Li / Lu Functional Nucleic Acids for Analytical Applications

1. Auflage 2009
ISBN: 978-0-387-73711-9
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 396 Seiten

Reihe: Integrated Analytical Systems

Nature has long used nucleic acid aptamers and enzymes for regulatory activities, such as the recently discovered 'riboswitches' involved in gene expression. The existence of a large array of natural and artificial functional nucleic acids has generated tremendous enthusiasm and new opportunities for molecular scientists from diverse disciplines to devise new concepts and real applications that take advantage of those nucleic acids for sensing and other analytical applications. This book provides a timely and comprehensive overview of recent advances in the field, from leading experts in biology, chemistry, and engineering. A variety of topics are covered, from fundamentals of functional nucleic acids, to their applications as sensors, to nanotechnologies; as well as integration of functional nucleic acids into practical analytical systems.

Autoren/Hrsg.

Li, Yingfu

Lu, Yi

Inhaltsverzeichnis

1;Title Page;3
2;Copyright Page;4
3;Preface;5
4;Contents;7
5;Part I: Overview of Functional Nucleic Acids and Their Analytical Applications;9
5.1;Chapter 1;10
5.1.1;Introductory Remarks;10
5.1.1.1;References;15
5.2;Chapter 2;17
5.2.1;Natural Functional Nucleic Acids: Ribozymes and Riboswitches;17
5.2.1.1;2.1 Introduction;17
5.2.1.2;2.2 Ribozymes;18
5.2.1.2.1;2.2.1 The Hammerhead Ribozyme;21
5.2.1.2.2;2.2.2 The Varkud Satellite Ribozyme;24
5.2.1.3;2.3 Riboswitches;27
5.2.1.3.1;2.3.1 The Adenine Riboswitch;31
5.2.1.3.2;2.3.2 The Sam Riboswitch;34
5.2.1.3.3;2.3.3 The TPP Riboswitch;36
5.2.1.4;2.4 The glmS Riboswitch Ribozyme;39
5.2.1.5;2.5 Summary and Conclusions;43
5.2.1.6;References;43
5.3;Chapter 3;53
5.3.1;Artificial Functional Nucleic Acids: Aptamers, Ribozymes, and Deoxyribozymes Identified by In Vitro Selection;53
5.3.1.1;3.1 Introduction to Artificial Functional Nucleic Acids;53
5.3.1.2;3.2 Methodology for In Vitro Selection of RNA and DNA Aptamers;54
5.3.1.2.1;3.2.1 In Vitro Selection of Aptamers by Affinity Chromatography;54
5.3.1.2.1.1;3.2.1.1 The Basic Procedures of In Vitro Selection (SELEX) of Aptamers;55
5.3.1.2.1.2;3.2.1.2 Additional Considerations for Aptamer Selection Procedures;57
5.3.1.2.2;3.2.2 Aptamer Selection Methods Other than Affinity Chromatography;60
5.3.1.3;3.3 Molecular Targets and Properties of RNA Aptamers;61
5.3.1.3.1;3.3.1 Molecular Targets Bound by RNA Aptamers;62
5.3.1.3.1.1;3.3.1.1 The First RNA Aptamers;62
5.3.1.3.1.2;3.3.1.2 Small-Molecule Targets of RNA Aptamers;62
5.3.1.3.1.3;3.3.1.3 Peptide and Protein Targets of RNA Aptamers;66
5.3.1.3.1.4;3.3.1.4 RNA Aptamers for In Vivo and Therapeutic Applications;68
5.3.1.3.1.5;3.3.1.5 Other Targets for RNA Aptamers;68
5.3.1.3.2;3.3.2 Biochemical Characterization of RNA Aptamers;69
5.3.1.3.2.1;3.3.2.1 Secondary Structure Analysis of RNA Aptamers;69
5.3.1.3.2.2;3.3.2.2 Binding Constants of RNA Aptamers: Methodology;70
5.3.1.3.2.3;3.3.2.3 Binding Constants of RNA Aptamers: Quantitative Data;70
5.3.1.3.2.4;3.3.2.4 Evolutionary Considerations for RNA Aptamers;71
5.3.1.3.3;3.3.3 RNA Aptamers with Chemical Modifications;71
5.3.1.3.4;3.3.4 Mirror-Image RNA Aptamers (Spiegelmers);72
5.3.1.4;3.4 Molecular Targets and Properties of DNA Aptamers;72
5.3.1.4.1;3.4.1 Molecular Targets Bound by DNA Aptamers;73
5.3.1.4.2;3.4.2 Biochemical Characterization of DNA Aptamers;74
5.3.1.4.3;3.4.3 Other Considerations for DNA Aptamers;74
5.3.1.5;3.5 Direct Structural Analysis of RNA and DNA Aptamers;74
5.3.1.5.1;3.5.1 NMR and X-Ray Crystallography Analysis of Aptamers;74
5.3.1.5.2;3.5.2 Case Study #1: Theophylline RNA Aptamer;75
5.3.1.5.3;3.5.3 Case Study #2: ATP RNA and DNA Aptamers;76
5.3.1.5.4;3.5.4 Case Study #3: Thrombin DNA Aptamer;76
5.3.1.6;3.6 In Vitro Selection of Ribozymes;76
5.3.1.6.1;3.6.1 Methodology to Identify Ribozymes;77
5.3.1.6.1.1;3.6.1.1 The Basic Procedures of In Vitro Selection of Ribozymes;77
5.3.1.6.1.2;3.6.1.2 Additional Considerations for Ribozyme Selections;79
5.3.1.6.1.3;3.6.1.3 Alternative Methods for Ribozyme Selections;80
5.3.1.6.2;3.6.2 Chemical Reactions Catalyzed by Ribozymes;81
5.3.1.6.3;3.6.3 Biochemical Characterization of Ribozymes;83
5.3.1.6.3.1;3.6.3.1 Secondary Structures and Minimization of Ribozymes;83
5.3.1.6.3.2;3.6.3.2 Ribozyme Mechanisms and Rate Enhancements;84
5.3.1.6.3.3;3.6.3.3 Ribozyme Structural Biology;85
5.3.1.6.3.4;3.6.3.4 Evolutionary Considerations for Ribozymes;85
5.3.1.6.4;3.6.4 Ribozymes with Chemical Modifications;86
5.3.1.7;3.7 In Vitro Selection of Deoxyribozymes;87
5.3.1.7.1;3.7.1 Methodology to Identify Deoxyribozymes;87
5.3.1.7.2;3.7.2 Chemical Reactions Catalyzed by Deoxyribozymes;88
5.3.1.7.3;3.7.3 Biochemical Characterization of Deoxyribozymes;88
5.3.1.8;3.8 In Vitro Selection of Aptazymes;89
5.3.1.8.1;3.8.1 Aptazymes Obtained by Rational Fusion of Aptamers with Nucleic Acid Enzymes;89
5.3.1.8.2;3.8.2 Aptazymes Obtained by In Vitro Selection for Regulated Catalysis;91
5.3.1.8.3;3.8.3 Mechanisms of Aptazyme Signal Transduction;92
5.3.1.9;3.9 Perspective on Artificial Functional Nucleic Acids;92
5.3.1.10;References;93
6;Part II: Functional Nucleic Acid sensors Based on Different Transduction Principles;115
6.1;Chapter 4;116
6.1.1;Fluorescent Aptamer Sensors;116
6.1.1.1;4.1 Overview;116
6.1.1.2;4.2 Fluorescent Aptamers Developed from Cell-Based SELEX for Recognition of Cancer Cells and Biomarker Discovery;118
6.1.1.3;4.3 FRET and Fluorescence Anisotropy-Based Aptamer Sensors for Protein Studies;124
6.1.1.4;4.4 Light-Switching Excimer-Based Aptamer Probes for Cancer Biomarker Detection in Complex Biological Fluids;130
6.1.1.5;4.5 Future Perspectives;133
6.1.1.6;References;133
6.2;Chapter 5;136
6.2.1;Fluorescent Ribozyme and Deoxyribozyme Sensors;136
6.2.1.1;5.1 Introduction;136
6.2.1.2;5.2 Synchronization of Catalytic Activity with Fluorescence Signals for Existing RNA-Cleaving Nucleic Acid Enzymes;139
6.2.1.3;5.3 Creating and Characterizing a Group of New Fluorescence-Signaling and RNA-Cleaving Deoxyribozymes;140
6.2.1.3.1;5.3.1 The In Vitro Selection Scheme;141
6.2.1.3.2;5.3.2 Fluorescence-Signaling and RNA-Cleaving Deoxyribozymes from the First In Vitro Selection Attempt;142
6.2.1.3.3;5.3.3 Evolution of a Fluorescence-Signaling and RNA-Cleaving Deoxyribozyme with a Five-Way Junction Structure;144
6.2.1.3.4;5.3.4 Fluorescence-Signaling and RNA-Cleaving Deoxyribozymes from the Second In Vitro Selection Attempt;145
6.2.1.3.5;5.3.5 Catalytic Relevance of F, Q, and rA Moieties Within the Substrate;148
6.2.1.4;5.4 Engineering Allostery into Fluorogenic RNA-Cleaving Nucleic Acid Enzymes;148
6.2.1.4.1;5.4.1 Communication Module Approach;149
6.2.1.4.2;5.4.2 Antisense Sequestration Approach;151
6.2.1.4.3;5.4.3 Catalytic Molecular Beacon Approach;153
6.2.1.5;5.5 Concluding Remarks;155
6.2.1.6;References;156
6.3;Chapter 6;159
6.3.1;Colorimetric and Fluorescent Biosensors Based on Directed Assembly of Nanomaterials with Functional DNA;159
6.3.1.1;6.1 Introduction;159
6.3.1.1.1;6.1.1 Functional DNA as Sensing Molecules;159
6.3.1.1.2;6.1.2 Optical Properties of Inorganic Nanomaterials;161
6.3.1.2;6.2 Colorimetric Sensors;162
6.3.1.2.1;6.2.1 Colorimetric Sensors for Metal Ions Based on Directed Assembly of Au NPs Using DNAzymes;162
6.3.1.2.2;6.2.2 Beyond Colorimetric Metal Sensors;166
6.3.1.2.3;6.2.3 Colorimetric Sensors with Tunable Dynamic Ranges;168
6.3.1.2.4;6.2.4 From Single Analyte Detection to Multiple Analyte Detection;170
6.3.1.3;6.3 Fluorescent Sensors;171
6.3.1.4;6.4 “One-Pot” Multiplex Colorimetric and Fluorescent Detection of Multiple Analytes Using Au NPs and QDs;172
6.3.1.5;6.5 Detection Based on Non-cross-Linking DNA;174
6.3.1.6;6.6 Toward More Practical Applications: Simple “Dipstick” Tests;176
6.3.1.7;6.7 Conclusions and Outlook;178
6.3.1.8;References;178
6.4;Chapter 7;183
6.4.1;Electrochemical Approaches to Aptamer-Based Sensing;183
6.4.1.1;7.1 Introduction;183
6.4.1.2;7.2 Sandwich or Competition-Based Electrochemical Techniques;185
6.4.1.3;7.3 Impedance-Based Electrochemical Aptasensors;188
6.4.1.4;7.4 Electrochemical Sensors Based on Target Binding-Induced Aptamer Folding;191
6.4.1.5;7.5 A Comparison: Optical Versus Electrochemical Aptasensors;195
6.4.1.6;7.6 Conclusions;197
6.4.1.7;References;197
6.5;Chapter 8;202
6.5.1;Amplified DNA Biosensors;202
6.5.1.1;8.1 Introduction;202
6.5.1.2;8.2 Enzyme-Amplified Electrochemical DNA Biosensors;207
6.5.1.2.1;8.2.1 Enzyme-Amplified Electrochemical Detection of DNA;208
6.5.1.2.2;8.2.2 Enzyme- and DNAzyme-Amplified Optical Detection of DNA;215
6.5.1.3;8.3 Amplified Electrochemical or Optical Detection of DNA Using Metal Nanoparticles (NPs);220
6.5.1.4;8.4 Amplified Electrochemical, Microgravimetric, and Optical Analysis of DNA Using Nanoparticles (NPs) as Labels;226
6.5.1.4.1;8.4.1 Amplified Electrochemical Analysis of DNA Using Nanoparticles;227
6.5.1.4.2;8.4.2 Amplified Microgravimetric Analysis of DNA with NPs;232
6.5.1.5;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
6.5.1.6;8.6 Amplified Optical Detection of DNA by DNA-Based Machines;242
6.5.1.7;8.7 Photoelectrochemical Detection of DNA;246
6.5.1.8;8.8 Conclusions and Perspectives;249
6.5.1.9;References;250
7;Part III: Other Emerging Analytical Applications;256
7.1;Chapter 9;257
7.1.1;Aptamers in Affinity Separations: Capillary Electrophoresis;257
7.1.1.1;9.1 Introduction;257
7.1.1.2;9.2 Aptamers;258
7.1.1.2.1;9.2.1 Aptamer Selection Using Capillary Electrophoresis;259
7.1.1.3;9.3 Assays Employing Aptamers in Capillary Electrophoresis;260
7.1.1.3.1;9.3.1 Competitive and Noncompetitive Assays;260
7.1.1.3.2;9.3.2 Fluorescence Polarization Assays;264
7.1.1.3.3;9.3.3 Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures;266
7.1.1.3.4;9.3.4 Affinity-Polymerase Chain Reaction CE Methods;268
7.1.1.4;9.4 Conclusions;269
7.1.1.5;References;270
7.2;Chapter 10;273
7.2.1;Aptamers in Affinity Separations: Stationary Separation;273
7.2.1.1;10.1 Introduction;273
7.2.1.2;10.2 Use of Aptamers as Specific Ligands for the Capture of Biopolymers;274
7.2.1.2.1;10.2.1 Aptamers as Affinity Tags;278
7.2.1.3;10.3 Use of Aptamers as Specific Ligands for the Separation/Capture of Small Molecules and Enantiomers;281
7.2.1.3.1;10.3.1 Immobilized Aptamers for the Separation/Capture of Small Molecules;281
7.2.1.3.2;10.3.2 Immobilized Aptamers for the Separation of Enantiomers;283
7.2.1.4;10.4 Conclusions;286
7.2.1.5;References;287
7.3;Chapter 11;289
7.3.1;Aptamer Microarrays;289
7.3.1.1;11.1 Introduction;289
7.3.1.2;11.2 Development of High-Throughput Selection Methods;290
7.3.1.2.1;11.2.1 The In Vitro Selection Scheme;290
7.3.1.2.2;11.2.2 High-Throughput Selection;291
7.3.1.2.2.1;11.2.2.1 Alternative Selection Modalities;292
7.3.1.2.2.2;11.2.2.2 Automated Selection;293
7.3.1.2.2.3;11.2.2.3 The Target Problem;295
7.3.1.2.2.3.1;In Vitro Transcription and Translation;295
7.3.1.2.2.3.2;Yeast Expression Libraries;296
7.3.1.3;11.3 Development of Aptamer Microarrays;296
7.3.1.3.1;11.3.1 Aptamer Immobilization on Arrays;297
7.3.1.3.2;11.3.2 Printing Aptamer Arrays;299
7.3.1.3.3;11.3.3 Assaying Aptamer Arrays;300
7.3.1.3.3.1;11.3.3.1 Incubating Arrays with Protein Targets;300
7.3.1.3.3.2;11.3.3.2 Aptamer Microarray Detection of Hen Egg White Lysozyme;300
7.3.1.3.3.3;11.3.3.3 Aptamer Microarray Detection of HIV-1 Reverse Transcriptase;303
7.3.1.4;11.4 Data Analysis;305
7.3.1.5;11.5 Other Approaches;306
7.3.1.6;References;307
7.4;Chapter 12;311
7.4.1;The Use of Functional Nucleic Acids in Solid-Phase Fluorimetric Assays;311
7.4.1.1;12.1 Introduction;311
7.4.1.2;12.2 Traditional Methods for DNA Immobilization;313
7.4.1.3;12.3 Assays Utilizing Immobilized Functional Nucleic Acids;315
7.4.1.3.1;12.3.1 Methods of Fluorescence Signaling;316
7.4.1.3.2;12.3.2 Fluorescence Sensors Based on Immobilized Functional Nucleic Acid Species;319
7.4.1.3.3;12.3.3 Multianalyte Arrays Utilizing Immobilized Molecular Beacon Species;320
7.4.1.3.4;12.3.4 Multianalyte Arrays Utilizing Immobilized Aptamers;323
7.4.1.4;12.4 Sol-gel Immobilization Methods;326
7.4.1.4.1;12.4.1 The Sol-gel Process for Biomolecule Entrapment;326
7.4.1.4.2;12.4.2 Immobilization of Molecular Beacons onto Sol-gel Materials;328
7.4.1.4.3;12.4.3 Entrapment of DNA Aptamers Within Sol-gel Materials;328
7.4.1.4.4;12.4.4 Entrapment of DNA Enzymes in Sol-gel Materials;330
7.4.1.4.5;12.4.5 Layered Structures for Aptamer-Based HTS Assays;332
7.4.1.5;12.5 Emerging Applications;336
7.4.1.6;12.6 Conclusions and Perspectives;338
7.4.1.7;References;339
7.5;Chapter 13;345
7.5.1;Functional Nucleic Acid Sensors as Screening Tools;345
7.5.1.1;13.1 Introduction;345
7.5.1.2;13.2 Aptamers as Screening Tools;347
7.5.1.2.1;13.2.1 DNA Aptamers;347
7.5.1.2.2;13.2.2 RNA Aptamers;349
7.5.1.3;13.3 Allosteric Ribozymes as Screening Tools;349
7.5.1.3.1;13.3.1 Generation of Allosteric Ribozymes;350
7.5.1.3.2;13.3.2 Indirect Screening;350
7.5.1.3.3;13.3.3 Direct Screening;351
7.5.1.4;13.4 Natural RNAs as Screening Tools;352
7.5.1.4.1;13.4.1 Riboswitches as Screening Tools;352
7.5.1.4.2;13.4.2 Pre-miRNAs as Screening Tools;354
7.5.1.5;13.5 Conclusions;354
7.5.1.6;References;355
7.6;Chapter 14;357
7.6.1;Nucleic Acids for Computation;357
7.6.1.1;14.1 Introduction;357
7.6.1.2;14.2 Logic Gates;358
7.6.1.2.1;14.2.1 Silicomimetic Approach;358
7.6.1.2.2;14.2.2 Principles Behind Deoxyribozyme-Based Logic Gates;359
7.6.1.2.3;14.2.3 Output Detection;361
7.6.1.3;14.3 Adders: Circuits for Basic Arithmetical Operations;363
7.6.1.3.1;14.3.1 A Molecular Half-Adder;363
7.6.1.3.2;14.3.2 A Molecular Full-Adder;364
7.6.1.4;14.4 Automata: Complex Decision Making and Scaled Integration;366
7.6.1.4.1;14.4.1 MAYA;366
7.6.1.4.2;14.4.2 MAYA-II;370
7.6.1.5;14.5 Engineering Interelement Interfaces;372
7.6.1.5.1;14.5.1 Ligase–Phosphodiesterase Cascades;372
7.6.1.5.2;14.5.2 Phosphodiesterase–Phosphodiesterase Cascades;373
7.6.1.5.2.1;14.5.2.1 Computational Control of Aptameric Actuators;374
7.6.1.6;14.6 Conclusions and Future Visions;375
7.6.1.7;References;376
7.7;Chapter 15;378
7.7.1;DNAzymes in DNA Nanomachines and DNA Analysis;378
7.7.1.1;15.1 Introduction;378
7.7.1.2;15.2 Autonomous DNA Nanomachines Powered by DNAzyme;379
7.7.1.2.1;15.2.1 Autonomous DNA Nanotweezers;379
7.7.1.2.2;15.2.2 An Autonomous and Processive DNA Walker;381
7.7.1.3;15.3 DNA Detection Systems Based on DNAzyme;383
7.7.1.3.1;15.3.1 DNAzyme-Mediated Amplification of Molecular Beacon Signal for DNA Detection;383
7.7.1.3.2;15.3.2 Cascade DNAzyme Signal Amplification for DNA Detection;385
7.7.1.4;15.4 Summary and Outlook;387
7.7.1.5;References;387
8;Index;390