Functional Nucleic Acids for Analytical Applications (eBook)

Title Page 3
Copyright Page 4
Preface 5
Contents 7
Part I: Overview of Functional Nucleic Acids and Their Analytical Applications 9
Chapter 1 10
Introductory Remarks 10
References 15
Chapter 2 17
Natural Functional Nucleic Acids: Ribozymes and Riboswitches 17
2.1 Introduction 17
2.2 Ribozymes 18
2.2.1 The Hammerhead Ribozyme 21
2.2.2 The Varkud Satellite Ribozyme 24
2.3 Riboswitches 27
2.3.1 The Adenine Riboswitch 31
2.3.2 The Sam Riboswitch 34
2.3.3 The TPP Riboswitch 36
2.4 The glmS Riboswitch Ribozyme 39
2.5 Summary and Conclusions 43
References 43
Chapter 3 53
Artificial Functional Nucleic Acids: Aptamers, Ribozymes, and Deoxyribozymes Identified by In Vitro Selection 53
3.1 Introduction to Artificial Functional Nucleic Acids 53
3.2 Methodology for In Vitro Selection of RNA and DNA Aptamers 54
3.2.1 In Vitro Selection of Aptamers by Affinity Chromatography 54
3.2.1.1 The Basic Procedures of In Vitro Selection (SELEX) of Aptamers 55
3.2.1.2 Additional Considerations for Aptamer Selection Procedures 57
3.2.2 Aptamer Selection Methods Other than Affinity Chromatography 60
3.3 Molecular Targets and Properties of RNA Aptamers 61
3.3.1 Molecular Targets Bound by RNA Aptamers 62
3.3.1.1 The First RNA Aptamers 62
3.3.1.2 Small-Molecule Targets of RNA Aptamers 62
3.3.1.3 Peptide and Protein Targets of RNA Aptamers 66
3.3.1.4 RNA Aptamers for In Vivo and Therapeutic Applications 68
3.3.1.5 Other Targets for RNA Aptamers 68
3.3.2 Biochemical Characterization of RNA Aptamers 69
3.3.2.1 Secondary Structure Analysis of RNA Aptamers 69
3.3.2.2 Binding Constants of RNA Aptamers: Methodology 70
3.3.2.3 Binding Constants of RNA Aptamers: Quantitative Data 70
3.3.2.4 Evolutionary Considerations for RNA Aptamers 71
3.3.3 RNA Aptamers with Chemical Modifications 71
3.3.4 Mirror-Image RNA Aptamers (Spiegelmers) 72
3.4 Molecular Targets and Properties of DNA Aptamers 72
3.4.1 Molecular Targets Bound by DNA Aptamers 73
3.4.2 Biochemical Characterization of DNA Aptamers 74
3.4.3 Other Considerations for DNA Aptamers 74
3.5 Direct Structural Analysis of RNA and DNA Aptamers 74
3.5.1 NMR and X-Ray Crystallography Analysis of Aptamers 74
3.5.2 Case Study #1: Theophylline RNA Aptamer 75
3.5.3 Case Study #2: ATP RNA and DNA Aptamers 76
3.5.4 Case Study #3: Thrombin DNA Aptamer 76
3.6 In Vitro Selection of Ribozymes 76
3.6.1 Methodology to Identify Ribozymes 77
3.6.1.1 The Basic Procedures of In Vitro Selection of Ribozymes 77
3.6.1.2 Additional Considerations for Ribozyme Selections 79
3.6.1.3 Alternative Methods for Ribozyme Selections 80
3.6.2 Chemical Reactions Catalyzed by Ribozymes 81
3.6.3 Biochemical Characterization of Ribozymes 83
3.6.3.1 Secondary Structures and Minimization of Ribozymes 83
3.6.3.2 Ribozyme Mechanisms and Rate Enhancements 84
3.6.3.3 Ribozyme Structural Biology 85
3.6.3.4 Evolutionary Considerations for Ribozymes 85
3.6.4 Ribozymes with Chemical Modifications 86
3.7 In Vitro Selection of Deoxyribozymes 87
3.7.1 Methodology to Identify Deoxyribozymes 87
3.7.2 Chemical Reactions Catalyzed by Deoxyribozymes 88
3.7.3 Biochemical Characterization of Deoxyribozymes 88
3.8 In Vitro Selection of Aptazymes 89
3.8.1 Aptazymes Obtained by Rational Fusion of Aptamers with Nucleic Acid Enzymes 89
3.8.2 Aptazymes Obtained by In Vitro Selection for Regulated Catalysis 91
3.8.3 Mechanisms of Aptazyme Signal Transduction 92
3.9 Perspective on Artificial Functional Nucleic Acids 92
References 93
Part II: Functional Nucleic Acid sensors Based on Different Transduction Principles 115
Chapter 4 116
Fluorescent Aptamer Sensors 116
4.1 Overview 116
4.2 Fluorescent Aptamers Developed from Cell-Based SELEX for Recognition of Cancer Cells and Biomarker Discovery 118
4.3 FRET and Fluorescence Anisotropy-Based Aptamer Sensors for Protein Studies 124
4.4 Light-Switching Excimer-Based Aptamer Probes for Cancer Biomarker Detection in Complex Biological Fluids 130
4.5 Future Perspectives 133
References 133
Chapter 5 136
Fluorescent Ribozyme and Deoxyribozyme Sensors 136
5.1 Introduction 136
5.2 Synchronization of Catalytic Activity with Fluorescence Signals for Existing RNA-Cleaving Nucleic Acid Enzymes 139
5.3 Creating and Characterizing a Group of New Fluorescence-Signaling and RNA-Cleaving Deoxyribozymes 140
5.3.1 The In Vitro Selection Scheme 141
5.3.2 Fluorescence-Signaling and RNA-Cleaving Deoxyribozymes from the First In Vitro Selection Attempt 142
5.3.3 Evolution of a Fluorescence-Signaling and RNA-Cleaving Deoxyribozyme with a Five-Way Junction Structure 144
5.3.4 Fluorescence-Signaling and RNA-Cleaving Deoxyribozymes from the Second In Vitro Selection Attempt 145
5.3.5 Catalytic Relevance of F, Q, and rA Moieties Within the Substrate 148
5.4 Engineering Allostery into Fluorogenic RNA-Cleaving Nucleic Acid Enzymes 148
5.4.1 Communication Module Approach 149
5.4.2 Antisense Sequestration Approach 151
5.4.3 Catalytic Molecular Beacon Approach 153
5.5 Concluding Remarks 155
References 156
Chapter 6 159
Colorimetric and Fluorescent Biosensors Based on Directed Assembly of Nanomaterials with Functional DNA 159
6.1 Introduction 159
6.1.1 Functional DNA as Sensing Molecules 159
6.1.2 Optical Properties of Inorganic Nanomaterials 161
6.2 Colorimetric Sensors 162
6.2.1 Colorimetric Sensors for Metal Ions Based on Directed Assembly of Au NPs Using DNAzymes 162
6.2.2 Beyond Colorimetric Metal Sensors 166
6.2.3 Colorimetric Sensors with Tunable Dynamic Ranges 168
6.2.4 From Single Analyte Detection to Multiple Analyte Detection 170
6.3 Fluorescent Sensors 171
6.4 “One-Pot” Multiplex Colorimetric and Fluorescent Detection of Multiple Analytes Using Au NPs and QDs 172
6.5 Detection Based on Non-cross-Linking DNA 174
6.6 Toward More Practical Applications: Simple “Dipstick” Tests 176
6.7 Conclusions and Outlook 178
References 178
Chapter 7 183
Electrochemical Approaches to Aptamer-Based Sensing 183
7.1 Introduction 183
7.2 Sandwich or Competition-Based Electrochemical Techniques 185
7.3 Impedance-Based Electrochemical Aptasensors 188
7.4 Electrochemical Sensors Based on Target Binding-Induced Aptamer Folding 191
7.5 A Comparison: Optical Versus Electrochemical Aptasensors 195
7.6 Conclusions 197
References 197
Chapter 8 202
Amplified DNA Biosensors 202
8.1 Introduction 202
8.2 Enzyme-Amplified Electrochemical DNA Biosensors 207
8.2.1 Enzyme-Amplified Electrochemical Detection of DNA 208
8.2.2 Enzyme- and DNAzyme-Amplified Optical Detection of DNA 215
8.3 Amplified Electrochemical or Optical Detection of DNA Using Metal Nanoparticles (NPs) 220
8.4 Amplified Electrochemical, Microgravimetric, and Optical Analysis of DNA Using Nanoparticles (NPs) as Labels 226
8.4.1 Amplified Electrochemical Analysis of DNA Using Nanoparticles 227
8.4.2 Amplified Microgravimetric Analysis of DNA with NPs 232
8.5 Amplified Electrochemical Analysis of DNA Using Micro-/Nano-carriers of Labels or Micro-/Nano-objects That Control the Interface Properties of Electrodes 234
8.6 Amplified Optical Detection of DNA by DNA-Based Machines 242
8.7 Photoelectrochemical Detection of DNA 246
8.8 Conclusions and Perspectives 249
References 250
Part III: Other Emerging Analytical Applications 256
Chapter 9 257
Aptamers in Affinity Separations: Capillary Electrophoresis 257
9.1 Introduction 257
9.2 Aptamers 258
9.2.1 Aptamer Selection Using Capillary Electrophoresis 259
9.3 Assays Employing Aptamers in Capillary Electrophoresis 260
9.3.1 Competitive and Noncompetitive Assays 260
9.3.2 Fluorescence Polarization Assays 264
9.3.3 Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures 266
9.3.4 Affinity-Polymerase Chain Reaction CE Methods 268
9.4 Conclusions 269
References 270
Chapter 10 273
Aptamers in Affinity Separations: Stationary Separation 273
10.1 Introduction 273
10.2 Use of Aptamers as Specific Ligands for the Capture of Biopolymers 274
10.2.1 Aptamers as Affinity Tags 278
10.3 Use of Aptamers as Specific Ligands for the Separation/Capture of Small Molecules and Enantiomers 281
10.3.1 Immobilized Aptamers for the Separation/Capture of Small Molecules 281
10.3.2 Immobilized Aptamers for the Separation of Enantiomers 283
10.4 Conclusions 286
References 287
Chapter 11 289
Aptamer Microarrays 289
11.1 Introduction 289
11.2 Development of High-Throughput Selection Methods 290
11.2.1 The In Vitro Selection Scheme 290
11.2.2 High-Throughput Selection 291
11.2.2.1 Alternative Selection Modalities 292
11.2.2.2 Automated Selection 293
11.2.2.3 The Target Problem 295
In Vitro Transcription and Translation 295
Yeast Expression Libraries 296
11.3 Development of Aptamer Microarrays 296
11.3.1 Aptamer Immobilization on Arrays 297
11.3.2 Printing Aptamer Arrays 299
11.3.3 Assaying Aptamer Arrays 300
11.3.3.1 Incubating Arrays with Protein Targets 300
11.3.3.2 Aptamer Microarray Detection of Hen Egg White Lysozyme 300
11.3.3.3 Aptamer Microarray Detection of HIV-1 Reverse Transcriptase 303
11.4 Data Analysis 305
11.5 Other Approaches 306
References 307
Chapter 12 311
The Use of Functional Nucleic Acids in Solid-Phase Fluorimetric Assays 311
12.1 Introduction 311
12.2 Traditional Methods for DNA Immobilization 313
12.3 Assays Utilizing Immobilized Functional Nucleic Acids 315
12.3.1 Methods of Fluorescence Signaling 316
12.3.2 Fluorescence Sensors Based on Immobilized Functional Nucleic Acid Species 319
12.3.3 Multianalyte Arrays Utilizing Immobilized Molecular Beacon Species 320
12.3.4 Multianalyte Arrays Utilizing Immobilized Aptamers 323
12.4 Sol-gel Immobilization Methods 326
12.4.1 The Sol-gel Process for Biomolecule Entrapment 326
12.4.2 Immobilization of Molecular Beacons onto Sol-gel Materials 328
12.4.3 Entrapment of DNA Aptamers Within Sol-gel Materials 328
12.4.4 Entrapment of DNA Enzymes in Sol-gel Materials 330
12.4.5 Layered Structures for Aptamer-Based HTS Assays 332
12.5 Emerging Applications 336
12.6 Conclusions and Perspectives 338
References 339
Chapter 13 345
Functional Nucleic Acid Sensors as Screening Tools 345
13.1 Introduction 345
13.2 Aptamers as Screening Tools 347
13.2.1 DNA Aptamers 347
13.2.2 RNA Aptamers 349
13.3 Allosteric Ribozymes as Screening Tools 349
13.3.1 Generation of Allosteric Ribozymes 350
13.3.2 Indirect Screening 350
13.3.3 Direct Screening 351
13.4 Natural RNAs as Screening Tools 352
13.4.1 Riboswitches as Screening Tools 352
13.4.2 Pre-miRNAs as Screening Tools 354
13.5 Conclusions 354
References 355
Chapter 14 357
Nucleic Acids for Computation 357
14.1 Introduction 357
14.2 Logic Gates 358
14.2.1 Silicomimetic Approach 358
14.2.2 Principles Behind Deoxyribozyme-Based Logic Gates 359
14.2.3 Output Detection 361
14.3 Adders: Circuits for Basic Arithmetical Operations 363
14.3.1 A Molecular Half-Adder 363
14.3.2 A Molecular Full-Adder 364
14.4 Automata: Complex Decision Making and Scaled Integration 366
14.4.1 MAYA 366
14.4.2 MAYA-II 370
14.5 Engineering Interelement Interfaces 372
14.5.1 Ligase–Phosphodiesterase Cascades 372
14.5.2 Phosphodiesterase–Phosphodiesterase Cascades 373
14.5.2.1 Computational Control of Aptameric Actuators 374
14.6 Conclusions and Future Visions 375
References 376
Chapter 15 378
DNAzymes in DNA Nanomachines and DNA Analysis 378
15.1 Introduction 378
15.2 Autonomous DNA Nanomachines Powered by DNAzyme 379
15.2.1 Autonomous DNA Nanotweezers 379
15.2.2 An Autonomous and Processive DNA Walker 381
15.3 DNA Detection Systems Based on DNAzyme 383
15.3.1 DNAzyme-Mediated Amplification of Molecular Beacon Signal for DNA Detection 383
15.3.2 Cascade DNAzyme Signal Amplification for DNA Detection 385
15.4 Summary and Outlook 387
References 387
Index 390