DNA- and RNA-Based Computing Systems

Evgeny Katz

• Publisher: Wiley-VCH
• Year: 2020
• Print ISBN: 9783527347209
• eBook ISBN: 9783527825417
• Edition: 1
• Topic: Scienze biologiche
• Subtopic: Biochimica

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.

1
DNA Computing: Origination, Motivation, and Goals – Illustrated Introduction

Evgeny Katz

Clarkson University, Department of Chemistry and Biomolecular Science, Potsdam, NY, 13699, USA

1.1 Motivation and Applications

Exponential development of computing systems based on silicon materials and binary algorithms formulated as “Moore's law” [1] (Figure 1.1) is coming to the end being limited by further component miniaturization and by the speed of operation. Conceptually novel ideas are needed to break through these limitations. The quest for novel ideas in the information processing has resulted in several exciting directions in the general area of unconventional computing [2–4], including research in quantum computing [5] and biologically inspired molecular computing [6–9]. Molecular computing systems, generally motivated by mimicking natural biological information processing [10,11], are not necessarily based on biomolecules and could be represented by synthetic molecules with signal‐controlled switchable properties. Synthetic molecular systems and nano‐species have been designed to mimic operation of Boolean logic gates and demonstrate basic arithmetic functions and memory units. However, despite progress achieved in assembling synthetic molecular systems performing basic Boolean operations and simple computations [6–9], these systems have limited complexity, and further increase of their complexity is very challenging. A new advance in the development of molecular information systems has been achieved with use of biomolecular species [12] (Figure 1.2) such as deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) [13–16], oligopeptides [17], proteins [18], enzymes [2,19,20], antigens/antibodies [21], and even whole biological cells/organisms [22–24] capable of operating in a biological environment [25], borrowing some ideas from systems biology [26]. The advantage of the biomolecular computing systems is their ability to be integrated in artificially designed complex reacting processes mimicking multistep information processing networks. These systems are still far away from the natural information processing in cells but are already much more complex than pure synthetic molecular systems. In fact, biochemical reactions are at the core of the mechanism of life itself, and therefore one could set rather ambitious expectations for how far can (bio)chemical reaction systems be scaled up in complexity, if not speed, for information processing. While in a long perspective a “biocomputer” might become a reality [27], particularly for some special applications, e.g., for solving complex combinatorial problems [28], potentially promising to have an advantage over silicon‐based electronic computers due to parallel computing performed by numerous biomolecular units, the present level of technology does not allow any practical use of biomolecular systems for real computational applications. For achieving any practical result soon, some other applications, different from making a biocomputer, should be considered using the (bio)molecular systems with a limited complexity. One of the immediate possible applications for molecular logic systems is a special kind of biosensing [29–31] where the multiple input signals are logically processed through chemical reactions resulting in YES/NO decisions in the binary (0,1) format. In this subarea of biomolecular logic systems, practical results are already possible at the present level of the system complexity, particularly for biomedical applications [32–35]. Overall, the research in molecular/biomolecular information processing, which has been motivated originally to progress unconventional computing applications, is broadly developing to areas not directly related to computing in its narrow definition. This research is bringing us to novel areas in sensing/biosensing [29–31], switchable “sm...

Table of contents

• Cover
• Table of Contents
• DNA- and RNA-Based Computing Systems
• Copyright
• Preface
• 1 DNA Computing: Origination, Motivation, and Goals – Illustrated Introduction
• 2 DNA Computing: Methodologies and Challenges
• 3 DNA Computing and Circuits
• 4 Connecting DNA Logic Gates in Computational Circuits
• 5 Development of Logic Gate Nanodevices from Fluorogenic RNA Aptamers
• 6 Programming Molecular Circuitry and Intracellular Computing with Framework Nucleic Acids
• 7 Engineering DNA Switches for DNA Computing Applications
• 8 Fluorescent Signal Design in DNA Logic Circuits
• 9 Nontraditional Luminescent and Quenching Materials for Nucleic Acid‐Based Molecular Photonic Logic
• 10 Programming Spatiotemporal Patterns with DNA‐Based Circuits
• 11 Computing Without Computing: DNA Version
• 12 DNA Computing: Versatile Logic Circuits and Innovative Bio‐applications
• 13 Nucleic Acid‐Based Computing in Living Cells Using Strand Displacement Processes
• 14 Strand Displacement in DNA‐Based Nanodevices and Logic
• 15 Development and Application of Catalytic DNA in Nanoscale Robotics
• 16 DNA Origami Transformers
• 17 Nanopore Decoding for DNA Computing
• 18 An Overview of DNA‐Based Digital Data Storage
• 19 Interfacing Enzyme‐Based and DNA‐Based Computing Systems: From Simple Boolean Logic to Sophisticated Reversible Logic Systems
• 20 Conclusions and Perspectives: Further Research Directions and Possible Applications
• Index
• End User License Agreement