Functional Nucleic Acid Based Biosensors for Food Safety Detection

360 Pages·2018·15.64 MB·English

by  Yunbo Luo

Yunbo Luo
Functional Nucleic
Acid Based
Biosensors for Food
Safety Detection
Functional Nucleic Acid Based Biosensors
for Food Safety Detection
Yunbo Luo
Functional Nucleic Acid
Based Biosensors for Food
Safety Detection
Yunbo Luo
Food Science & Nutritional Engineering
China Agricultural University
Beijing, China
ISBN 978-981-10-8218-4 ISBN 978-981-10-8219-1 (eBook)
https://doi.org/10.1007/978-981-10-8219-1
Library of Congress Control Number: 2018931890
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Preface
I have been engaged in food science research for more than two decades. In the
1990s of the last century, I led our group to research nucleic acids’ function which
mainly focused on regulating effect, such as interference effect, degradation, and
abnormal expression. Later, we learned that many functions of nucleic acids are
natural functional nucleic acid structures. For examples, the formation of
G-quadruplex represses the expression of some cancer-related genes, while the con-
struction of G-quadruplex also has amazing horseradish peroxidase-like function.
In the last decade, our group showed great interest in the research of functional
nucleic acids, which are not limited to their genetic character. For instance, aptam-
ers are termed “chemical antibodies” with a high affinity and specificity, which are
selected by means of in vitro selection and systematic evolution of systematic evo-
lution of ligands by exponential enrichment (SELEX). DNAzyme is another inter-
esting case, which is a type of catalytic nucleic acid that cleaves specific substrates
in the presence of cofactors, such as metal ions (UO 2+, Pb2+, Ni2+, Cu2+, Zn2+) and
2
amino acids, coexist. The third case in point is the transformation from G-rich
sequence into a G-quadruplex with the help of some metal ions such as K+, Pb2+, and
NH4+, which could employ hemin to mimic the peroxidase activity. In the traditional
sense, antibodies and enzymes belong to the domain of protein molecules. However,
these functional nucleic acids open the door for nucleic acid molecules.
There is no doubt that functional nucleic acid has become a hot research field in
the world. Nowadays, thousands of studies related to the functional nucleic acid-
based biosensors have been developed for food safety detection because they can
act as excellent signal recognition elements, the probes for signal amplification, or
framework of nanostructure due to their unique properties. The detection targets
cover almost all of the food safety risk factors from farm to table. However, the
concept, recent advances, and perspectives of functional nucleic acid-based biosen-
sor for the use of food safety detection have not been comprehensively reviewed.
According to various types of food safety risk factors, this monograph is comprised
of the following six parts: definition and basic theories of functional nucleic acids
(Chap. 1), functional nucleic acids biosensors for microorganisms detection (Chap.
2), genetically modified food detection (Chap. 3), heavy metal ion detection (Chap.
v
vi Preface
4), chemical small molecule detection (Chap. 5), and nucleic acid biomarker detec-
tion (Chap. 6). Each chapter explains the technologies and strategies for functional
nucleic acid-based biosensors regarding specific food risk factor detection with
such sensing performances. Moreover, their advantages and limitations are also
compared and discussed in each chapter. Meanwhile, challenges and future perspec-
tives on enabling strategies for the development of desirable functional nucleic acid-
based biosensors are provided.
This book is the first monograph to discuss functional nucleic acid based biosen-
sors for food safety detection, and this classification is very easy for readers engaged
in different fields to read. The completion of this book should be grateful to all
participants in our group for their hard work on organizing documents, drawings,
proofreading, and modification. The book was fulfilled through the joint efforts of
all contributors: Wentao Xu, Nan Cheng, Weiran Wang, Ying Shang, Longjiao Zhu,
Liye Zhu, Boyang Zhang, Jingjing Tian, Chenqi Niu, Hongyu Li, Xiangli Shao,
Bing Xiao, Yuan Zhang, Guishan Li, Huan Song, Zaihui Du, Wanchong He, Yinxia
Xie, and Miao Miao. I am very grateful for their suggestions and kind help in pre-
paring the manuscripts. Of course, shortcomings in the writing process are unavoid-
able, and we are eager for reader’s criticism to make the book better. I believe that
new technology will inevitably lead to the promotion of biosensors due to the fur-
ther development of functional nucleic acid. Therefore, I hope this book will inspire
more food safety researchers’ interests on functional nucleic acid biosensors.
Beijing, China Yunbo Luo
01/03/2018
Contents
1 Functional Nucleic Acid Based Biosensors
for Food Safety Detection ....................................................................... 1
1.1 Food Safety Burden: Safer Food Saves Lives .................................. 1
1.2 Food Safety Risk Factors: Significant Proportion
Can Be Prevented ............................................................................. 1
1.2.1 Microorganisms ................................................................... 2
1.2.2 Genetically Modified Organism (GMO) .............................. 2
1.2.3 Heavy Metal Ion................................................................... 2
1.2.4 Chemical Small Molecules .................................................. 3
1.2.5 Nucleic Acid Biomarkers ..................................................... 3
1.3 Biosensor: A Trend Toward Rapid and On-Site Detection .............. 4
1.3.1 Optical Biosensor ................................................................. 4
1.3.2 Electrochemical Biosensor ................................................... 5
1.3.3 Gravimetric Biosensor ......................................................... 6
1.4 Functional Nucleic Acid: Powerful Tools to Improve
Performance ..................................................................................... 6
1.4.1 Nucleic Acid as Target Recognition Element ...................... 7
1.4.2 Nucleic Acid as Signal Amplification .................................. 12
1.4.3 Nucleic Acid as 3D Nanostructure ....................................... 13
References ................................................................................................. 13
2 Functional Nucleic Acid Based Biosensor
for Microorganism Detection ................................................................. 15
2.1 Introduction ...................................................................................... 15
2.2 The Construction of Functional Nucleic Acid Based Biosensors
for Microorganism Detection and Its Technological Element ......... 17
2.2.1 Signal Recognization and Transduction
of Functional Nucleic Acid Based Biosensor ...................... 19
2.2.2 Signal Transduction Elements.............................................. 21
vii
viii Contents
2.2.3 Signal Amplification of Functional Nucleic
Acid Based Biosensor .......................................................... 22
2.2.4 Signal Output Systems of Functional Nucleic
Acid Based Biosensor .......................................................... 25
2.3 Functional Nucleic Acid Based Biosensors
for Microorganism Detection ........................................................... 30
2.3.1 Aptamer Based Biosensors for Microorganism
Detection .............................................................................. 30
2.3.2 Functional Nucleic Acid Based Colorimetric
Biosensors for Microorganism Detection ............................ 34
2.3.3 Lateral Flow Nucleic Acid Based Biosensors
(LFNABs) for Microorganism Detection ............................. 38
2.3.4 PCR-Functional Nucleic Acid Based Biosensors
for Microorganisms Quantitative Detection ......................... 40
2.3.5 Isothermal Amplification-Functional Nucleic
Acid Based Biosensors for Microorganism
Detection .............................................................................. 42
2.3.6 Functional Nucleic Acid Based High-Throughput
Biosensors for Microorganism Detection ............................ 44
2.3.7 Functional Nucleic Acid Based Biosensor
for Living or Dead Bacteria Detection ................................. 50
2.3.8 Artificial Nucleic Acid Based Biosensors
for Microorganism Detection ............................................... 53
2.3.9 DNAzyme Based Biosensors for Microorganism
Detection .............................................................................. 55
2.3.10 Gold Nanoparticle (AuNP)-Functional Nucleic
Acid Based Biosensors for Microorganism Detection ......... 56
2.3.11 Silver Nanoparticle (AgNP)-Functional Nucleic Acid
Based Biosensors for Microorganism Detection ................. 58
2.3.12 Nanozyme-Functional Nucleic Acid Based
Biosensors for Microorganism Detection ............................ 59
2.3.13 Magnetic Nanoparticle (MNP)-Functional
Nucleic Acid Based Biosensors for Microorganism
Detection .............................................................................. 62
2.3.14 Functional Nucleic Acid Based Fluorescence
Biosensors for Microorganism Detection ............................ 62
2.3.15 Functional Nucleic Acid Based Electrochemical
Biosensors for Microorganism Detection ............................ 66
2.3.16 Surface-Enhanced Raman Spectroscopy-Functional
Nucleic Acid Based Biosensors for Microorganism
Detection .............................................................................. 67
2.3.17 Surface Plasmon Resonance (SPR)-Functional
Nucleic Acid Based Biosensors for Microorganism
Detection .............................................................................. 68
Contents ix
2.3.18 Flow Cytometry-Functional Nucleic Acid Based
Biosensors for Microorganism Detection ............................ 69
2.3.19 Gene Chip-Functional Nucleic Acid Based Biosensors
for Microorganism Detection ............................................... 70
2.3.20 Functional Nucleic Acid Based Biosensors
for Microorganisms Diversity Analysis ............................... 71
2.4 Conclusion and Prospects ................................................................ 72
References ................................................................................................. 73
3 Functional Nucleic Acid Based Biosensors for GMO Detection ......... 81
3.1 The Introduction of Functional Nucleic Acid
Based Biosensors (FNAB) for GMO Detection .............................. 81
3.2 Functional Nucleic Acid Based Biosensors
for GMO Detection .......................................................................... 82
3.2.1 Functional Nucleic Acid Surface Plasmon
Resonance (SPR) Biosensors for GMO Detection .............. 82
3.2.2 Functional Nucleic Acid Nanoparticle Biosensors
for GMO Detection .............................................................. 83
3.2.3 Functional Nucleic Acid Electrochemical Biosensors
for GMO Detection .............................................................. 84
3.2.4 Functional Nucleic Acid Colorimetric Biosensors
for GMO Detection .............................................................. 85
3.2.5 Functional Nucleic Acid Lateral Flow Biosensor
for GMO Detection .............................................................. 87
3.2.6 PCR-Based Functional Nucleic Acid Biosensors
for GMO Quantitative Detection ......................................... 88
3.2.7 Isothermal Amplification-Based Functional
Nucleic Acid Biosensors for GMO Detection ..................... 99
3.2.8 Functional Nucleic Acid High-Throughput
Biosensors for GMO Detection ........................................... 100
References ................................................................................................. 106
4 Functional Nucleic Acid Based Biosensors
for Post-transition Metal Ion Detection ................................................ 111
4.1 Specific Functional Nucleic Acid for Lead Ion Detection ............... 111
4.2 Colorimetric Biosensor for Lead Ion Detection ............................... 113
4.3 Fluorescent Biosensor for Lead Ion Detection ................................ 115
4.4 Quantum Dot Biosensor for Lead Ion Detection ............................. 116
4.5 Electrochemical Biosensor for Lead Ion Detection ......................... 117
4.6 Graphene Oxide-Based Biosensor for Lead Ion Detection .............. 119
References ................................................................................................. 120
5 Functional Nucleic Acid Based Biosensors
for Transition Metal Ion Detection ........................................................ 125
5.1 FNAs for Zinc Ion Detection ........................................................... 125
5.1.1 Specific Functional Nucleic Acid for Zinc
Ion Detection ........................................................................ 125
x Contents
5.1.2 Fluorescent Biosensor for Zinc Ion Detection ..................... 127
5.1.3 Electrochemical Biosensor for Zinc Ion Detection .............. 127
5.1.4 Graphene Oxide-Based Biosensor for Zinc
Ion Detection ........................................................................ 128
5.2 FNAs for Copper Ion ....................................................................... 130
5.2.1 G-Quadruplex DNAzyme for Copper (II)
Ion Sensing ........................................................................... 131
5.2.2 Gold Nanoparticles for Copper (II) Ion Sensing .................. 132
5.2.3 Lateral Flow Biosensor for Copper (II) Ion Sensing ........... 133
5.2.4 Hydrogel for Copper (II) Ion Sensing .................................. 134
5.2.5 Graphene for Copper (II) Ion Sensing ................................. 135
5.2.6 Copper Nanoparticles (CuNPs) for Copper (II)
Ion Sensing ........................................................................... 136
5.3 FNAs for Mercury Ion ..................................................................... 136
5.3.1 G-Quadruplex DNAzyme for Mercury (II)
Ion Sensing ........................................................................... 137
5.3.2 Gold Nanoparticles for Mercury (II) Ion Sensing ................ 138
5.3.3 Fluorescence for Mercury (II) Ion Sensing .......................... 140
5.3.4 Carbon Nanomaterials for Mercury (II) Ion Sensing ........... 141
5.3.5 Electrochemistry for Mercury (II) Ion Sensing ................... 142
5.3.6 Lateral Flow Biosensor for Mercury (II) Ion Sensing ......... 143
5.3.7 Hydrogels for Mercury (II) Ion Sensing .............................. 145
5.4 FNAs for Cadmium Ion ................................................................... 146
5.4.1 Toxicity of Cadmium Ion ..................................................... 146
5.4.2 DNAzyme Biosensor for Cadmium Ion Detection .............. 146
5.4.3 Aptamer Biosensor for Cadmium Ion Detection ................. 148
5.4.4 Summary .............................................................................. 150
5.5 FNAs for Chromium Ions ................................................................ 151
5.5.1 Toxicity of Chromium Ion ................................................... 151
5.5.2 Screen of Chromium-Dependent DNAzyme ....................... 151
5.5.3 Fluorescent Biosensor for Chromium Ions .......................... 152
5.5.4 Summary .............................................................................. 154
References ................................................................................................. 155
6 Functional Nucleic Acid Based Biosensors for Noble Metal
Ion Detection ............................................................................................ 161
6.1 Functional Nucleic Acid Sensors for Silver Ions ............................. 161
6.1.1 RNA-Cleaving DNAzyme ................................................... 161
6.1.2 C−C Mismatch .................................................................... 161
6.1.3 Quadruplex and i-Motif ....................................................... 162
6.2 Signaling Methods ........................................................................... 163
6.2.1 Colorimetric Biosensor for Silver Ion Detection ................. 163
6.2.2 Fluorescent Biosensor for Silver Ion Detection ................... 167
6.2.3 Electrochemical Biosensor for Silver Ion Detection............ 173