Details

Aptamers for Analytical Applications


Aptamers for Analytical Applications

Affinity Acquisition and Method Design
1. Aufl.

von: Yiyang Dong

124,99 €

Verlag: Wiley-VCH
Format: PDF
Veröffentl.: 15.10.2018
ISBN/EAN: 9783527806829
Sprache: englisch
Anzahl Seiten: 352

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Beschreibungen

An essential guide that puts the focus on method developments and applications in aptamers In recent years, aptamer-based systems have been developed for a wide-range of analytical and medical applications. Aptamers for Analytical Applications offers an introduction to the topic, outlines the common protocols for aptamer synthesis, as well as providing information on the different optimization strategies that can obtain higher affinities to target molecules. The contributors?noted experts on the topic?provide an in-depth review of the characterization of aptamer-target molecule interaction and immobilization strategies and discuss the developments of methods for all the relevant applications. The book outlines different schemes to efficiently immobilize aptamers on substrates as well as summarizing the characterization methods for aptamer-ligand complexes. In addition, aptamer-based colorimetric, enzyme-linked, fluorescent, electrochemical, lateral flow and non-labeling analytical methods are presented. The book also reflects state-of-the-art and emerging applications of aptamer-based methods. This important resource: -Provides a guide to aptamers which provide highly specific and sensitive molecular recognition, with affinities in the range of antibodies and are much cheaper to produce -Offers a discussion of the analytical method developments and improvements with established systems and beyond -Offers a comprehensive guide to all the relevant application areas -Presents an authoritative book from contributors who are noted experts in the field Written for analytical chemists, biochemists, analytical researchers, Aptamers for Analytical Applications is a comprehensive book that adopts a methodological point of view to the important aspects of aptamer generation and modification with a strong emphasis on method developments for relevant applications.
About the Author xv Foreword xvii Preface xix 1 Introduction of SELEX and Important SELEX Variants 1Yiyang Dong, ZhuoWang, SaiWang, YehuiWu, YufanMa, and Jiahui Liu 1.1 SELEX 1 1.2 Negative SELEX and Its Analogs 3 1.3 One-Round SELEX 5 1.4 CE-SELEX 6 1.5 Microfluidic SELEX 8 1.6 Cell-SELEX 10 1.7 In Silico-SELEX 12 1.8 Post-SELEX and In Chemico-SELEX 14 1.9 Auto-SELEX 17 1.10 Primer-Free SELEX 17 1.11 Genomic SELEX 18 1.12 Photo-SELEX 19 1.13 qPCR-SELEX 19 1.14 Perspectives 20 References 21 2 In Chemico Modification of Nucleotides for Better Recognition 27Przemyslaw Jurek, MartaMatusiewicz,MaciejMazurek, and Filip Jelen 2.1 Introduction 27 2.1.1 Beyond ATGC 27 2.1.2 The Scope of This Chapter 29 2.2 Modified Functional Nucleic Acids 30 2.2.1 The “Hows” 30 2.2.1.1 Post-SELEX Optimization 30 2.2.1.2 In-line Modifications 30 2.2.2 The “Whys” 31 2.2.2.1 The Hurdles 31 2.2.2.2 The Gains 32 2.2.3 The “Ifs” 33 2.3 Backbone Modifications 35 2.3.1 2?-OH Modifications 36 2.3.2 Phosphodiester Bond Modifications 36 2.3.3 Xeno Nucleic Acids 38 2.3.3.1 TNA 39 2.3.3.2 FANAs 39 2.3.3.3 HNA, CeNA, LNA, ANA 39 2.3.3.4 Other Modifications 40 2.4 Nucleobase Modifications 40 2.4.1 General Information 40 2.4.2 Modified Aptamers and Catalysts 42 2.4.2.1 Introduction of Cationic Moieties 42 2.4.2.2 Catalysts with Protein-like Sidechains 43 2.4.2.3 Nucleobase-linked Nucleobases 44 2.4.2.4 Glycans Targeting with Boronic Acids 44 2.4.2.5 “Click Chemistry”–Based Versatile Approach 45 2.4.2.6 Nonenzymatic Selection – X-aptamers 45 2.4.2.7 Slow Off-rate Modified Aptamers 46 2.5 Aptamers with Expanded Genetic Alphabet 48 2.5.1 GACTZP Aptamers 48 2.5.2 Aptamers with a Hydrophobic Fifth Base 50 2.6 Summary 52 2.A Appendix 52 References 68 3 Immobilization of Aptamers on Substrates 85Annalisa De Girolamo, Maureen McKeague,Michelangelo Pascale, Marina Cortese, andMaria C. DeRosa 3.1 Introduction 85 3.2 Methods for Immobilization of Aptamers 87 3.2.1 Physical Adsorption 87 3.2.2 Covalent Binding 88 3.2.2.1 Covalent Immobilization of Activated Aptamers on a Functionalized Surface 88 3.2.2.2 Covalent Immobilization of Modified Aptamers on Activated Surfaces 92 3.2.2.3 Covalent Immobilization by Entrapment 95 3.2.2.4 Covalent Immobilization by Electrografting 97 3.2.3 Self-assembled Monolayers 98 3.2.4 Avidin–Biotin Binding (Affinity Coupling) 100 3.2.5 Electrochemical Adsorption 101 3.2.6 Hybridization 101 3.3 Immobilization of Aptamers on Substrates for Diagnostic Applications 102 3.3.1 Flat Gold 102 3.3.1.1 Surface Plasmon Resonance Detection 109 3.3.1.2 Electrochemical Detection 109 3.3.2 Solid Phase 111 3.3.2.1 Optical Detection 112 3.3.2.2 Sample Cleanup 114 3.3.3 Nanomaterials 115 3.4 Future Perspectives on New Substrates and New Immobilization Chemistries 116 3.5 Conclusions 117 References 119 4 Characterization of Aptamer–Ligand Complexes 127RebecaMiranda-Castro, Noemí de-los-Santos-Álvarez, and María J. Lobo-Castañón 4.1 Introduction 127 4.2 Equilibrium Characterization:Thermodynamics 128 4.2.1 Basic Principles 128 4.2.2 Separation-Based Methods 133 4.2.2.1 Equilibrium Dialysis and Related Techniques 133 4.2.2.2 High-Performance Liquid Chromatography 135 4.2.2.3 Electrophoresis 136 4.2.3 Direct Methods 137 4.2.3.1 Isothermal Titration Calorimetry 138 4.2.3.2 Fluorescence-Based Methods 140 4.3 Kinetic Characterization 146 4.3.1 Heterogeneous Methods 148 4.3.1.1 Surface Plasmon Resonance 148 4.3.1.2 Electrochemical Impedance Spectroscopy 152 4.3.2 Homogeneous Methods 154 4.3.2.1 Rotating Droplet Electrochemistry 154 4.3.2.2 Capillary Electrophoresis 157 4.3.2.3 Nanopore-Based Studies 159 4.4 Concluding Remarks 162 Acknowledgments 163 References 164 5 Utilization of Aptamers for Sample Preparation in Analytical Methods 173Zhiyong Yan and Yang Liu 5.1 Introduction 173 5.2 Substrate Materials Developed for Immobilization of Aptamers 175 5.3 Utilization of Aptamers for Sample Preparation in SPE 177 5.3.1 Aptamers Utilized in Affinity Column for SPE 181 5.3.2 Aptamers Utilized in Other SPE 182 5.4 Aptamers Utilized in SPME 182 5.4.1 Aptamers Utilized in Fiber SPME 183 5.4.2 Aptamers Utilized in SBSE 184 5.4.3 Aptamers Utilized in Other Formats of SPME 185 5.5 Aptamers Utilized in Other Affinity Chromatography 185 5.6 Aptamers Utilized in Microfluidic Separation System 187 5.7 Aptamers Utilized in Magnetic Separation System 189 5.7.1 Aptamers Utilized in Magnetic Solid-Phase Extraction (MSPE) 190 5.7.2 Aptamers Utilized in Other Magnetic Separation Formats 190 5.8 Aptamers Utilized in CE 191 5.9 Aptamers Utilized in Other Sample SeparationMethods 192 5.10 Conclusion and Outlook 192 References 192 6 Development of Aptamer-Based Colorimetric Analytical Methods 205Subash C.B. Gopinath, Thangavel Lakshmipriya,M.K.Md Arshad, and Chun Hong Voon 6.1 Introduction 205 6.2 Aptamer Generation for Colorimetric Assay 206 6.3 Aptasensor 206 6.4 Aptamer-AuNP-Based Colorimetric Assays 207 6.5 Applications of AuNP-Aptamer-Based Colorimetric Assays 211 6.6 Conclusions 213 References 213 7 Enzyme-Linked Aptamer Assay (ELAA) 219Yiyang Dong and SaiWang 7.1 Introduction 219 7.2 Enzyme-Linked Immunosorbent Assay 219 7.3 AnalyticalMerits of Aptamer vs Antibody 221 7.4 Enzyme-Linked Aptamer Assay (ELAA) 223 7.5 Comparison of Direct-Competitive ELAA (dc-ELAA), Indirect-Competitive ELAA (ic-ELAA), and ELISA 225 7.6 Conclusion 226 References 227 8 Development of Aptamer-Based Fluorescence Sensors 229SeyedM. Taghdisi, Rezvan Yazdian-Robati, Mona Alibolandi, Mohammad Ramezani, and Khalil Abnous 8.1 Introduction 229 8.2 Fluorescent-Dye-Based Aptasensors 230 8.3 Nanoparticle-Based Aptasensors 231 8.3.1 Fluorescent Aptasensors Based on Gold Nanoparticles 231 8.3.2 Fluorescent Aptasensors Based on Carbon Nanomaterials 234 8.3.3 Fluorescent Aptasensors Based on Silica Nanoparticles 236 8.3.4 Fluorescent Aptasensors Based on Silver Nanoparticles 238 8.3.5 Fluorescent Aptasensors Based on DNA Structures 239 8.3.5.1 Fluorescent Aptasensors Based on DNA Nanostructures 239 8.3.5.2 Fluorescent Aptasensors Based on Triple-Helix Molecular Switch (THMS) 240 8.4 Conclusion 241 Acknowledgment 241 SuggestedWebsites 242 References 242 9 Development of Aptamer-Based Electrochemical Methods 247Jian-guo Xu, Li Yao, Lin Cheng, Chao Yan, andWei Chen 9.1 Introduction 247 9.2 Classification of Electrochemical Aptasensors 247 9.3 Amperometric Aptasensors 248 9.3.1 Covalent Labels 248 9.3.1.1 Enzyme Labels 248 9.3.1.2 Other Covalently Linked Redox Species 250 9.3.2 Non-covalent Labels 256 9.3.2.1 Intercalated Redox Species 256 9.3.2.2 Cationic Redox Species 260 9.3.3 Label-Free Aptasensors 263 9.4 Potentiometric Aptasensors 265 9.5 Impedimetric Aptasensors 266 9.6 Electrochemiluminescence Aptasensors 268 9.7 Conclusion 268 References 269 10 Development of Aptamer-Based Lateral Flow Assay Methods 273Miriam Jauset-Rubio, Mohammad S. El-Shahawi, Abdulaziz S. Bashammakh, Abdulrahman O. Alyoubi, and Ciara K. O’Sullivan 10.1 Introduction 273 10.2 Development of Aptamer-Based Lateral Flow Assay – Strategy 275 10.2.1 Analogies and Differences Compared to Lateral flow Immunoassays (LFIAs) 275 10.2.2 Fundamental Assay Considerations 276 10.2.3 Fundamental Analytical Considerations 277 10.3 Lateral Flow Aptamer Assays 278 10.3.1 Sandwich Assay 278 10.3.2 Competitive Assay 281 10.3.3 Signal Amplification 283 10.4 Summary and Perspectives 291 References 294 11 Development of Aptamer-Based Non-labeling Methods 301Huajie Gu, Liling Hao, and ZhoupingWang 11.1 Introduction 301 11.2 Surface Plasmon Resonance (SPR)-Based Aptasensor 302 11.2.1 Introduction 302 11.2.2 The Principle of SPR Technique 302 11.2.3 The Classification of SPR Biosensors 303 11.2.3.1 SPR Biosensors Based on Angular Modulation 303 11.2.3.2 SPR Biosensors Based onWavelength Modulation 304 11.2.3.3 SPR Biosensors Based on Amplitude Modulation 304 11.2.3.4 SPR Biosensors Based on Phase Modulation 304 11.2.4 The Application of Aptamer-Based SPR Technique 304 11.2.4.1 Determination of the Affinity of Aptamers 305 11.2.4.2 Detection Analyte Concentrations 305 11.2.5 Summary and Prospects of SPR Aptasensors 310 11.3 Quartz Crystal Microbalance (QCM)-Based Aptasensor 311 11.3.1 Introduction 311 11.3.2 The Principle of QCM Technique 311 11.3.3 The Application of Aptamer-Based QCM Technique 312 11.3.3.1 Determination of the Affinity of Aptamers 312 11.3.3.2 Detection of Analyte Concentrations 313 11.3.4 Summary and Prospect of QCM Aptasensors 318 11.4 Isothermal Titration Calorimetry (ITC) 319 11.4.1 Introduction 319 11.4.2 The Principle of ITC Technique 319 11.4.3 Thermodynamic Parameters Obtained from ITC Experiment 320 11.4.4 Application of ITC in Association Between Aptamer and Target 322 11.4.4.1 Interaction Between the Aptamer Domain of the Purine Riboswitch and Ligands 322 11.4.4.2 Interaction Between the Cocaine-Binding Aptamer and Quinine 324 11.4.4.3 Affinity Test by ITC After Systemic Evolution of Ligands by EXponential Enrichment (SELEX) 327 11.4.5 Summary 329 11.5 MicroScaleThermophoresis (MST) 329 11.5.1 Introduction 329 11.5.2 The Principle of MST Technique 330 11.5.3 Application of MST in Association Between Aptamer and Target 332 11.5.3.1 Interaction Between Steroid Hormones and Aptamers 332 11.5.3.2 Affinity Test by MST After Systemic Evolution of Ligands by EXponential Enrichment (SELEX) 333 11.5.4 Summary 335 References 335 12 Challenges of SELEX and Demerits of Aptamer-Based Methods 345Haiyun Liu and Jinghua Yu 12.1 Introduction 345 12.2 Challenges of SELEX 347 12.2.1 Aptamer Degradation 347 12.2.2 Purification 348 12.2.3 Binding Affinity (Kd) 348 12.2.4 Target Immobilization 349 12.2.5 Cross-Reactivity 350 12.2.6 Time and Cost 350 12.2.7 Interaction of Aptamers with Intracellular Targets 351 12.2.8 Bioinformatics Tools 352 12.3 Demerits of Aptamer-Based Methods 352 12.3.1 Sensitivity 352 12.3.2 Selectivity and Specificity 354 12.3.3 Reproducibility 355 12.3.4 Calibration and Uncertainty 355 12.3.5 Regeneration 355 12.3.6 Immobilization of Aptamers 356 12.4 Summary and Perspectives 356 References 357 13 State of the Art and Emerging Applications 365Lin-Chi Chen, Jui-HongWeng, and Pei-Wei Lee 13.1 Introduction 365 13.2 Frontiers of Analytical Aptamer Selection and Probe Design 368 13.2.1 Biochip-Based Aptamer Selection 368 13.2.2 SELEX with Next-Generation Sequencing (NGS) 372 13.2.3 Aptamer Optimization and Specialized Selection 373 13.2.4 In Silico Aptamer Design 376 13.3 Novel Aptasensing Platforms – From Assays and Sensors to Instrumental Analyses 378 13.3.1 Aptamer Assays 378 13.3.2 Aptasensors 380 13.3.3 Aptamer Chips 382 13.3.4 Cell-Based Aptasensing 384 13.4 Emerging Applications of Aptamer Diagnostics 385 13.4.1 Human Disease Diagnosis 386 13.4.2 Food/EnvironmentalMonitoring – Mycotoxins, Pesticides, Heavy Metal Ions 387 13.4.3 Therapeutic Drug Assessment – Organ-on-a-Chip 387 13.4.4 New Molecular Biology Applications – CRISPR/Cas9, Stem Cells, IHC 388 13.5 Concluding Remarks – Frontiers of Frontiers 389 Acknowledgments 389 References 390 Index 397
Yiyang Dong, PhD, is Professor and Director of the Food Safety & Risk Assessment Laboratory of Beijing University of Chemical Technology (BUCT) in Beijing, China.
An essential guide that puts the focus on method developments and applications in aptamers In recent years, aptamer-based systems have been developed for a wide-range of analytical and medical applications. Aptamers for Analytical Applications offers an introduction to the topic, outlines the common protocols for aptamer synthesis, as well as providing information on the different optimization strategies that can obtain higher affinities to target molecules. The contributors—noted experts on the topic—provide an in-depth review of the characterization of aptamer-target molecule interaction and immobilization strategies and discuss the developments of methods for all the relevant applications. The book outlines different schemes to efficiently immobilize aptamers on substrates as well as summarizing the characterization methods for aptamer-ligand complexes. In addition, aptamer-based colorimetric, enzyme-linked, fluorescent, electrochemical, lateral flow and non-labeling analytical methods are presented. The book also reflects state-of-the-art and emerging applications of aptamer-based methods. This important resource: Provides a guide to aptamers which provide highly specific and sensitive molecular recognition, with affinities in the range of antibodies and are much cheaper to produce Offers a discussion of the analytical method developments and improvements with established systems and beyond Offers a comprehensive guide to all the relevant application areas Presents an authoritative book from contributors who are noted experts in the field Written for analytical chemists, biochemists, analytical researchers, Aptamers for Analytical Applications is a comprehensive book that adopts a methodological point of view to the important aspects of aptamer generation and modification with a strong emphasis on method developments for relevant applications.

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