Table Of ContentEdited by Marco Mascini and Ilaria Palchetti
Nucleic Acid Biosensors
for Environmental Pollution
Monitoring
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Nucleic Acid Biosensors for Environmental Pollution
Monitoring
Nucleic Acid Biosensors for
Environmental Pollution
Monitoring
Edited by
Marco Mascini and Ilaria Palchetti
Dipartimento di Chimica, Universita` degli Studi di Firenze, Italy
ISBN: 978-1-84973-131-7
A catalogue record for this book is available from the British Library
r Royal Society of Chemistry 2011
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Preface
Nucleic acids are the fundamental bricks of life. They are universal in living
things, as they are found in all cells and also in viruses. Their role in nature
is of tremendous importance since they are responsible for carrying genetic
information from one generation to another.
However,inrecentyears,thefunctionofnucleicacidshasbeenrecognizedto
extend beyond the Watson–Crick base pair recognition of complementary
strands.Theirchemicalcharacteristicofbeingamacromoleculecomposedofa
chainofnucleotideshasbeenusedtocreateuniquechemicalcompounds.Since
the early 1990s, many nucleic acid-based molecules, consisting of 40–50
nucleotides—known as aptamers—have been isolated from large libraries that
are able to bind a broad range of molecules with high affinity and specificity.
Themoleculesandentitiesthatcanberecognizedbyaptamersrangefromsmall
organic molecules to proteins, cells, and even intact viral particles. A further
advancewasmadein1994,whenforthefirsttimeDNAwasshowntoactasa
catalyst. These catalytic DNA molecules are called DNAzymes. DNAzymes
and aptamers can be combined to form aptazymes.
In this book we have attempted to demonstrate the incredible opportunities
that nucleic acids can offer to analytical chemistry, and in particular to envir-
onmental analytical chemistry. These innovative biomolecules can, in fact, be
used to develop smart and innovative biosensors for environmental analysis.
Monitoring of contaminants in the air, water, and soil is instrumental in
understandingandmanagingriskstohumanhealthandecosystems.Giventhis
requirement, as well as the time and cost involved in traditional chemical
analysisofenvironmentalsamples(e.g.,chromatographicmethods),thereisan
expanding need for simple, rapid, cost-effective, and field portable screening
methods.Abiosensorisacompactanalyticaldeviceincorporating abiological
or biologically derived sensing element either integrated within or intimately
associated with a physicochemical transducer. The peculiar characteristics of
biosensors allow them to complement current environmental field screening
NucleicAcidBiosensorsforEnvironmentalPollutionMonitoring
EditedbyMarcoMasciniandIlariaPalchetti
rRoyalSocietyofChemistry2011
PublishedbytheRoyalSocietyofChemistry,www.rsc.org
v
vi Preface
and monitoring methods, especially when continuous, real-time, in situ mon-
itoringisrequired.Asdescribedinthisbook,nucleicacidshaveapivotalrolein
development of smart biosensors for environmental monitoring.
Chapter1(byPalchettiandMascini)describesthecrucialroleofbiosensors
forenvironmentalmonitoring,withspecialemphasisontheproblemsinvolved
and the attempts to solve the basic requirements for increased stability,
detection sensitivity, and reliability of the biomolecular recognition element.
Theopportunitiesthatnucleicacidsofferinthisfieldsarehighlighted.Chapter
2 (by Erdem and Oszoz) provides a description and classification of nucleic
acidsandtheirroleinlivingorganisms.Chapter3(byPalchetti,Marrazza,and
Mascini) deals with the use of nucleic acid based biosensors for hybridization
and their role in environmental monitoring. Chapter 4 (by Cella, Chen, and
Mulchandani)andChapter5(byNagrajandLu)focusonthedevelopmentof
biosensors based on aptamers and nucleic acid enzymes respectively for the
detectionoforganicandinorganicpollutants.Chapter6(byRogersandGary)
and Chapter 7 (by Labuda) deal with the use of nucleic acid based biosensors
for environmental toxicity screening, and Chapter 8 (by Escosura-Mun˜iz,
Medina, and Merkoc¸i) focuses on the use of nanomaterials (nanoparticles,
quantum dots, nanotubes, etc.) as well as miniaturization and lab-on-a-chip
technologies for nucleic acid based biosensing systems with interest for
environmental applications.
We are fortunate to have assembled contributions from world-class autho-
ritiesinthisfield,andwesincerelythankallofthem.Sharingtheirenthusiasm
for the field of nucleic acid based biosensors, we have brought their contribu-
tions together in this book, which we believe, will be of great help to the
increasing number of researchers in this field.
Marco Mascini and Ilaria Palchetti
Sesto Fiorentino
Contents
Chapter 1 Biosensor Techniques for Environmental Monitoring 1
Ilaria Palchetti and Marco Mascini
1.1 Introduction: Role of Biosensors in Environmental
Analysis 1
1.2 Biosensors: Definition, Classification and a Brief
History 3
1.3 InnovativeBiorecognitionElementsforEnvironmental
Analysis 6
1.4 Conclusions 14
References 15
Chapter 2 Nucleic Acids as Biorecognition Element in Biosensor
Development 17
Arzum Erdem and Mehmet Ozsoz
2.1 Description and Classification of Nucleic Acids 17
2.1.1 Natural Nucleic Acids 17
2.1.2 Synthetic Nucleic Acids 18
2.2 Applications of Nucleic Acid Based Biosensor
Technologies 21
2.2.1 DNA Biosensors 25
2.2.2 RNA Biosensors 27
2.2.3 PNA Biosensors 28
2.2.4 LNA Biosensors 29
2.3 Conclusion 30
References 30
NucleicAcidBiosensorsforEnvironmentalPollutionMonitoring
EditedbyMarcoMasciniandIlariaPalchetti
rRoyalSocietyofChemistry2011
PublishedbytheRoyalSocietyofChemistry,www.rsc.org
vii
viii Contents
Chapter 3 Genosensing Environmental Pollution 34
Ilaria Palchetti, Giovanna Marrazza and Marco Mascini
3.1 Introduction 34
3.2 Genosensor Development 35
3.2.1 Probe Design 36
3.2.2 Probe Immobilization 37
3.2.3 Sample Treatment and Hybridization 40
3.2.4 Detection 47
3.3 Genosensors for Environmental Monitoring 51
3.4 Conclusions 57
References 57
Chapter 4 Aptamer-based Biosensor for Environmental Monitoring 61
Lakshmi N. Cella, Wilfred Chen and Ashok Mulchandani
4.1 Introduction to Aptamers 61
4.2 Aptamer Properties 62
4.3 SELEX and its Variants 63
4.3.1 Bound-state SELEX Variants 64
4.3.2 Solution-based SELEX Variants 66
4.3.3 Specialized Variants 66
4.4 Aptamer-based Biosensors for Environmental
Monitoring 67
4.4.1 DetectionofOrganicandInorganicPollutants 68
4.4.2 Detection of Drugs, EDCs, and PPCPs 70
4.4.3 Detection of Toxins 72
4.4.4 Detection of Pathogens 75
4.4.5 Detection of Nitroaromatic Explosives 77
4.5 Future Prospects 77
References 78
Chapter 5 Catalytic Nucleic Acid Biosensors for Environmental
Monitoring 82
Nandini Nagraj and Yi Lu
5.1 Discovery of Catalytic Nucleic Acids 82
5.2 Detection of Trace Contaminants using Catalytic
Nucleic Acids as Sensing Platforms 83
5.3 Isolation of Catalytic Nucleic Acids Using in vitro
Selection 84
5.4 ConversionofCatalyticNucleicAcidsintoBiosensors 85
5.4.1 Fluorescence Sensing 86
5.4.2 Colorimetric Sensors 89
Contents ix
5.4.3 Dipstick Tests based on AuNP-DNAzyme
Conjugates 91
5.4.4 Electrochemical Sensors 93
5.5 Expanding the Scope of the Sensing Targets of
Catalytic Nucleic Acids by Employing Aptazymes 93
5.6 Summary and Future Perspectives 95
Acknowledgments 95
References 95
Chapter 6 Nucleic Acid-based Biosensors for the Detection of DNA
Damage 99
Kim R. Rogers and Ronald K. Gary
6.1 Introduction 99
6.2 Optical Transduction Schemes 107
6.3 Whole-Cell Based Biosensors 110
6.4 Field Capability and Stage of Development 116
6.5 Future Trends and Summary 117
Disclaimer 118
References 118
Chapter 7 Detection of Damage to DNA Using Electrochemical and
Piezoelectric DNA-Based Biosensors 121
Jan Labuda
7.1 Introduction 121
7.2 Electrochemical Biosensors 123
7.2.1 Construction of Biosensors for DNA Damage
Detection 123
7.2.2 TechniquesUsed forDNADamageDetection 124
7.3 Piezoelectric Biosensors 133
7.4 Conclusions 134
References 134
Chapter8 NewTrendsinDNASensorsforEnvironmentalApplications:
Nanomaterials, Miniaturization, and Lab-on-a-Chip
Technology 141
Alfredo de la Escosura-Muniz, Mariana Medina and
Arben Merkoc¸i
8.1 Introduction 141
8.2 Nanomaterial-based Sensors for DNA Detection 142
8.2.1 Optical Sensors 142
8.2.2 Electrochemical Sensors 146
8.3 DNA and Nanomaterial-based Sensing Platforms 148
