Comparison of continuous-flow and static-chamber μPCR devices through a computational study: the potential of flexible polymeric substrates

Papadopoulos, Vasileios; Kokkoris, George; Kefala, Ioanna N.; Tserepi, Angeliki

doi:10.1007/s10404-015-1613-1

Cited by 19 publications

(55 citation statements)

References 35 publications

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“…c) The same PCR protocol and the same number of cycles (10) are considered for both devices. The chosen PCR protocols is 3s:4.2s:6.2s [denaturation (95 o C), annealing (55 o C), and extension (72 o C) step duration, respectively] which allows for the temperature uniformity in the CF device [13,22]. Calculations do not take into account the energy required for pumping, and the energy for preheating and final extension of the PCR mixture.…”

Section: Results and Discussion Of The Computational Studymentioning

confidence: 99%

Miniaturized devices towards an integrated lab-on-a-chip platform for DNA diagnostics

et al. 2015

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Microfluidics is an emerging technology enabling the development of Lab-on-a-chip (LOC) systems for clinical diagnostics, drug discovery and screening, food safety and environmental analysis. LOC systems integrate and scale down one or several laboratory functions on a single chip of a few mm 2 to cm 2 in size, and account for many advantages on biochemical analyses, such as low sample and reagent consumption, low cost, reduced analysis time, portability and point-of-need compatibility. Currently, available nucleic acid diagnostic tests take advantage of Polymerase Chain Reaction (PCR) that allows exponential amplification of portions of nucleic acid sequences that can be used as indicators for the identification of various diseases. Here, we present a comparison between static chamber and continuous flow miniaturized PCR devices, in terms of energy consumption for devices fabricated on the same material stack, with identical sample volume and channel dimensions. The comparison is implemented by a computational study coupling heat transfer in both solid and fluid, mass conservation of species, and joule heating. Based on the conclusions of this study, we develop low-cost and fast DNA amplification devices for both PCR and isothermal amplification, and we implement them in the detection of mutations related to breast cancer. The devices are fabricated by mass production amenable technologies on printed circuit board (PCB) substrates, where copper facilitates the incorporation of on-chip microheaters, defining the thermal zones necessary for PCR or isothermal amplification methods.

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Section: Results and Discussion Of The Computational Studymentioning

confidence: 99%

Miniaturized devices towards an integrated lab-on-a-chip platform for DNA diagnostics

et al. 2015

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“…The mathematical model utilized for the computational study consists of the continuity equation, the momentum conservation equation, the heat transfer equation in both solid and fluid, and the joule heating equations on both devices, coupled with a Proportional-Integral-Derivative (PID) temperature controller for the case of SC device. More details on the devices and the mathematical model can be found in (Papadopoulos et al 2015).…”

Section: Computational Study-simulationsmentioning

confidence: 99%

“…The difference in the energy consumption can be explained by the heat losses to the ambient at each device; the SC device has lower heat losses due to the smaller area in contact to the ambient compared to the CF device (Papadopoulos et al 2015). At low substrate thickness, the constant heat losses at the CF device exceed the energy required for the thermal cycling of the SC device.…”

Section: Computational Study-simulationsmentioning

confidence: 99%

“…To guide our device design, SC and CF μ-PCR devices fabricated on polymeric substrates with integrated microheaters are simulated. Comparison is made in terms of energy consumption of devices fabricated on the same material stack, with identical sample volume and channel dimensions, and is implemented by a computational study coupling heat transfer in both solid and fluid, mass conservation of species, and joule heating (Papadopoulos et al 2015). The pros and cons of each configuration are compared and discussed and the conclusions drawn are used as a guide for the devices to be realized and implemented for efficient DNA amplification.…”

Section: Introductionmentioning

confidence: 99%

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Miniaturized devices for isothermal DNA amplification addressing DNA diagnostics

et al. 2015

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Microfluidics is an emerging technology enabling the development of Lab-on-a-chip (LOC) systems for clinical diagnostics, drug discovery and screening, food safety and environmental analysis. Currently, available nucleic acid diagnostic tests take advantage of Polymerase Chain Reaction (PCR) that allows exponential amplification of portions of nucleic acid sequences that can be used as indicators for the identification of various diseases. At the same time, isothermal methods for DNA amplification are being developed and are preferred for their simplified protocols and the elimination of thermocycling. Here, we present a low-cost and fast DNA amplification device for isothermal Helicase Dependent Amplification (HDA) implemented in the detection of mutations related to breast cancer as well as the detection of Salmonella pathogens. The device is fabricated by mass production amenable technologies on printed circuit board (PCB) substrates, where copper facilitates the incorporation of on-chip microheaters, defining the thermal zone necessary for isothermal amplification methods.

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“…The PCR kinetics was incorporated into the flow model to obtain the time-dependent concentration profiles of some individual species. Papadopoulos et al [ 22 ] proposed a comparison of the CFPCR and the chamber-type PCR devices through a computational investigation. The implementation of PCR kinetics to evaluate the performance of DNA amplification was shown.…”

Section: Introductionmentioning

confidence: 99%

Analysis of PCR Kinetics inside a Microfluidic DNA Amplification System

Chen

2018

Micromachines

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In order to analyze the DNA amplification numerically with integration of the DNA kinetics, three-dimensional simulations, including flow and thermal fields, and one-dimensional polymerase chain reaction (PCR) kinetics are presented. The simulated results are compared with experimental data that have been applied to the operation of a continuous-flow PCR device. Microchannels fabricated by Micro Electro-Mechanical Systems (MEMS) technologies are shown. Comprehensive simulations of the flow and thermal fields and experiments measuring temperatures during thermal cycling are presented first. The resultant velocity and temperature profiles from the simulations are introduced to the mathematical models of PCR kinetics. Then kinetic equations are utilized to determine the evolution of the species concentrations inside the DNA mixture along the microchannel. The exponential growth of the double-stranded DNA concentration is investigated numerically with the various operational parameters during PCR. Next a 190-bp segment of Bartonella DNA is amplified to evaluate the PCR performance. The trends of the experimental results and numerical data regarding the DNA amplification are similar. The unique architecture built in this study can be applied to a low-cost portable PCR system in the future.

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Comparison of continuous-flow and static-chamber μPCR devices through a computational study: the potential of flexible polymeric substrates

Cited by 19 publications

References 35 publications

Miniaturized devices towards an integrated lab-on-a-chip platform for DNA diagnostics

Miniaturized devices towards an integrated lab-on-a-chip platform for DNA diagnostics

Miniaturized devices for isothermal DNA amplification addressing DNA diagnostics

Analysis of PCR Kinetics inside a Microfluidic DNA Amplification System

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