Cover -- Title Page -- Copyright -- Contents -- Preface -- Chapter 1 DNA Computing: Origination, Motivation, and Goals - Illustrated Introduction -- 1.1 Motivation and Applications -- 1.2 DNA- and RNA-Based Biocomputing Systems in Progress -- 1.3 DNA-Based Information Storage Systems -- 1.4 Short Conclusions and Comments on the Book -- References -- Chapter 2 DNA Computing: Methodologies and Challenges -- 2.1 Introduction to DNA Computing Methodologies -- 2.2 Key Developments in DNA Computing -- 2.2.1 Adleman Model -- 2.2.2 Lipton's Model -- 2.2.3 Smith's Model -- 2.2.4 Sakamoto's Model

2.2.5 Ouyang's Model -- 2.2.6 Chao's Model -- 2.2.7 DNA Origami -- 2.2.8 DNA-Based Data Storage -- 2.3 Challenges -- Acknowledgment -- References -- Chapter 3 DNA Computing and Circuits -- 3.1 From Theory to DNA Implementations -- 3.2 Application-Specific DNA Circuits -- Acknowledgments -- References -- Chapter 4 Connecting DNA Logic Gates in Computational Circuits -- 4.1 DNA Logic Gates in the Context of Molecular Computation -- 4.2 Connecting Deoxyribozyme Logic Gates -- 4.3 Connecting Gates Based on DNA Strand Displacement -- 4.4 Logic Gates Connected Via DNA Four-Way Junction (4WJ)

4.5 Conclusion -- References -- Chapter 5 Development of Logic Gate Nanodevices from Fluorogenic RNA Aptamers -- 5.1 Nucleic Acid: The Material of Choice for Nanotechnology -- 5.2 RNA Aptamers are Modular and Programmable Biosensing Units -- 5.3 Construction of RNA Nanoparticles with Integrated Logic Gate Operations Using Light-Up Aptamers -- 5.3.1 Implementation of MG-Binding RNA Aptamer to Design Binary Logic Gates -- 5.3.2 Implementation of MG-Binding RNA Aptamer and Broccoli RNA Aptamer to Design Half-Adder Circuit -- 5.4 Conclusion -- Acknowledgments -- References

Chapter 6 Programming Molecular Circuitry and Intracellular Computing with Framework Nucleic Acids -- 6.1 Framework Nucleic Acids -- 6.2 A Toolbox for Biomolecular Engineering of Living Systems -- 6.2.1 Biomolecular Scaffolds -- 6.2.2 Logic Units -- 6.2.3 Cell Entry Vehicles -- 6.2.4 Isothermal Construction -- 6.2.5 Targeting and Editing -- 6.2.6 Signal Readout -- 6.2.7 Triggers and Switches -- 6.2.8 Error Correction and Resilience -- 6.3 Targeted Applications -- 6.3.1 Drug Delivery -- 6.3.2 Cellular Imaging -- 6.3.3 Metabolic Engineering and Cellular Pathway Investigation

6.4 Nucleic Acid Nanotechnology-Enabled Computing Kernel -- 6.5 I/O and Human-Computer Interfacing -- 6.6 Information Storage -- 6.7 Perspectives -- 6.8 Conclusion -- 6.8.1 Terminology -- References -- Chapter 7 Engineering DNA Switches for DNA Computing Applications -- 7.1 Introduction -- 7.2 Selecting Recognition Element Based on Input -- 7.3 Engineering Switching Mechanisms -- 7.4 Engineering Logic Output Function Response -- 7.5 Optimizing Switch Response -- 7.6 Perspective -- Acknowledgments -- References -- Chapter 8 Fluorescent Signal Design in DNA Logic Circuits

8.1 Basic Signal Generation Strategies Based on DNA Structures.