Microfluidic Polymerase Chain Reaction Device Research Articles

Miniaturized and IoT Enabled Continuous-Flow-Based Microfluidic PCR Device for DNA Amplification.

Herein, a continuous-flow driven microfluidic device has been designed and fabricated using the CO2 laser ablation method for polymerase chain reaction (PCR). The device consists of a polymethyl methacrylate (PMMA) microfluidic channel with 30 serpentine thermal cycles, an arduino board, two custom-made cartridge heaters, and thermocouple sensors. The portable thermal management system, with aluminium blocks placed on a wooden substrate, working on the PID controller principle, is low-cost, battery-powered, automated, integrated, and IoT-enabled. The device with dimensions 80×72×36 mm3 (L × W × H) has a temperature accuracy of ±0.2 °C. The IoT module enables accessing and storage of real-time temperature values directly onto the smartphone through ThingSpeak analytics. It was developed to achieve desirable accurate temperature at two thermal zones, denaturation and annealing (95 °C and 60 °C) on the microfluidic thermal management platform. A PCR mixture of [Formula: see text] was infused into the serpentine-based microchannel using a syringe pump. Amplification of DNA template with 594-base pair (bp) fragment of the rat GAPDH gene was successfully performed on the miniaturized thermal management system. The total time required for a complete PCR reaction was 32 min at an optimum flow rate of [Formula: see text]/min. The amplified sample of the target DNA obtained from the PCR microchannel was then separated by agarose gel electrophoresis and was further analyzed using a gel-doc system. Finally, the obtained results were compared to the conventional PCR instrument showing excellent performance.

Plasmonic and label-free real-time quantitative PCR for point-of-care diagnostics.

In response to the world's medical community's need for accurate and immediate infectious pathogen detection, many researchers have focused on adapting the standard molecular diagnostic method of polymerase chain reaction (PCR) for point-of-care (POC) applications. PCR technology is not without its shortcomings; current platforms can be bulky, slow, and power-intensive. Although there have been some advances in microfluidic PCR devices, a simple-to-operate and fabricate PCR device is still lacking. In the first part of this paper, we introduce a compact plasmonic PCR thermocycler in which fast DNA amplification is derived from efficient photothermal heating of a colloidal reaction mixture containing gold nanorods (AuNRs) using a small-scale vertical-cavity surface-emitting laser (VCSEL). Using this method, we demonstrate 30 cycle-assay time of sub-ten minutes for successful Chlamydia trachomatis DNA amplification in 20 μL total PCR sample volume. In the second part, we report an ultrasensitive real-time amplicon detection strategy which is based on cycle-by-cycle monitoring of 260 nm absorption of the PCR sample. This was accomplished by irradiating the PCR sample using a UV LED and collecting the transmitted optical power with a photodetector. The UV absorption dependency on the nucleotides' structural degree of freedom gives rise to distinctive features in the shape of UV amplification curves for the determination of PCR results, thus circumventing the need for the complicated design of target-specific probes or intercalating fluorophores. This amplicon quantification method has a high detection sensitivity of one DNA copy. This is the first demonstration of a compact plasmonic thermocycler combined with a real-time fluorophore-free quantitative amplicon detection system. The small footprint of our PCR device stems from hardware miniaturization, while abundant sample volume facilitates highly sensitive detection and fluid handling required for in-field sample analysis, thereby making it an excellent candidate for POC molecular diagnostics.

Miniaturized Thermal Monitoring Module With CO₂ Laser Ablated Microfluidic Device for Electrochemically Validated DNA Amplification

Polymerase chain reaction (PCR) is the gold standard method to amplify deoxyribonucleic acid (DNA) fragments. Several methods have been used to miniaturize and integrate PCR to execute in a microfluidic platform. A continuous-flow-based microfluidic PCR device permits the required rapid thermal cycling and multiplexing, which are hard to realize in a benchtop PCR or microchamber PCR. This work aims to develop a microfluidic PCR platform using a custom-made Internet of Things (IoT)-enabled portable thermal monitoring module. The microfluidic device was fabricated on polymethyl methacrylate (PMMA) using a CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> laser. Apart from 30 serpentine cycles, the PCR microchannel also had initial denaturation and final elongation regions to enhance the overall amplification. As a proof-of-application, rat GAPDH gene, with a fragment size of 594 base pair, has been amplified on the miniaturized platform. Furthermore, the agarose gel electrophoresis technique was used to separate the DNA molecules validated using a gel-doc system. Subsequently, the acquired results were quantitatively compared with the conventional thermocycler using ImageJ software. Furthermore, this was also validated with electrochemical DNA detection using differential pulse voltammetry (DPV). The results from the smart low-power device showed promising performance for the nucleic acid amplification process while reducing the overall amplification time and achieving benchmarked efficiency.

Shunting microfluidic PCR device for rapid bacterial detection

Polymerase chain reaction (PCR) is commonly used for the analysis of nucleic acids in a variety of applications including clinical. There is, however, a need for a low cost portable PCR device that allows rapid identification of pathogenic bacteria. We report a shunting PCR microfluidic device comprising: polycarbonate microfluidic PCR chip; shunting thermal cycler and fluorescence detector. The microfluidic PCR chip – fabricated using micro-milling and thermal fusion bonding for sealing of the cover – was shunted between three double side temperature zones for thermal cycling. Rapid amplification was observed with heating and cooling rates of 1.8 °C/s and 2 °C/s respectively. Lock-in photodetector for fluorescence detection of the microfluidic PCR chip achieved at 95% confidence an LOD of 75pM FITC and 0.7 ng μl−1 of dsDNA using a QuantiFluor assay kit. The device was validated using universal primers - based on chromosomal DNA extracted from non-pathogenic K-12 subtype of Escherichia coli (E. coli) – for amplification of fragments of 250, 552 and 1500 bp. PCR amplification was demonstrated, with annealing temperatures ranging between 54 °C and 68 °C, and confirmed using gel electrophoresis. The developed shunting PCR microfluidic device will allow for low cost and portable nucleic acid amplification for the detection of infectious diseases.

Peanut Detection Using Droplet Microfluidic Polymerase Chain Reaction Device

In this study, we integrated genetic detection for polymerase chain reaction (PCR) with microfluidics technology for the detection of peanut DNA. A cross-junction microchannel was used to induce emulsion droplets of water in oil for PCR on a chip. Compared with the single-phase flow, the emulsion droplet flow exhibited a 7.24% lower evaporation amount and prevented air bubble generation. PCR results of the droplet microfluidic PCR chip for peanut DNA fragment detection was verified by comparison with a commercial PCR thermal cycler and increased fluorescence intensity in SYBR Green reagent-based PCR. Moreover, PCR on the microfluidic PCR chip was successful for sesame, Salmonella spp., and Staphylococcus aureus. The droplet microfluidic PCR device developed in this study can be applied for peanut detection in the context of food allergy.

Bubble-free rapid microfluidic PCR

Microfluidic polymerase chain reaction (PCR) has been of great interest owing to its ability to perform rapid and specific nucleic acid amplification and analysis on small volumes of samples. One of the major drawbacks of microfluidic PCR is bubble generation and reagent evaporation, which can cause malfunctions. Here, through theoretical modeling and characterization of bubble behavior, we propose a bubble-free microfluidic PCR device via controlled fluid transfer. Our approach exploits a thin impermeable polyethylene (PE) top layer that minimizes the generation of bubbles by inhibiting mass transport along a vertical direction. Simulation results demonstrate that a calculated mass flow difference of approximately 370% can be obtained by utilizing an impermeable membrane as the vertical barrier layer. To demonstrate proof-of-concept, two nanoporous polymeric materials, poly(dimethylsiloxane) (PDMS) and PE, were used for stand-alone self-powered sample loading (approximately 70 s) and for use as a vertical barrier layer, respectively. Consequently, we demonstrate successful amplification of the cMET gene, a nucleic acid (NA) biomarker for lung cancer, and complete an ultrafast PCR test in less than 3 min using a high powered Peltier-based thermal cycler under bubble-free conditions. This approach will result in a new paradigm for ultrafast molecular diagnosis and can facilitate NA-based nearly instantaneous diagnostics for point-of-care testing and for personalized and preventive medicine.

Centrifugation-Controlled Thermal Convection and Its Application to Rapid Microfluidic Polymerase Chain Reaction Devices

Here, we report the developed cyclo olefin polymer (COP) microfluidic chip on a fabricated rotating heater stage that utilizes centrifugation-assisted thermal cycle in a ring-structured microchannel for polymerase chain reaction (PCR). The PCR solution could be driven by thermal convection and continuously exchanged high/low temperatures in a ring structured microchannel without the use of typical syringe pump. More importantly, the flow rate was controlled by the relative gravitational acceleration only. The platform enables amplification within 10 min at 5G and has a detection limit of 70.5 pg/channel DNA concentration (β-actin, 295 bp). The current rotating system is capable of testing four different samples in parallel. The microfluidic chip can be preloaded with the PCR premix solution for on-site utility, and, with all of the features integrated to the system, the test can be conducted without the need for specialized laboratory and trained laboratory staff. In addition, this innovative chemical reaction technique has the potential to be utilized in other micromixing applications.

Integration of a microfluidic polymerase chain reaction device and surface plasmon resonance fiber sensor into an inline all-in-one platform for pathogenic bacteria detection

We presented the integration of polymerase chain reaction (PCR) microdevice and surface plasmon resonance (SPR) optical fiber sensor into an inline all-in-one device for fluorophore-free detection of PCR amplification. The proposed integrated device consisted of the microfluidic PCR reactor that used channel position-dependent temperature change and the optical fiber SPR sensor with bimetallic (Ag/Al) coating. This all-in-one device performed not only the amplification of DNA of Salmonella spp. (injected volume of 20 microlitter) within 30min, but also the immediately subsequent measurement of the DNA amplicon by the SPR fiber sensor part.Results showed that the SPR sensor signal increased with the cycle number due to the amplicon refractive index smaller than the sum of its constituent dNTP molecules and its minimum resolvable DNA amplicon was that generated at the 15th cycle. The integrated device could serve as a DNA amplification-to-detection instrument. Both the label-free nature that could allow reusability of the presented device and further miniaturization of the whole system can find use in a point-of-care testing with early diagnosis genetic analysis.

Polymerase chain reaction in microfluidic devices.

The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.

A Prototype Continuous Flow Polymerase Chain Reaction LTCC Device

There is a growing need for remote biological sensing in both laboratory and harsh field environments. Sensing and detection of biological entities such as anthrax, Ebola and other micro-organisms of interest involves sampling of the environment, amplification, analysis and identification of the target DNA. A key component of such a sensor is a low cost, portable, reusable, continuous flow polymerase chain reaction (PCR) thermal cycler. Fabrication with low temperature co-fired ceramics (LTCC) can provide a reusable low cost device capable of operating in a wide range of environments The design and manufacture of a prototype continuous flow micro-fluidic PCR device using low temperature co-fired ceramic is presented. Initial modeling of flow characteristics and heat transfer was carried out in SolidWorks™. The prototype device employs resistance heaters below the channels, buried and surface thermocouples for temperature monitoring, and air gaps for thermal isolation.