Discover the science of biocomputing with this comprehensive and forward-looking new resource DNA- and RNA-Based Computing Systems delivers an authoritative overview of DNA- and RNA-based biocomputing systems that touches on cutting-edge advancements in computer science, biotechnology, nanotechnology, and materials science. Accomplished researcher, academic, and author Evgeny Katz offers readers an examination of the intersection of computational, chemical, materials, and engineering aspects of biomolecular information processing. A perfect companion to the recently published Enzyme-Based Computing by the same editor, the book is an authoritative reference for those who hope to better understand DNA- and RNA-based logic gates, multi-component logic networks, combinatorial calculators, and related computational systems that have recently been developed for use in biocomputing devices. DNA- and RNA-Based Computing Systems summarizes the latest research efforts in this rapidly evolving field and points to possible future research foci. Along with an examination of potential applications in biosensing and bioactuation, particularly in the field of biomedicine, the book also includes topics like: A thorough introduction to the fields of DNA and RNA computing, including DNA/enzyme circuits A description of DNA logic gates, switches and circuits,  and how to program them An introduction to photonic logic using DNA and RNA The development and applications of DNA computing for use in databases and robotics  Perfect for biochemists, biotechnologists, materials scientists, and bioengineers, DNA- and RNA-Based Computing Systems also belongs on the bookshelves of computer technologists and electrical engineers who seek to improve their understanding of biomolecular information processing. Senior undergraduate students and graduate students in biochemistry, materials science, and computer science will also benefit from this book.

Table of Contents:
Preface xiii 1 DNA Computing: Origination,Motivation, and Goals -- Illustrated Introduction 1 Evgeny Katz 1.1 Motivation and Applications 1 1.2 DNA- and RNA-Based Biocomputing Systems in Progress 3 1.3 DNA-Based Information Storage Systems 8 1.4 Short Conclusions and Comments on the Book 10 2 DNA Computing: Methodologies and Challenges 15 Deepak Sharma and Manojkumar Ramteke 2.1 Introduction to DNA Computing Methodologies 15 2.2 Key Developments in DNA Computing 16 2.3 Challenges 26 3 DNA Computing and Circuits 31 Chuan Zhang 3.1 FromTheory to DNA Implementations 31 3.2 Application-Specific DNA Circuits 35 4 Connecting DNA Logic Gates in Computational Circuits 45 Dmitry M. Kolpashchikov and Aresenij J. Kalnin 4.1 DNA Logic Gates in the Context of Molecular Computation 45 4.2 Connecting Deoxyribozyme Logic Gates 46 4.3 Connecting Gates Based on DNA Strand Displacement 47 4.4 Logic Gates Connected Via DNA Four-Way Junction (4WJ) 50 4.5 Conclusion 53 5 Development of Logic Gate Nanodevices from Fluorogenic RNA Aptamers 57 Trinity Jackson, Rachel Fitzgerald, Daniel K.Miller, and Emil F. Khisamutdinov 5.1 Nucleic Acid: The Material of Choice for Nanotechnology 57 5.2 RNA Aptamers are Modular and Programmable Biosensing Units 58 5.3 Construction of RNA Nanoparticles with Integrated Logic Gate Operations Using Light-Up Aptamers 64 5.4 Conclusion 70 6 ProgrammingMolecular Circuitry and Intracellular Computing with Framework Nucleic Acids 77 Jiang Li and Chunhai Fan 6.1 Framework Nucleic Acids 77 6.2 A Toolbox for Biomolecular Engineering of Living Systems 80 6.3 Targeted Applications 85 6.4 Nucleic Acid Nanotechnology-Enabled Computing Kernel 86 6.5 I/O and Human-Computer Interfacing 89 6.6 Information Storage 90 6.7 Perspectives 91 6.8 Conclusion 95 6.8.1 Terminology 96 7 Engineering DNA Switches for DNA Computing Applications 105 Dominic Lauzon, Guichi Zhu, and Alexis Vallée-Bélisle 7.1 Introduction 105 7.2 Selecting Recognition Element Based on Input 107 7.3 Engineering Switching Mechanisms 108 7.4 Engineering Logic Output Function Response 116 7.5 Optimizing Switch Response 117 7.6 Perspective 120 8 Fluorescent Signal Design in DNA Logic Circuits 125 Dan Huang, Shu Yang, and Qianfan Yang 8.1 Basic Signal Generation Strategies Based on DNA Structures 126 8.2 Designs for Constructing Multi-output Signals 138 8.3 Summary and Outlook 147 9 Nontraditional Luminescent and Quenching Materials for Nucleic Acid-Based Molecular Photonic Logic 155 Rehan Higgins,Melissa Massey, andW. Russ Algar 9.1 Introduction 155 9.2 DNA Molecular Photonic Logic Gates 156 9.3 Nontraditional Luminescent Materials 158 9.4 Semiconductor "Quantum Dot" Nanocrystals 159 9.5 Lanthanide-Based Materials 161 9.6 Gold Nanoparticles 166 9.7 Metal Nanoclusters 169 9.8 Carbon Nanomaterials 171 9.9 Conjugated Polymers 175 9.10 Conclusions and Perspective 177 10 Programming Spatiotemporal Patterns with DNA-Based Circuits 185 Marc Van Der Hofstadt, Guillaume Gines, Jean-Christophe Galas, and André Estevez-Torres 10.1 Introduction 185 10.2 Experimental Implementation of DNA Analog Circuits 188 10.3 Time-Dependent Spatial Patterns 193 10.4 Steady-State Spatial Patterns 202 10.5 Conclusion and Perspectives 206 11 ComputingWithout Computing: DNA Version 213 Vladik Kreinovich and Julio C. Urenda 11.1 Introduction 213 11.2 ComputingWithout Computing -- Quantum Version: A Brief Reminder 214 11.3 ComputingWithout Computing -- Version Involving Acausal Processes: A Reminder 215 11.4 ComputingWithout Computing -- DNA Version 217 11.5 DNA ComputingWithout Computing Is Somewhat Less Powerful than Traditional DNA Computing: A Proof 222 11.6 First Related Result: Security Is More Difficult to Achieve than Privacy 224 11.7 Second Related Result: Data Storage Is More Difficult than Data Transmission 226 12 DNA Computing: Versatile Logic Circuits and Innovative Bio-applications 231 Daoqing Fan, ErkangWang, and Shaojun Dong 12.1 Definition, Logical Principle, and Classification of DNA Computing 231 12.2 Advanced Arithmetic DNA Logic Devices 232 12.3 Advanced Non-arithmetic DNA Logic Devices 235 12.4 Concatenated Logic Circuits 239 12.5 InnovativeMultifunctional DNA Logic Library 241 12.6 Intelligent Bio-applications 241 12.7 Prospects 244 13 Nucleic Acid-Based Computing in Living Cells Using Strand Displacement Processes 247 Lukas Oesinghaus and Friedrich C. Simmel 13.1 Nucleic Acid Strand Displacement 247 13.2 Synthetic Riboregulators 251 13.3 Combining Strand Displacement and CRISPR Mechanisms 255 13.4 Computing Via Nucleic Acid Strand Displacement in Mammalian Cells 258 13.5 Outlook 260 14 Strand Displacement in DNA-Based Nanodevices and Logic 265 Antoine Bader and Scott L. Cockroft 14.1 An Introduction to Strand Displacement Reactions 265 14.2 Dynamic Reconfiguration of Structural Devices 268 14.3 Stepped and Autonomous DNAWalkers 271 14.4 Early Breakthroughs in DNA Computing 274 14.5 DNA-Based Molecular Logic 279 14.6 Future Prospects for Strand Displacement-Based Devices 286 15 Development and Application of Catalytic DNA in Nanoscale Robotics 293 David Arredondo, Matthew R. Lakin, Darko Stefanovic, andMilan N. Stojanovic 15.1 Introduction 293 15.2 Brief History of DNAzymes 293 15.3 Experimental Implementations 296 15.4 DNAzymeWalkers 298 15.5 StatisticalMechanics and Simulation 300 15.6 Conclusions 302 16 DNA Origami Transformers 307 Reem Mokhtar, Tianqi Song, Daniel Fu, Shalin Shah, Xin Song,Ming Yang, and John Reif 16.1 Introduction 307 16.2 Design 312 16.3 Experimental Demonstrations 316 16.4 Applications 318 16.5 Conclusion 322 17 Nanopore Decoding for DNA Computing 327 Hiroki Yasuga, Kan Shoji, and Ryuji Kawano 17.1 Introduction 327 17.2 Application of Nanopore Technology for Rapid and Label-Free Decoding 330 17.3 Application of Nanopore Decoding in Medical Diagnosis 335 17.4 Conclusions 339 18 An Overview of DNA-Based Digital Data Storage 345 Xin Song, Shalin Shah, and John Reif 18.1 Introduction 345 18.2 Components of a DNA Storage System 346 18.3 Conclusions and Outlook 350 19 Interfacing Enzyme-Based and DNA-Based Computing Systems: FromSimple Boolean Logic to Sophisticated Reversible Logic Systems 353 Evgeny Katz 19.1 Interfacing Enzyme-Based and DNA-Based Computing Systems is a Challenging Goal: Motivations and Approaches 353 19.2 Bioelectronic Interface Transducing Logically Processed Signals from an Enzymatic System to a DNA System 354 19.3 The Bioelectronic Interface Connecting Enzyme-Based Reversible Logic Gates and DNA-Based Reversible Logic Gates: Realization in a Flow Device 362 19.4 Enzyme-Based Fredkin Gate Processing Biomolecular Signals Prior to the Bioelectronic Interface 363 19.5 Reversible DNA-Based Feynman Gate Activated by Signals Produced by the Enzyme-Based Fredkin Gate 368 19.6 Conclusions and Perspectives 371 19.A Appendix 373 19.A.1 Oligonucleotides Used in the System Mimicking Feynman Gate 373 References 374 20 Conclusions and Perspectives: Further Research Directions and Possible Applications 379 Evgeny Katz Index 383