Abstract
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.
Highlights
Since the polymerase chain reaction (PCR) was invented in the early 1980s, PCR has become one of the most important techniques in gene analysis, identification of infectious diseases, clinical diagnostics, and so on [1]
A PCR process goes through three major steps: double-stranded deoxyribonucleic acid (DNA) is separated into two single strands at about 95 ◦ C
The microfluidic chip is exposed to one heater and one Peltier element in order to create several temperature regions for PCR
Summary
Since the polymerase chain reaction (PCR) was invented in the early 1980s, PCR has become one of the most important techniques in gene analysis, identification of infectious diseases, clinical diagnostics, and so on [1]. PCR is a procedure that exponentially amplifies a small amount of deoxyribonucleic acid (DNA) fragments into a lot of sample products during several thermal cycles. DNA at about 55 ◦ C during annealing; and DNA strands are extended by a thermostable DNA polymerase at about 72 ◦ C during the extension These steps complete one PCR cycle, and ideally each piece of DNA in the mixture is duplicated. The small-scale thermocycling devices can be categorized into two groups: a chamber type and a continuous-flow type. These devices shorten the PCR reaction time from hours to minutes and have been reported for decades [2]
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