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Table of Contents
Preface; Contents; 1: Programming Biology: Expanding the Toolset for the Engineering of Transcription; 1.1 Introduction; 1.2 Reengineering Natural Systems for New Applications; 1.2.1 The Beginnings; 1.2.2 Engineering Controlled Transcription: Mining for Parts; 1.2.3 Tandem Gene Duplication; 1.2.4 Decoy Operators Modulate Transcription Factors; 1.2.5 Choose the Gene Location Wisely; 1.3 Engineering Transcription: Above and Beyond Nature; 1.3.1 Engineered Promoter Binding; 1.3.2 Attenuation: Regulation Through Termination; 1.3.3 Transcription Machinery Engineering
1.3.3.1 Hacking the Polymerase1.3.3.2 Global Transcription Machinery Engineering; 1.3.4 Artificial Transcription Factors; 1.3.4.1 Zinc Finger Proteins; 1.3.4.2 A Tale of Transcription Activator-Like Effectors (TALEs): Adversaries Turned Allies; 1.3.4.3 RNA-Guided DNA Binding with CRISPR Technology; 1.4 Complex Behavior Through Genetic Circuits; 1.4.1 Biosensors Provide Circuit Inputs; 1.4.2 Boole Meets Biology: Genetic Logic Gates; 1.4.3 Towards Building a Biochemical Computer; 1.4.3.1 Volatile and Nonvolatile Memory; 1.4.3.2 Clock Generators: Biological Metronomes
1.4.3.3 Network Interfaces Enable Multicellular Computing1.4.4 Design Principles; 1.4.4.1 Turning the Control Knobs of Discrete Components; 1.4.4.2 Serial Signal Processing Parts; 1.4.4.3 Parallel Network Loops; 1.4.5 Caveats and Perspectives; 1.5 Transcription Engineering for New Advances in the Fields of Medicine and Industrial Biotechnology; 1.5.1 Transcriptional Engineering in Medicine; 1.5.1.1 Combatting Infectious Diseases: Fighting Fire with Fire; 1.5.1.2 Microscopic Doctors that Diagnose and Medicate; 1.5.1.3 Target the Tumor and Nothing But the Tumor
1.5.2 Industrial Applications: Synthetic Biology Meets Metabolic Engineering1.6 Outlook; References; 2: Novel DNA and RNA Elements; 2.1 Introduction; 2.2 Synthetic Promoters; 2.2.1 Hybrid Promoters; 2.2.2 Common Strategies for the Engineering of Prokaryotic Promoters; 2.2.3 Common Methods for the Engineering of Eukaryotic Promoters; 2.3 Terminators; 2.4 Ribozymes; 2.5 Riboswitches; 2.6 Small RNAs; 2.6.1 Detection, Prediction, and Classification of Small RNAs; 2.6.2 Small RNA Processing Pathways; 2.6.3 Functions and Applications of Small RNAs; 2.7 Long Noncoding RNAs
2.8 Aptamers and Adaptamers2.9 DNA Barcodes; 2.10 DNA Machines; 2.11 DNA Walker; References; 3: Key Methods for Synthetic Biology: Genome Engineering and DNA Assembly; 3.1 Genome Engineering Technologies; 3.1.1 Non-programmable Genome Engineering; 3.1.1.1 Site-Specific Recombinases (Cre/loxP, FLP/FRT); 3.1.1.2 Transposons; 3.1.2 RNA Interference and Translational Repression; 3.1.3 Prokaryotic Genome Engineering; 3.1.3.1 Group II Introns: Targetrons; 3.1.3.2 Recombineering; 3.1.4 Universally Applicable Genome Editing Strategies; 3.1.4.1 Homing Endonucleases; 3.1.4.2 Zinc-Finger Nucleases
1.3.3.1 Hacking the Polymerase1.3.3.2 Global Transcription Machinery Engineering; 1.3.4 Artificial Transcription Factors; 1.3.4.1 Zinc Finger Proteins; 1.3.4.2 A Tale of Transcription Activator-Like Effectors (TALEs): Adversaries Turned Allies; 1.3.4.3 RNA-Guided DNA Binding with CRISPR Technology; 1.4 Complex Behavior Through Genetic Circuits; 1.4.1 Biosensors Provide Circuit Inputs; 1.4.2 Boole Meets Biology: Genetic Logic Gates; 1.4.3 Towards Building a Biochemical Computer; 1.4.3.1 Volatile and Nonvolatile Memory; 1.4.3.2 Clock Generators: Biological Metronomes
1.4.3.3 Network Interfaces Enable Multicellular Computing1.4.4 Design Principles; 1.4.4.1 Turning the Control Knobs of Discrete Components; 1.4.4.2 Serial Signal Processing Parts; 1.4.4.3 Parallel Network Loops; 1.4.5 Caveats and Perspectives; 1.5 Transcription Engineering for New Advances in the Fields of Medicine and Industrial Biotechnology; 1.5.1 Transcriptional Engineering in Medicine; 1.5.1.1 Combatting Infectious Diseases: Fighting Fire with Fire; 1.5.1.2 Microscopic Doctors that Diagnose and Medicate; 1.5.1.3 Target the Tumor and Nothing But the Tumor
1.5.2 Industrial Applications: Synthetic Biology Meets Metabolic Engineering1.6 Outlook; References; 2: Novel DNA and RNA Elements; 2.1 Introduction; 2.2 Synthetic Promoters; 2.2.1 Hybrid Promoters; 2.2.2 Common Strategies for the Engineering of Prokaryotic Promoters; 2.2.3 Common Methods for the Engineering of Eukaryotic Promoters; 2.3 Terminators; 2.4 Ribozymes; 2.5 Riboswitches; 2.6 Small RNAs; 2.6.1 Detection, Prediction, and Classification of Small RNAs; 2.6.2 Small RNA Processing Pathways; 2.6.3 Functions and Applications of Small RNAs; 2.7 Long Noncoding RNAs
2.8 Aptamers and Adaptamers2.9 DNA Barcodes; 2.10 DNA Machines; 2.11 DNA Walker; References; 3: Key Methods for Synthetic Biology: Genome Engineering and DNA Assembly; 3.1 Genome Engineering Technologies; 3.1.1 Non-programmable Genome Engineering; 3.1.1.1 Site-Specific Recombinases (Cre/loxP, FLP/FRT); 3.1.1.2 Transposons; 3.1.2 RNA Interference and Translational Repression; 3.1.3 Prokaryotic Genome Engineering; 3.1.3.1 Group II Introns: Targetrons; 3.1.3.2 Recombineering; 3.1.4 Universally Applicable Genome Editing Strategies; 3.1.4.1 Homing Endonucleases; 3.1.4.2 Zinc-Finger Nucleases