Amplification of Escherichia coli in a Continuous-Flow-PCR Microfluidic Chip and Its Detection with a Capillary Electrophoresis System

Summary

This protocol describes how to build a continuous-flow-polymerase chain system based on a microfluidic chip and how to build a capillary electrophoresis system in the lab. It presents a simple method for the analysis of nucleic acids in the lab.

Abstract

Polymerase chain reaction (PCR) is a traditional method employed for the amplification of a target gene that has played an important role in biomolecular diagnostics. However, traditional PCR is very time-consuming because of the low-temperature variation efficiency. This work proposes a continuous-flow-PCR (CF-PCR) system based on a microfluidic chip. The amplification time can be greatly reduced by running the PCR solution into a microchannel placed on heaters set at different temperatures. Moreover, as capillary electrophoresis (CE) is an ideal way to differentiate positive and false-positive PCR products, a CE system was built to achieve efficient separation of the DNA fragments. This paper describes the process of amplification of Escherichia coli (E. coli) by the CF-PCR system built in-house and the detection of the PCR products by CE. The results demonstrate that the target gene of E. coli was successfully amplified within 10 min, indicating that these two systems can be used for the rapid amplification and detection of nucleic acids.

Introduction

Polymerase chain reaction (PCR) is a molecular biology technique used to amplify specific DNA fragments, thereby amplifying trace amounts of DNA hundreds of millions of times. It has been widely used in clinical diagnosis, medical research, food safety, forensic identification, and other fields. The PCR process mainly consists of three steps: denaturation at 90-95 °C, annealing at 50-60 °C, and extension at 72-77 °C. Thermal cycling is an important part of the PCR process; however, the traditional PCR thermal cycler is not only bulky but also inefficient, requiring approximately 40 min to complete 25 cycles. To overcome these limitations, a continuous-f....

Protocol

NOTE: See the Table of Materials for details related to all materials, reagents, and equipment used in this protocol.

1. Fabrication of CF-PCR microfluidic chip

1. Heat the silicon wafer at 200 °C for 25 min to remove the moisture.
2. Dispense 1 mL of SU-8-2075 photoresist per inch of the wafer. Spin it on the silicon wafer using a spin coater at 500 rpm for 5-10 s with an acceleration of 100 rpm/s, and then at 2,000 rpm for 30 s with an acceleration of 500 rpm/s.
3. Soft bake the silicon wafer at 65 °C for 3 min, then at 95 °C for 15 min.
4. Set 150 - 21....

Results

Figure 5 represents the electropherogram of the PCR products and the DNA markers. Trace (Figure 5A) is the CE result of the CF-PCR amplified product, trace (Figure 5B) is the CE result of the product amplified by thermal cycling, and trace (Figure 5C) is the CE result of the 100 bp DNA ladder. We first amplified the target gene of E. coli in the CF-PCR system; the PCR solution took ~10 min.......

Discussion

Both PCR and CE are two popular biotechnologies in the analysis of nucleic acids. This paper describes the amplification of E. coli and the detection of the PCR products using the CF-PCR and CE systems, both built in-house. The target gene of E. coli was successfully amplified within 10 min because of the high heat transfer rates. The DNA fragments smaller than 1,500 bp were separated within 8 min (Figure 5). The great advantage of these two techniques is that it can greatl.......

Materials

Name	Company	Catalog Number	Comments
100 bp DNA ladder	Takara Bio Inc.	3422A
10x Fast Buffer I	Takara Bio Inc.	RR070A
10x TBE	Beijing Solarbio Science & Technology Co., Ltd.	T1051
developer solution	Alfa Aesar, USA	L15459
dNTP mixture (2.5 μM)	Takara Bio Inc.	RR070A
EC-F	Sangon Biotech, Shanghai, China
EC-R	Sangon Biotech, Shanghai, China
HEC,1300K	Sigma-Aldrich, USA	9004-62-0
isopropanol	Aladdin, Shanghai, China	67-63-0
microscope	Olympus, Japan	BX51
photolithography	SUSS MicroTec, Germany	MJB4
photomultiplier tube	Hamamatsu Photonics, Japan	R928
photoresist	MicroChem, USA	SU-8 2075
PID temperature controllers	Shanghai, China	XH-W2023
plasma cleaner	Harrick Plasma	PDC-32G-2
polyvinyl pyrrolidone (PVP)	Aladdin, Shanghai, China	P110608
pump	Harvard Apparatus	PHD2000
silicone tubing	BIO-RAD,USA	7318210
solid-state relays	KZLTD, China	KS1-25LA
SpeedSTAR HS DNA Polymerase	Takara Bio Inc.	RR070A
steel needle	zhongxinqiheng,Suzhou,China
SYBR GREEN	Solarbio, Beijing, China	SY1020
temperature sensors	EasyShining Technology, Chengdu, China	TCM-M207
Template (E. coli)	Takara Bio Inc.	AK601
Tween 20	Aladdin, Shanghai, China	T104863
voltage power supply	Medina, NY, USA	TREK MODEL 610E