Details

Aptamers for Analytical Applications


Aptamers for Analytical Applications

Affinity Acquisition and Method Design
1. Aufl.

von: Yiyang Dong

133,99 €

Verlag: Wiley-VCH
Format: PDF
Veröffentl.: 15.10.2018
ISBN/EAN: 9783527806829
Sprache: englisch
Anzahl Seiten: 432

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Beschreibungen

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