Aptamers in Bioanalysis

MARCO MASCINI, PhD, is a Full Professor of Analytical Chemistry in the Department of Chemistry at the University of Firenze, Italy. He has been one of the pioneers of biosensor technology. His research interests are related to electrochemical, piezoelectric, and optical biosensors. He pioneered several practical applications of these devices in industrial prototypes for use in bioanalysis, medicine, the environment, and food quality and safety. Some of these devices are commercialized today. Dr. Mascini is the author of more than 300 publications and has taken part in several European Commission projects and steering committees.

• Preface xiContributors xvI Introduction1 Aptamers: Ligands for All Reasons 3Jean-Jacques Toulmé, Jean-Pierre Daguer, and Eric Dausse1.1 Introduction 31.2 The Power of Selection and Aptamer Refinement 51.3 The Chemistry Drives the Shape 71.4 Aptaregulators 111.5 Aptasensors 151.6 Prospects 18References 202 Selex and Its Recent Optimizations 31Beate Strehlitz and Regina Stoltenburg2.1 Introduction 312.2 Aptamers and Their Selection by SELEX 322.3 Modifications of SELEX Technology 352.4 Advantages and Limitations of Aptamers and Their Selection Technology 412.5 Applications of Aptamers Being Developed for the Market 432.6 Future Perspectives 45References 50II Biosensors3 Electrochemical Aptasensors 63Itamar Willner and Maya Zayats3.1 Introduction 633.2 Electrochemical Aptasensor Based on Redox-Active Aptamer Monolayers Linked to Electrodes 663.3 Enzyme-Based Amplified Electrochemical Aptasensors 693.4 Amplified Electrochemical Aptasensors Based on Nanoparticles 723.5 Label-Free Electrochemical Aptasensors 753.6 Field-Effect Transistor–Based Aptasensors 783.7 Conclusions and Perspectives 81References 814 Aptamers: Hybrids Between Nature And Technology 87Moritz K. Beissenhirtz, Eik Leupold, Walter Stöcklein, Ulla Wollenberger, Oliver Pänke, Fred Lisdat, and Frieder W. Scheller4.1 Introduction 874.2 Specific Features of Aptamers 884.3 Electrochemical Detection of Nucleic Acids 884.4 Cytochrome c Binding by Aptamers 904.5 DNA Machines and Aptamers 92References 985 Detection of Protein–aptamer Interactions By Means of Electrochemical Indicators And Transverse Shear Mode Method 101Tibor Hianik5.1 Introduction 1015.2 Immobilization of Aptamers on a Solid Support 1025.3 Detection of Aptamer–Ligand Interactions 1045.3.1 Electrochemical Methods 1055.3.2 Acoustic Methods 1175.4 Conclusions 124References 1256 Biosensors Using the Aptameric Enzyme Subunit: the Use of Aptamers in the Allosteric Control of Enzymes 129Kazunori Ikebukuro, Wataru Yoshida, and Koji Sode6.1 Aptamers as Molecular Recognition Elements of Biosensors 1296.1.1 Comparing Aptamers to Antibodies 1296.1.2 Signaling Aptamers 1316.2 Homogeneous Sensing 1336.2.1 Biosensor Systems That Do Not Require Bound–Free Separation 1336.2.2 Aptameric Enzyme Subunit 1336.3 Evolution-mimicking Algorithm for the Improvement of Aptamers 136References 1377 Nanomaterial-based Label-free Aptasensors 139Kagan Kerman and Eiichi Tamiya7.1 Introduction 1397.2 Label-Free Electrochemical Aptasensors 1397.3 Field-Effect Transistor–Based Aptasensors 1437.4 Label-Free Aptasensors Based on Localized Surface Plasmon Resonance 1477.5 Forthcoming Challenges and Concluding Remarks 151References 1518 Aptamer-based Bioanalytical Assays: Amplification Strategies 159Sara Tombelli, Maria Minunni, and Marco Mascini8.1 Introduction 1598.2 Bioanalytical Assays Based on Aptamer-Functionalized Nanoparticles 1608.3 Aptamers and Quantum Dot–Based Assays 1648.4 Aptazymes and Aptamer-Based Machines 1688.5 Polymerase Chain Reaction as an Amplification Method in Aptamer-Based Assays 1738.6 Conclusions 176References 177III Applications9 Kinetic Capillary Electrophoresis for Selection, Characterization, and Analytical Utilization of Aptamers 183Sergey N. Krylov9.1 Introduction 1839.1.1 Kinetic Capillary Electrophoresis 1839.1.2 The Concept of NECEEM and ECEEM 1859.2 Selection of Aptamers Using KCE Methods for Partitioning and Affinity Control 1889.2.1 NECEEM-Based Selection of Aptamers 1889.2.2 ECEEM-Based Selection of Aptamers 1979.2.3 Optimization of PCR 1989.2.4 Future of KCE Methods for Aptamer Selection 2009.3 Measurements of Binding Parameters of Target–Aptamer Interaction by KCE Methods 2009.3.1 Foundation 2009.3.2 Temperature Control Inside the Capillary 2029.3.3 Examples 2039.4 Quantitative Affinity Analysis of a Target Using Aptamer as an Affinity Probe 2059.4.1 Foundation 2059.4.2 Example 2089.5 Conclusions 209References 21010 Aptamers for Separation of Enantiomers 213Corinne Ravelet and Eric Peyrin10.1 Introduction 21310.2 Generation and Properties of Enantioselective Aptamers 21410.3 Immobilized Aptamers for Enantiomeric Separation by Liquid Chromatography 21510.3.1 Stationary-Phase Preparation and Column Packing 21610.3.2 DNA Aptamer-Based CSPs 21610.3.3 RNA Aptamer-Based CSPs and the Mirror-Image Strategy 21710.3.4 Class-Specific Aptamer-Based CSPs 21910.4 Aptamers for Analysis of Enantiomers by Capillary Electrophoresis 22110.4.1 Aptamers as Chiral Additives in the Background Electrolyte for CE Enantiomeric Separation 22110.4.2 Aptamers for the Design of an Affinity CE-Based Enantioselective Competitive Assay 22310.5 Conclusions 226References 22611 Aptamer-modified Surfaces for Affinity Capture and Detection of Proteins in Capillary Electrophoresis and Maldi–mass Spectrometry 229Linda B. McGown11.1 Introduction 22911.2 Aptamer-Modified Capillaries in Affinity Capillary Electrophoresis 23011.3 Aptamer-Modified Surfaces for Affinity MALDI-MS 23211.3.1 Overview 23211.3.2 Affinity MALDI-MS of Thrombin 23311.3.3 Affinity MALDI-MS of IgE 23511.3.4 Summary 24211.4 Beyond Aptamers: Genome-Inspired DNA Binding Ligands 242References 24812 Strategy for Use of Smart Routes to Prepare Label-free Aptasensors for Bioassay Using Different Techniques 251Bingling Li, Hui Wei, and Shaojun Dong12.1 Introduction 25112.2 Electrochemical Aptasensors 25412.2.1 POSOALF Mode 25412.2.2 PFSOALF Mode 25712.2.3 Electrochemical Impedimetric Aptasensors 25712.2.4 Electrochemical Aptasensors with Nonlabeled Redox Probes 26312.3 Fluorescent Molecular Switches 26512.3.1 POSFALF Mode 26612.3.2 PFSFALF Mode 26812.4 Colorimetry 27212.4.1 POSFALF Mode 27312.4.2 PFSFALF Mode 27412.5 Hemin–Aptamer DNAzyme-Based Aptasensor 28112.6 Liquid Chromatography, Electrochromatography, and Capillary Electrophoresis Applications 28412.7 Other Aptasensors 29012.8 Conclusions 290References 290Index 299

?This book provides descriptions of many applications of aptamers for biosensing, and for this reason, it is very useful and an interesting read.? (JACS , August 2009)