Preface xi
Contributors xv
I Introduction
1 Aptamers: Ligands for All Reasons 3
Jean-Jacques Toulm©, Jean-Pierre Daguer, and Eric Dausse
1.1 Introduction 3
1.2 The Power of Selection and Aptamer Refinement 5
1.3 The Chemistry Drives the Shape 7
1.4 Aptaregulators 11
1.5 Aptasensors 15
1.6 Prospects 18
References 20
2 Selex and Its Recent Optimizations 31
Beate Strehlitz and Regina Stoltenburg
2.1 Introduction 31
2.2 Aptamers and Their Selection by SELEX 32
2.3 Modifications of SELEX Technology 35
2.4 Advantages and Limitations of Aptamers and Their Selection Technology 41
2.5 Applications of Aptamers Being Developed for the Market 43
2.6 Future Perspectives 45
References 50
II Biosensors
3 Electrochemical Aptasensors 63
Itamar Willner and Maya Zayats
3.1 Introduction 63
3.2 Electrochemical Aptasensor Based on Redox-Active Aptamer Monolayers Linked to Electrodes 66
3.3 Enzyme-Based Amplified Electrochemical Aptasensors 69
3.4 Amplified Electrochemical Aptasensors Based on Nanoparticles 72
3.5 Label-Free Electrochemical Aptasensors 75
3.6 Field-Effect Transistorâ"Based Aptasensors 78
3.7 Conclusions and Perspectives 81
References 81
4 Aptamers: Hybrids Between Nature And Technology 87
Moritz K. Beissenhirtz, Eik Leupold, Walter St¶cklein, Ulla Wollenberger, Oliver P¤nke, Fred Lisdat, and Frieder W. Scheller
4.1 Introduction 87
4.2 Specific Features of Aptamers 88
4.3 Electrochemical Detection of Nucleic Acids 88
4.4 Cytochrome c Binding by Aptamers 90
4.5 DNA Machines and Aptamers 92
References 98
5 Detection of Proteinâ"aptamer Interactions By Means of Electrochemical Indicators And Transverse Shear Mode Method 101
Tibor Hianik
5.1 Introduction 101
5.2 Immobilization of Aptamers on a Solid Support 102
5.3 Detection of Aptamerâ"Ligand Interactions 104
5.3.1 Electrochemical Methods 105
5.3.2 Acoustic Methods 117
5.4 Conclusions 124
References 125
6 Biosensors Using the Aptameric Enzyme Subunit: the Use of Aptamers in the Allosteric Control of Enzymes 129
Kazunori Ikebukuro, Wataru Yoshida, and Koji Sode
6.1 Aptamers as Molecular Recognition Elements of Biosensors 129
6.1.1 Comparing Aptamers to Antibodies 129
6.1.2 Signaling Aptamers 131
6.2 Homogeneous Sensing 133
6.2.1 Biosensor Systems That Do Not Require Boundâ"Free Separation 133
6.2.2 Aptameric Enzyme Subunit 133
6.3 Evolution-mimicking Algorithm for the Improvement of Aptamers 136
References 137
7 Nanomaterial-based Label-free Aptasensors 139
Kagan Kerman and Eiichi Tamiya
7.1 Introduction 139
7.2 Label-Free Electrochemical Aptasensors 139
7.3 Field-Effect Transistorâ"Based Aptasensors 143
7.4 Label-Free Aptasensors Based on Localized Surface Plasmon Resonance 147
7.5 Forthcoming Challenges and Concluding Remarks 151
References 151
8 Aptamer-based Bioanalytical Assays: Amplification Strategies 159
Sara Tombelli, Maria Minunni, and Marco Mascini
8.1 Introduction 159
8.2 Bioanalytical Assays Based on Aptamer-Functionalized Nanoparticles 160
8.3 Aptamers and Quantum Dotâ"Based Assays 164
8.4 Aptazymes and Aptamer-Based Machines 168
8.5 Polymerase Chain Reaction as an Amplification Method in Aptamer-Based Assays 173
8.6 Conclusions 176
References 177
III Applications
9 Kinetic Capillary Electrophoresis for Selection, Characterization, and Analytical Utilization of Aptamers 183
Sergey N. Krylov
9.1 Introduction 183
9.1.1 Kinetic Capillary Electrophoresis 183
9.1.2 The Concept of NECEEM and ECEEM 185
9.2 Selection of Aptamers Using KCE Methods for Partitioning and Affinity Control 188
9.2.1 NECEEM-Based Selection of Aptamers 188
9.2.2 ECEEM-Based Selection of Aptamers 197
9.2.3 Optimization of PCR 198
9.2.4 Future of KCE Methods for Aptamer Selection 200
9.3 Measurements of Binding Parameters of Targetâ"Aptamer Interaction by KCE Methods 200
9.3.1 Foundation 200
9.3.2 Temperature Control Inside the Capillary 202
9.3.3 Examples 203
9.4 Quantitative Affinity Analysis of a Target Using Aptamer as an Affinity Probe 205
9.4.1 Foundation 205
9.4.2 Example 208
9.5 Conclusions 209
References 210
10 Aptamers for Separation of Enantiomers 213
Corinne Ravelet and Eric Peyrin
10.1 Introduction 213
10.2 Generation and Properties of Enantioselective Aptamers 214
10.3 Immobilized Aptamers for Enantiomeric Separation by Liquid Chromatography 215
10.3.1 Stationary-Phase Preparation and Column Packing 216
10.3.2 DNA Aptamer-Based CSPs 216
10.3.3 RNA Aptamer-Based CSPs and the Mirror-Image Strategy 217
10.3.4 Class-Specific Aptamer-Based CSPs 219
10.4 Aptamers for Analysis of Enantiomers by Capillary Electrophoresis 221
10.4.1 Aptamers as Chiral Additives in the Background Electrolyte for CE Enantiomeric Separation 221
10.4.2 Aptamers for the Design of an Affinity CE-Based Enantioselective Competitive Assay 223
10.5 Conclusions 226
References 226
11 Aptamer-modified Surfaces for Affinity Capture and Detection of Proteins in Capillary Electrophoresis and Maldiâ"mass Spectrometry 229
Linda B. McGown
11.1 Introduction 229
11.2 Aptamer-Modified Capillaries in Affinity Capillary Electrophoresis 230
11.3 Aptamer-Modified Surfaces for Affinity MALDI-MS 232
11.3.1 Overview 232
11.3.2 Affinity MALDI-MS of Thrombin 233
11.3.3 Affinity MALDI-MS of IgE 235
11.3.4 Summary 242
11.4 Beyond Aptamers: Genome-Inspired DNA Binding Ligands 242
References 248
12 Strategy for Use of Smart Routes to Prepare Label-free Aptasensors for Bioassay Using Different Techniques 251
Bingling Li, Hui Wei, and Shaojun Dong
12.1 Introduction 251
12.2 Electrochemical Aptasensors 254
12.2.1 POSOALF Mode 254
12.2.2 PFSOALF Mode 257
12.2.3 Electrochemical Impedimetric Aptasensors 257
12.2.4 Electrochemical Aptasensors with Nonlabeled Redox Probes 263
12.3 Fluorescent Molecular Switches 265
12.3.1 POSFALF Mode 266
12.3.2 PFSFALF Mode 268
12.4 Colorimetry 272
12.4.1 POSFALF Mode 273
12.4.2 PFSFALF Mode 274
12.5 Heminâ"Aptamer DNAzyme-Based Aptasensor 281
12.6 Liquid Chromatography, Electrochromatography, and Capillary Electrophoresis Applications 284
12.7 Other Aptasensors 290
12.8 Conclusions 290
References 290
Index 299
