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
