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

Portable Heating System Based on a Liquid Metal Bath for Rapid PCR

With the outbreak of COVID-19 around the world, rapid and accurate detection of new coronaviruses is the key to stop the transmission of the disease and prevent and control the novel coronavirus, among which polymerase chain reaction (PCR) is the mainstream nucleic acid detection method. A temperature cycling device is the core of the PCR amplification micro-device. The precision of the temperature control and temperature change rate directly affect the efficiency of PCR amplification. This study proposes a new PCR method based on rapid PCR chip optimization of a liquid metal bath, which realizes precise and rapid temperature rise and fall control. We systematically explored the feasibility of using liquid metals with different melting points in the system and proposed a 47 °C bismuth-based liquid metal bath as the heat conduction medium of the system to optimize the system. The heat conduction properties of the thermally conductive silicone oil bath were compared. Compared with the thermally conductive silicone oil bath, thermal cycle efficiency is improved nearly 3 times. The average heating rate of the liquid metal bath is fast, and the temperature control stability is good, which can significantly reduce the hysteresis, and the temperature change curve is more gentle, which can greatly improve the efficiency of PCR amplification. The results of gene amplification using rat DNA as the template and SEC61A as the target also indicate that the system can be successfully used in PCR devices, and the types of PCR containers can be not limited to PCR tubes. Based on the experiment, we proved that the PCR method optimized by the liquid metal bath multi-gene rapid PCR chip can further improve the temperature response speed. It has the advantages of accurate data, fast response speed, low price, safety, and environmental protection and can effectively reduce the time of PCR and improve the application efficiency. As far as we know, this is the first international report on using a liquid metal bath to do rapid-cooling PCR.

Light Energy Conversion Surface with Gold Dendritic Nanoforests/Si Chip for Plasmonic Polymerase Chain Reaction

Surfaces with gold dendritic nanoforests (Au DNFs) on Si chips demonstrate broadband-light absorption. This study is the first to utilize localized surface plasmons of Au DNFs/Si chips for polymerase chain reaction (PCR) applications. A convenient halogen lamp was used as the heating source to illuminate the Au DNFs/Si chip for PCR. A detection target of Salmonella spp. DNA fragments was reproduced in this plasmonic PCR chip system. By semi-quantitation in gel electrophoresis analysis, the plasmonic PCR with 30 cycles and a largely reduced processing time provided results comparable with those of a commercial PCR thermal cycler with 40 cycles in more than 1 h. In the presence of an Au DNFs/Si chip, the plasmonic PCR provides superior results in a short processing time.

Review of Experimental Setups for Plasmonic Photocatalytic Reactions

Plasmonic photocatalytic reactions have been substantially developed. However, the mechanism underlying the enhancement of such reactions is confusing in relevant studies. The plasmonic enhancements of photocatalytic reactions are hard to identify by processing chemically or physically. This review discusses the noteworthy experimental setups or designs for reactors that process various energy transformation paths for enhancing plasmonic photocatalytic reactions. Specially designed experimental setups can help characterize near-field optical responses in inducing plasmons and transformation of light energy. Electrochemical measurements, dark-field imaging, spectral measurements, and matched coupling of wavevectors lead to further understanding of the mechanism underlying plasmonic enhancement. The discussions herein can provide valuable ideas for advanced future studies.

Numerical Investigation of Design and Operating Parameters of Thermal Gradient Continuous-Flow PCR Microreactor Using One Heater

To respond to the dire need for miniaturization and process simplification of continuous-flow PCR (CF-PCR) device, this paper represents design and operation guide of a novel metal alloy assisted hybrid microdevice (polydimethylsiloxane (PDMS) and glass) for CF-PCR employing one heater. In this research, the specific objectives are to determine whether one heater chip design will be flexible enough when the size of DNA base pair is varied and to investigate whether one heater CF-PCR device will be able to resolve the longstanding problem of thermal crosstalk. Furthermore, the parametric study is performed to determine which of the fourteen parameters have the greatest impact on the performance of one heater CF-PCR device. The main objective of this parametric study is to distinguish between the parameters that are either critical to the chip performance or can be freely specified. It is found that substrate thickness, flow rate, channel spacing, aspect ratio, channel pass length and external heat transfer coefficient are the most limiting parameters that can either improve or deteriorate the chip’s thermal performance. Overall, the impact of design and operating parameters are observed to be least on thermocycling profile at low Reynolds number (≤0.37 Re). However, in addition to the primary metric advantages of CF-PCR, one heater chip design helps in minimizing the thermal crosstalk effects by a factor of 4 in comparison to dual heater PCR while still maintaining a critical criteria of chip flexibility in terms of handling various sizes of DNA fragments. Hence, the proposed scheme paves the way for low-cost point-of-care diagnostics, system integration, and device miniaturization, realizing a portable microfluidic device applicable for on-site and direct field uses.

Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology

Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.

Fabrication of 3D continuous-flow reverse-transcription polymerase chain reaction microdevice integrated with on-chip fluorescence detection for semi-quantitative assessment of gene expression

We fabricate a three-dimensional (3D) microdevice operated with minimal peripheral accessories, including a portable pump for semi-automated sample delivery and a single heater for temperature control, for performing reverse transcription polymerase chain reaction (RT-PCR) integrated with a downstream fluorescence detection module for semi-quantitative assessment of gene expression. The microdevice was fabricated by wrapping a polytetrafluoroethylene (PTFE) tube around a pre-designed polycarbonate mold to create a seamless microchannel for both the reverse transcription (RT) of RNA and the amplification of complementary DNA. In addition, a silicone tube, which underwent a two-step surface modification mediated by polyethyleneimine and glutaraldehyde coating, was connected at the outlet to capture amplicons downstream of the PTFE tube for on-site fluorescence detection. This fabrication method enabled continuous-flow RT-PCR (CF RT-PCR) using the 3D CF RT-PCR microdevice as a reactor, a single heater for the temperature control of both RT and PCR processes, and a disposable plastic syringe for semi-automated sample delivery. The microdevice was successfully implemented for the identification of the β-actin gene, a constitutively expressed gene in all cells, and the sphingosine-1-phosphate lyase 1 gene, a potential pharmacological target gene in the diagnosis of cancer, diabetes, and atherosclerosis. This portable integrated microdevice offers a potential approach towards preliminary studies of gene expression and identification of RNA viruses.

Sequence-specific sepsis-related DNA capture and fluorescent labeling in monoliths prepared by single-step photopolymerization in microfluidic devices

Fast determination of antibiotic resistance is crucial in selecting appropriate treatment for sepsis patients, but current methods based on culture are time consuming. We are developing a microfluidic platform with a monolithic column modified with oligonucleotides designed for sequence-specific capture of target DNA related to the Klebsiella pneumoniae carbapenemase (KPC) gene. We developed a novel single-step monolith fabrication method with an acrydite-modified capture oligonucleotide in the polymerization mixture, enabling fast monolith preparation in a microfluidic channel using UV photopolymerization. These prepared columns had a threefold higher capacity compared to monoliths prepared in a multistep process involving Schiff-base DNA attachment. Conditions for denaturing, capture and fluorescence labeling using hybridization probes were optimized with synthetic 90-mer oligonucleotides. These procedures were applied for extraction of a PCR amplicon from the KPC antibiotic resistance gene in bacterial lysate obtained from a blood sample spiked with E. coli. The results showed similar eluted peak areas for KPC amplicon extracted from either hybridization buffer or bacterial lysate. Selective extraction of the KPC DNA was verified by real time PCR on eluted fractions. These results show great promise for application in an integrated microfluidic diagnostic system that combines upstream blood sample preparation and downstream single-molecule counting detection.

Analysis of PCR Kinetics inside a Microfluidic DNA Amplification System

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.

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.