Entropy-driven DNA logic circuits regulated by DNAzyme (original) (raw)
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DNA computing circuits using libraries of DNAzyme subunits
Nature Nanotechnology, 2011
Biological systems that are capable of performing computational operations 1-3 could be of use in bioengineering and nanomedicine 4,5 , and DNA and other biomolecules have already been used as active components in biocomputational circuits . There have also been demonstrations of DNA/RNA-enzyme-based automatons 12 , logic control of gene expression 14 , and RNA systems for processing of intracellular information 15,16 . However, for biocomputational circuits to be useful for applications it will be necessary to develop a library of computing elements, to demonstrate the modular coupling of these elements, and to demonstrate that this approach is scalable. Here, we report the construction of a DNA-based computational platform that uses a library of catalytic nucleic acids (DNAzymes) 10 , and their substrates, for the input-guided dynamic assembly of a universal set of logic gates and a half-adder/half-subtractor system. We demonstrate multilayered gate cascades, fan-out gates and parallel logic gate operations. In response to input markers, the system can regulate the controlled expression of anti-sense molecules, or aptamers, that act as inhibitors for enzymes.
Chemical communications (Cambridge, England), 2015
This feature article addresses the implementation of catalytic nucleic acids as functional units for the construction of logic gates and computing circuits, and discusses the future applications of these systems. The assembly of computational modules composed of DNAzymes has led to the operation of a universal set of logic gates, to field programmable logic gates and computing circuits, to the development of multiplexers/demultiplexers, and to full-adder systems. Also, DNAzyme cascades operating as logic gates and computing circuits were demonstrated. DNAzyme logic systems find important practical applications. These include the use of DNAzyme-based systems for sensing and multiplexed analyses, for the development of controlled release and drug delivery systems, for regulating intracellular biosynthetic pathways, and for the programmed synthesis and operation of cascades.
Automated Design of Programmable Enzyme-Driven DNA Circuits
ACS Synthetic Biology, 2014
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Chemical Reviews, 2014
CONTENTS 1. Introduction 2881 2. Enzyme-Free Nucleic Acid-Activated Chain Reactions 2883 2.1. Hybridization Chain Reactions (HCR) for Sensing and Tailoring Nanostructures 2884 2.2. Catalytic Hairpin Assembly (CHA) Reactions for Amplified Sensing and Programmed Nanostructuring 2888 2.3. Cascaded Strand-Displacement Processes for Logic Gates and DNA Machines 2893 3. DNAzyme-Activated Chain Reactions 2896 3.1. Isothermal DNAzyme-Activated Catalytic Cascades 2896 3.2. Isothermal Autonomous DNAzyme-Activated Catalytic Cascades 2899 3.3. DNAzyme-Activated Autonomous Cascaded Logic Gates and DNA Machines 2903 4. Enzyme/DNAzyme Coupled Catalytic Cascades 2906 4.1. Biocatalytic Cascades Driven by Coupled DNAzymes and Rolling Circle Amplification (RCA) Processes 2906 4.2. Biocatalytic Cascades Driven by Coupled DNAzymes and Endonucleases/Nicking Enzymes 2910 4.3. Biocatalytic Transformations Driven by Coupled Polymerase/Nicking Enzyme DNAzyme Cascades 2913 4.4. Coupled Ligation-Triggered DNAzyme Cascades 2915 4.5. DNAzyme-Amplified Detection of Telomerase Activity 2917 4.6. Logic Gates with Cascaded Enzyme/DNAzyme Systems 2919 5. Enzyme−Nucleic Acid Systems for Controlled Chemical Processes 2919 5.1.
Catalyst-Based Biomolecular Logic Gates
Catalysts
Regulatory processes in biology can be re-conceptualized in terms of logic gates, analogous to those in computer science. Frequently, biological systems need to respond to multiple, sometimes conflicting, inputs to provide the correct output. The language of logic gates can then be used to model complex signal transduction and metabolic processes. Advances in synthetic biology in turn can be used to construct new logic gates, which find a variety of biotechnology applications including in the production of high value chemicals, biosensing, and drug delivery. In this review, we focus on advances in the construction of logic gates that take advantage of biological catalysts, including both protein-based and nucleic acid-based enzymes. These catalyst-based biomolecular logic gates can read a variety of molecular inputs and provide chemical, optical, and electrical outputs, allowing them to interface with other types of biomolecular logic gates or even extend to inorganic systems. Conti...
Journal of the American Chemical Society, 2004
A conceptually new logic gate based on DNA has been devised. Methoxybenzodeazaadenine (MD A), an artificial nucleobase which we recently developed for efficient hole transport through DNA, formed stable base pairs with T and C. However, a reasonable hole-transport efficiency was observed in the reaction for the duplex containing an MD A/T base pair, whereas the hole transport was strongly suppressed in the reaction using a duplex where the base opposite MD A was replaced by C. The influence of complementary pyrimidines on the efficiency of hole transport through MD A was quite contrary to the selectivity observed for hole transport through G. The orthogonality of the modulation of these hole-transport properties by complementary pyrimidine bases is promising for the design of a new molecular logic gate. The logic gate system was executed by hole transport through short DNA duplexes, which consisted of the "logic gate strand", containing hole-transporting nucleobases, and the "input strand", containing pyrimidines which modulate the hole-transport efficiency of logic bases. A logic gate strand containing multiple MD A bases in series provided the basis for a sharp AND logic action. On the other hand, for OR logic and combinational logic, conversion of Boolean expressions to standard sum-of-product (SOP) expressions was indispensable. Three logic gate strands were designed for OR logic according to each product term in the standard SOP expression of OR logic. The hole-transport efficiency observed for the mixed sample of logic gate strands exhibited an OR logic behavior. This approach is generally applicable to the design of other complicated combinational logic circuits such as the full-adder.
Synthetic Metals, 2003
DNA is one of the most promising molecules as the scaffold for molecular nanotechnology and nanoelectronics. For realizing the molecular devices constructed with DNA, three kinds of function is required such as (1) circuit and control of the conductivity, (2) switching and (3) storage. We have found that the electrical conducting properties of the DNA networks are strongly depended on the doping condition. Photoswitching (current enhancement with shining the light) and magnetoresistance effect are observed in the dye-modified DNA and Co ions doped DNA, respectively. Furthermore, DNA network pattern can be patterned on the Si/SiO 2 surface. These results have significant implications for the application of DNA in electronic devices and in DNA-based electrochemical biosensors.