coatings gave more suppressed and repeatable EOF with RSDs of less than 2.3%. The vacuum-drying method was also applicable to polyanions and polycations to provide accelerated and inversed EOF, respectively, with acceptable RSDs of less than 4.9%. In the microchip electrophoresis (MCE) analysis of bovine serum albumin (BSA) in the vacuum-dried and thermally-treated PVA coating channel, an almost symmetric peak of BSA was obtained, while in the native microchannel a significantly skewed peak was observed. The results demonstrated that the vacuum-dried polymer coatings were effective to control the EOF, and reduced the surface adsorption of proteins in MCE.

The effect of a capillary bridge on the crack opening of a penny crack

Young's relation is based on the equilibrium of horizontal components of surface tensions for a liquid droplet on a "rigid" substrate without addressing the substrate deformation induced by the net vertical component of surface tensions. Upon realizing the importance of wetting in controlling the integrity of flexible structures and electronics, the effect of a capillary bridge or a liquid droplet on the crack opening of a penny crack under the action of a far-field tensile stress is analyzed. Closed-form solutions are derived for both the crack opening and the stress intensity factor, which are functions of the size of the capillary bridge or the droplet, surface tension, and the contact angle. Both the capillary bridge and the droplet can introduce the crack closure. The minimum far-field tensile stresses needed for complete crack opening, i.e. no crack closure, are obtained analytically. The net vertical component of the surface tensions introduces the formation of a surface ridge on the crack face at the edge of the droplet for an open crack. The amplitude of the surface ridge increases with the increase of the net vertical component of the surface tensions and the decrease of the breadth width.

One-heater flow-through polymerase chain reaction device by heat pipes cooling

This study describes a novel microfluidic reactor capable of flow-through polymerase chain reactions (PCR). For one-heater PCR devices in previous studies, comprehensive simulations and experiments for the chip geometry and the heater arrangement were usually needed before the fabrication of the device. In order to improve the flexibility of the one-heater PCR device, two heat pipes with one fan are used to create the requisite temperature regions in our device. With the integration of one heater onto the chip, the high temperature required for the denaturation stage can be generated at the chip center. By arranging the heat pipes on the opposite sides of the chip, the low temperature needed for the annealing stage is easy to regulate. Numerical calculations and thermal measurements have shown that the temperature distribution in the five-temperature-region PCR chip would be suitable for DNA amplification. In order to ensure temperature uniformity at specific reaction regions, the Re of the sample flow is less than 1. When the microchannel width increases and then decreases gradually between the denaturation and annealing regions, the extension region located in the enlarged part of the channel can be observed numerically and experimentally. From the simulations, the residence time at the extension region with the enlarged channel is 4.25 times longer than that without an enlarged channel at a flow rate of 2 μl/min. The treated surfaces of the flow-through microchannel are characterized using the water contact angle, while the effects of the hydrophilicity of the treated polydimethylsiloxane (PDMS) microchannels on PCR efficiency are determined using gel electrophoresis. By increasing the hydrophilicity of the channel surface after immersing the PDMS substrates into Tween 20 (20%) or BSA (1 mg/ml) solutions, efficient amplifications of DNA segments were proved to occur in our chip device. To our knowledge, our group is the first to introduce heat pipes into the cooling module that has been designed for a PCR device. The unique architecture utilized in this flow-through PCR device is well applied to a low-cost PCR system.

Solar thermal polymerase chain reaction for smartphone-assisted molecular diagnostics

Nucleic acid-based diagnostic techniques such as polymerase chain reaction (PCR) are used extensively in medical diagnostics due to their high sensitivity, specificity and quantification capability. In settings with limited infrastructure and unreliable electricity, however, access to such devices is often limited due to the highly specialized and energy-intensive nature of the thermal cycling process required for nucleic acid amplification. Here we integrate solar heating with microfluidics to eliminate thermal cycling power requirements as well as create a simple device infrastructure for PCR. Tests are completed in less than 30 min, and power consumption is reduced to 80 mW, enabling a standard 5.5 Wh iPhone battery to provide 70 h of power to this system. Additionally, we demonstrate a complete sample-to-answer diagnostic strategy by analyzing human skin biopsies infected with Kaposi's Sarcoma herpesvirus (KSHV/HHV-8) through the combination of solar thermal PCR, HotSHOT DNA extraction and smartphone-based fluorescence detection. We believe that exploiting the ubiquity of solar thermal energy as demonstrated here could facilitate broad availability of nucleic acid-based diagnostics in resource-limited areas.

Analytical study of a microfludic DNA amplification chip using water cooling effect

A novel continuous-flow polymerase chain reaction (PCR) chip has been analyzed in our work. Two temperature zones are controlled by two external controllers and the other temperature zone at the chip center is controlled by the flow rate of the fluid inside a channel under the glass chip. By employing a water cooling channel at the chip center, the sequence of denaturation, annealing, and extension can be created due to the forced convection effect. The required annealing temperature of PCR less than 313 K can also be demonstrated in this chip. The Poly(methyl methacrylate) (PMMA) cooling channel with the thin aluminum cover is utilized to enhance the temperature uniformity. The size of this chip is 76 mm × 26 mm × 3 mm. This device represents the first demonstration of water cooling thermocycling within continuous-flow PCR microfluidics. The commercial software CFD-ACE+(TM) is utilized to determine the distances between the heating assemblies within the chip. We investigate the influences of various chip materials, operational parameters of the cooling channel and geometric parameters of the chip on the temperature uniformity on the chip surface. Concerning the temperature uniformity of the working zones and the lowest temperature at the annealing zone, the air gap spacing of 1 mm and the cooling channel thicknesses of 1 mm of the PMMA channel with an aluminum cover are recommended in our design. The hydrophobic surface of the PDMS channel was modified by filling it with 20 % Tween 20 solution and then adding bovine serum albumin (BSA) solution to the PCR mixture. DNA fragments with different lengths (372 bp and 478 bp) are successfully amplified with the device.

Detection of influenza virus using a lateral flow immunoassay for amplified DNA by a microfluidic RT-PCR chip

Influenza virus RNA was amplified by a continuous-flow polydimethylsiloxane microfluidic RT-PCR chip within 15-20 min. The amplified influenza virus RNA was observed with the naked eye, as the red color at the test line, using a lateral flow immunoassay within 1 min.

Highly efficient capillary polymerase chain reaction using an oscillation droplet microreactor

The current work presents the development of a capillary-based oscillation droplet approach to maximize the potential of a continuous-flow polymerase chain reaction (PCR). Through the full utilization of interfacial chemistry, a water-in-oil (w/o) droplet was generated by allowing an oil-water plug to flow along a polytetrafluoroethylene (PTFE) capillary. The w/o droplet functioned as the reactor for oscillating-flow PCR to provide a stable reaction environment, accelerate reagent mixing, and eliminate surface adsorption. The capillary PCR approach proposed in the current research offers high amplification efficiency, fast reaction speed, and easy system control attributable to the oscillation droplet reactor. Experimental results show that the droplet-based micro-PCR assay requires lower reaction volume (2 μL) and shorter reaction time (12 min) compared with conventional PCR methods. Taking the amplification of the New Delhi metallo-beta-lactamase (NDM-1) gene as an example, the present work demonstrates that the oscillation droplet PCR assay is capable of achieving high efficiency up to 89.5% and a detection limit of 10 DNA copies. The miniature PCR protocol developed in the current work is fast, robust, and low-cost, thus exhibiting the potential for expansion into various practical applications.

Solid phase DNA extraction on PDMS and direct amplification

In this paper we report an innovative use of Poly(DiMethyl)Siloxane (PDMS) to design a microfluidic device that combines, for the first time, in one single reaction chamber, DNA purification from a complex biological sample (blood) without elution and PCR without surface passivation agents. This result is achieved by exploiting the spontaneous chemical structure and nanomorphology of the material after casting. The observed surface organization leads to spontaneous DNA adsorption. This property allows on-chip complete protocols of purification of complex biological samples to be performed directly, starting from cells lysis. Amplification by PCR is performed directly on the adsorbed DNA, avoiding the elution process that is normally required by DNA purification protocols. The use of one single microfluidic volume for both DNA purification and amplification dramatically simplifies the structure of microfluidic devices for DNA preparation. X-Ray Photoelectron Spectroscopy (XPS) was used to analyze the surface chemical composition. Atomic Force Microscopy (AFM) and Field Emission Scanning Electron Microscopy (FESEM) were employed to assess the morphological nanostructure of the PDMS-chips. A confocal fluorescence analysis was utilized to check DNA distribution inside the chip.

Long target droplet polymerase chain reaction with a microfluidic device for high-throughput detection of pathogenic bacteria at clinical sensitivity

In this article we present a long target droplet polymerase chain reaction (PCR) microsystem for the amplification of the 16S ribosomal RNA gene. It is used for detecting Gram-positive and Gram-negative pathogens at high-throughput and is optimised for downstream species identification. The miniaturised device consists of three heating plates for denaturation, annealing and extension arranged to form a triangular prism. Around this prism a fluoropolymeric tubing is coiled, which represents the reactor. The source DNA was thermally isolated from bacterial cells without any purification, which proved the robustness of the system. Long target sequences up to 1.3 kbp from Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa have successfully been amplified, which is crucial for the successive species classification with DNA microarrays at high accuracy. In addition to the kilobase amplicon, detection limits down to DNA concentrations equivalent to 10(2) bacterial cells per reaction were achieved, which qualifies the microfluidic device for clinical applications. PCR efficiency could be increased up to 2-fold and the total processing time was accelerated 3-fold in comparison to a conventional thermocycler. Besides this speed-up, the device operates in continuous mode with consecutive droplets, offering a maximal throughput of 80 samples per hour in a single reactor. Therefore we have overcome the trade-off between target length, sensitivity and throughput, existing in present literature. This qualifies the device for the application in species identification by PCR and microarray technology with high sample numbers. Moreover early diagnosis of infectious diseases can be implemented, allowing immediate species specific antibiotic treatment. Finally this can improve patient convalescence significantly.

Ultra-rapid flow-through polymerase chain reaction microfluidics using vapor pressure

A novel flow-through polymerase chain reaction (PCR) microfluidic system using vapor pressure was developed that can achieve ultra-rapid, small-volume DNA amplification on a chip. The 40-cycle amplification can be completed in as little as 120 s, making this device the fastest PCR system in the world. The chip device is made of a pressure-sensitive polyolefin (PSP) film and cyclo-olefin polymer (COP) substrate which was processed by cutting-work to fabricate the microchannel. The enclosed structure of the microchannel was fabricated solely by weighing the PSP film on the COP substrate, resulting in superior practical application. The vapor pressure in the denaturation zone of the destabilizing flow source was applied to the flow force, and ultra-rapid, efficient amplification was accomplished with a minimal amount of PCR reagents for detection. The flowing rhythm created by vapor pressure minimized the residual PCR products, leading to highly efficient amplification. For field test analysis, airborne dust was collected from a public place and tested for the presence of anthrax. The PCR chip had sufficient sensitivity for anthrax identification. The fastest time from aerosol sampling to detection was theoretically estimated as 8 min.

Genetic analysis of H1N1 influenza virus from throat swab samples in a microfluidic system for point-of-care diagnostics

The ability to obtain sequence-specific genetic information about rare target organisms directly from complex biological samples at the point-of-care would transform many areas of biotechnology. Microfluidics technology offers compelling tools for integrating multiple biochemical processes in a single device, but despite significant progress, only limited examples have shown specific, genetic analysis of clinical samples within the context of a fully integrated, portable platform. Herein we present the Magnetic Integrated Microfluidic Electrochemical Detector (MIMED) that integrates sample preparation and electrochemical sensors in a monolithic disposable device to detect RNA-based virus directly from throat swab samples. By combining immunomagnetic target capture, concentration, and purification, reverse-transcriptase polymerase chain reaction (RT-PCR) and single-stranded DNA (ssDNA) generation in the sample preparation chamber, as well as sequence-specific electrochemical DNA detection in the electrochemical cell, we demonstrate the detection of influenza H1N1 in throat swab samples at loads as low as 10 TCID(50), 4 orders of magnitude below the clinical titer for this virus. Given the availability of affinity reagents for a broad range of pathogens, our system offers a general approach for multitarget diagnostics at the point-of-care.

Rapid detection for primary screening of influenza A virus: microfluidic RT-PCR chip and electrochemical DNA sensor

Rapid and definitive diagnosis is critical to the prevention of the spread of endemic human pathogenic viruses. Detection of variant specific genes by reverse transcription polymerase chain reaction (RT-PCR) has become a routine diagnostic test for accurate subtyping of RNA viruses, such as influenza. In this paper, we demonstrate the use of a continuous-flow polydimethylsiloxane (PDMS) microfluidic RT-PCR chip and disposable electrical printed (DEP) chips for rapid amplification and sensing of new influenza (AH1pdm) virus of swine-origin. The RT-PCR chip consisted of four zones: RT reaction zone, initial denaturation zone, thermal cycle zone for PCR (2-step PCR) and pressurizing-channel zone for preventing air-bubble formation. In order to measure electrochemical signals, methylene blue (MB), an electro-active DNA intercalator, was added to the RT-PCR mixture. The RT-PCR was completed within 15 min which was the total flow-through time from the inlet to the outlet, and the reduction signals from amplifications could be detected quickly on the DEP chip. The MB reduction current on the DEP chip with the amplicon significantly reduced compared to non-amplified controls. This microfluidic platform for rapid RT-PCR and the DEP chip for quick electrochemical sensing are suitable for integration, and have the potential to be a portable system for diagnostic tests.

In-gel technology for PCR genotyping and pathogen detection

This work describes the use of polyacrylamide gel and PCR reagents photopolymerized in a mold to create an array of semisolid posts that serve as reaction vessels for parallel PCR amplification of an externally added template. DNA amplification occurred in a cylindrical, self-standing 9 × 9 array of gel posts each less than 1 μL in volume. Photopolymerization of the gel with an intercalating dye added prior to polymerization permitted acquisition of real-time PCR data and melting curve analysis data without the need for any type of post-PCR staining procedures. PCR was equally efficient and reproducible when template DNA was polymerized within the gel or when exogenous template was added atop precast gel posts. PCR amplification occurred with template from purified DNA or from raw urine of patients with BK viruria. Multiple primer sets can be utilized per gel post array with no detectable cross contamination. As few as 34 BK virus templates were consistently detected by PCR in an individual gel post. Amplification of HPA1 and FGFR2 genes in human genomic DNA (gDNA) required as little as 2-5 ng of gDNA template/gel post. The device prototype includes a Peltier element for PCR thermal cycling and a CCD camera to capture fluorescence for product detection. Our technology is amenable to integration in point of care microdevices.

Reduction of water evaporation in polymerase chain reaction microfluidic devices based on oscillating-flow

Producing polymeric or hybrid microfluidic devices operating at high temperatures with reduced or no water evaporation is a challenge for many on-chip applications including polymerase chain reaction (PCR). We study sample evaporation in polymeric and hybrid devices, realized by glass microchannels for avoiding water diffusion toward the elastomer used for chip fabrication. The method dramatically reduces water evaporation in PCR devices that are found to exhibit optimal stability and effective operation under oscillating-flow. This approach maintains the flexibility, ease of fabrication, and low cost of disposable chips, and can be extended to other high-temperature microfluidic biochemical reactors.

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.

Microfluidic DNA amplification--a review

The application of microfluidic devices for DNA amplification has recently been extensively studied. Here, we review the important development of microfluidic polymerase chain reaction (PCR) devices and discuss the underlying physical principles for the optimal design and operation of the device. In particular, we focus on continuous-flow microfluidic PCR on-chip, which can be readily implemented as an integrated function of a micro-total-analysis system. To overcome sample carryover contamination and surface adsorption associated with microfluidic PCR, microdroplet technology has recently been utilized to perform PCR in droplets, which can eliminate the synthesis of short chimeric products, shorten thermal-cycling time, and offers great potential for single DNA molecule and single-cell amplification. The work on chip-based PCR in droplets is highlighted.

Rapid detection of genetically modified organisms on a continuous-flow polymerase chain reaction microfluidics

The ability to perform DNA amplification on a microfluidic device is very appealing. In this study, a compact continuous-flow polymerase chain reaction (PCR) microfluidics was developed for rapid analysis of genetically modified organisms (GMOs) in genetically modified soybeans. The device consists of three pieces of copper and a transparent polytetrafluoroethylene capillary tube embedded in the spiral channel fabricated on the copper. On this device, the P35S and Tnos sequences were successfully amplified within 9min, and the limit of detection of the DNA sample was estimated to be 0.005 ng microl(-1). Furthermore, a duplex continuous-flow PCR was also reported for the detection of the P35S and Tnos sequences in GMOs simultaneously. This method was coupled with the intercalating dye SYBR Green I and the melting curve analysis of the amplified products. Using this method, temperature differences were identified by the specific melting temperature values of two sequences, and the limit of detection of the DNA sample was assessed to be 0.01 ng microl(-1). Therefore, our results demonstrated that the continuous-flow PCR assay could discriminate the GMOs in a cost-saving and less time-consuming way.

Photobleaching absorbed Rhodamine B to improve temperature measurements in PDMS microchannels

Rhodamine B based fluorescence thermometry is commonly used in microfluidics to measure fluid temperatures in microchannels. Notable absorption of Rhodamine B into PDMS channel walls, however, causes difficulties in obtaining accurate temperature measurements due to a steady increase in the overall fluorescent signal. A simple and effective technique is reported that removes the fluorescent signal from absorbed Rhodamine B dye by means of photobleaching with a high intensity light source before taking images for thermometry analysis. The temperature field at the convergence of hot and cold streams in a Y-channel fabricated in PDMS/glass microfluidic chip is studied to demonstrate the execution of the photobleaching technique.

Flow-induced thermal effects on spatial DNA melting

Continuous-flow temperature gradient microfluidics can be used to perform spatial DNA melting analysis. To accurately characterize the melting behavior of PCR amplicon across a spatial temperature gradient, the temperature distribution along the microfluidic channel must be both stable and known. Although temperature change created by micro-flows is often neglected, flow-induced effects can cause significant local variations in the temperature profile within the fluid and the closely surrounding substrate. In this study, microfluidic flow within a substrate with a quasi-linear temperature gradient has been examined experimentally and numerically. Serpentine geometries consisting of 10 mm long channel sections joined with 90 degrees and/or 180 degrees bends were studied. Infrared thermometry was used to characterize the surface temperature variations and a 3-D conjugate heat transfer model was used to predict interior temperatures for multiple device configurations. The thermal interaction between adjacent counter-flow channel sections, which is related to their spacing and substrate material properties, contributes significantly to the temperature profile within the microchannel and substrate. The volumetric flow rate and axial temperature gradient are directly proportional to the thermal variations within the device, while these flow-induced effects are largely independent of the cross-sectional area of the microchannel. The quantitative results and qualitative trends that are presented in this study are applicable to temperature gradient heating systems as well as other microfluidic thermal systems.