The Aptamer Handbook: Functional Oligonucleotides and Their Applications

Abstract

Part 1: History and Theoretical Background. 1 In Vitro Selection of Functional Oligonucleotides and the Origins of Biochemical Activity (James M. Carothers and Jack W. Szostak). 1.1 Introduction. 1.2 A Brief History of In Vitro Selection. 1.3 Lessons from the Aptamers, Ribozymes, Deoxyribozymes Generated by In Vitro Selection. 1.4 Synthetic Approaches to Understanding the Natural Origins of Function. 1.5 Recent Technological Developments and Future Directions. 1.6 Conclusion. 2 Mathematical Models on RNA Evolution, Simulations In Silico, and Concepts for In Vitro Selection (Peter Schuster). 2.1 From Early Experiments and Theories to the Concept of Neutral Networks. 2.2 RNA Structures, Thermodynamics and Kinetic Folding. 2.3 Neutral Networks and In Silico Evolution of Molecules. 2.4 Designed and Natural RNA Switches. 2.5 Outlook on Future Problems in RNA Design. 3 Fitness Landscapes, Error Thresholds, and Cofactors in Aptamer Evolution (Adam Kun, Marie-Christine Maurel, Mauro Santos, and Eors Szathmary). 3.1 Introduction. 3.2 Functionality Landscapes Inferred from Examples. 3.3 Error Thresholds Inferred from Functional Landscapes: The Realistic Error Threshold of the Neurospora VS Ribozyme. 3.4 Looking for Catalytic Partners: Cofactors and Aptamers. 3.5 The Use of Coenzymes: From the RNA World to the Protein World via Translation and the Genetic Code. 3.6 Outlook. Part 2: In Vitro Selection of Target-binding Oligonucleotides. 4 Aptamers to Small Molecules (Heiko Fickert, Iris G. Fransson, and Ulrich Hahn). 4.1 Introduction. 4.2 Aptamers to Nucleotides/Nucleosides/Nucleobases. 4.3 Aptamers to Cofactors. 4.4 Aptamers to Amino Acids. 4.5 Aptamers to Carbohydrates. 4.6 Aptamers to Natural Products. 4.7 Aptamers to Organic or Fluorescent Dyes. 4.8 The Chimeric Approach for Aptamer Selection. 4.9 Conclusion. 5 Aptamers to Antibiotics (Christina Lorenz and Renee Schroeder). 5.1 Introduction. 5.2 RNA-binding Antibiotics. 5.3 Aptamers to Tetracyclines. 5.4 Aptamers to Streptomycin. 5.5 Aptamers to Aminoglycosides. 5.6 Aptamers to Chloramphenicol. 5.7 Aptamers to the Peptide Antibiotic Viomycin. 5.7.1 The Peptide Antibiotic Viomycin as a Primordial Lead Molecule. 5.8 What Have We Learned From the Antibiotic-binding Aptamers? 6 Aptamers to Proteins (Shahid M. Nimjee, Christopher P. Rusconi, and Bruce A. Sullenger). 6.1 Introduction. 6.2 Properties of Aptamers as Protein Inhibitors. 6.3 Cytokines/Growth Factors. 6.4 Nucleic Acid Binding Proteins. 6.5 Serine Proteases. 6.6 Antibodies/Immunoglobulins. 6.7 Cell Surface Receptor/Cell Adhesion Molecules. 6.8 Complement Proteins - Human Complement C5. 6.9 Extracellular Membrane Protein - Tenascin-C. 6.10 Lipoproteins - Human Non-pancreatic Secretory Phospholipase A2. 6.11 Prion Proteins - Prion Protein PrP Sc . 6.12 Peptides. 6.13 Conclusion. 7 Aptamers to Nucleic Acid Structures (Jean-Jacques Toulme, Fabien Darfeuille, Carmelo Di Primo, and Eric Dausse). 7.1 Introduction. 7.2 Targeting Double-stranded Nucleic Acids. 7.3 Loop-Loop Interactions. 7.4 Chemically Modified Aptamers Recognizing RNA Targets. 7.5 Biological Properties of Aptamers Targeted to Nucleic Acids. 7.6 Conclusion. 8 Riboswitches: Natural Metabolite-binding RNAs Controlling Gene Expression (Adam Roth, Rdiger Welz, and Ronald R. Breaker). 8.1 Introduction. 8.2 Genetic Control by Riboswitches. 8.3 Aptamer Domains of Riboswitches. 8.4 Natural Aptamers Specific for Guanine and Adenine. 8.5 High-resolution Aptamer Structures. 8.6 The Glycine Riboswitch. Part 3: In Vitro Selection of Short, Catalytically Active Oligonucleotides. 9 Catalytically Active RNA Molecules: Tools in Organic Chemistry (Barbara-Sylvia Weigand, Andreas Zerressen, Jrg C. Schlatterer, Mark Helm, and Andres Jaschke). 9.1 Introduction. 9.2 Catalytic Biopolymers. 9.3 De Novo Creation of Ribozymes. 9.4 The Catalytic Spectrum of Ribozymes. 9.5 Summary and Outlook. 10 Deoxyribozymes: Catalytically Active DNA Molecules (Kenny Schlosser, Simon A. McManus, and Yingfu Li). 10.1 Initial Demonstration of DNA's Catalytic Ability. 10.2 A Tale of Two Deoxyribozymes that Cleave RNA. 10.3 Other Deoxyribozymes. 10.4 Outlook. References. 11 In Vivo and In Vitro Target Validation with Nucleic Acid Aptamers as Pharmacological Probes (P. Shannon Pendergrast and David M. Epstein). 11.1 Introduction. 11.2 Target Validation with Aptamers as Pharmacological Probes. 11.3 Limitations of Target Validation by Gene or mRNA Knockout. 11.4 Target Validation Using Nucleic Acid Aptamers. 11.5 Summary. 12 Intramers for Protein Function Analysis and Drug Discovery (Michael Famulok and Gnter Mayer). 12.1 Introduction. 12.2 Intramers: Intracellular Aptamers. 12.3 Aptamers as Probes for Inhibitor Screening. 12.4 Summary. 13 Aptazymes: Allosteric Ribozymes and Deoxyribozymes as Biosensors (Scott M. Knudsen and Andrew D. Ellington). 13.1 Introduction. 13.2 Creating Aptazymes via Rational Design and In Vitro Selection Methodologies. 13.3 Effector Activation. 13.4 Aptazyme Structural and