Implementing Molecular Logic Gates, Circuits, and Cascades Using DNAzymes

Lakin, Matthew R.; Stojanović, Milan N.; Stefanović, Darko

doi:10.1007/978-3-319-33921-4_1

Cited by 3 publications

(4 citation statements)

References 141 publications

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“…Instead of the toehold-mediated strand displacement mechanism described above, logic gates can also be constructed by using strand displacement to allosterically regulate the catalytic activity of DNAzymes [97][98][99] (Figure 8). Early work with DNAzymes used the E6 DNAzyme, which cleaves a fluorogenic RNA substrate.…”

Section: Using Dnazymes As Part Of Logic Gatesmentioning

confidence: 99%

Catalyst-Based Biomolecular Logic Gates

Winston

Boehr

2022

Catalysts

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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. Continued advances in molecular modeling and engineering will facilitate the construction of new logic gates, further expanding the utility of biomolecular computing.

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Section: Using Dnazymes As Part Of Logic Gatesmentioning

confidence: 99%

Catalyst-Based Biomolecular Logic Gates

Winston

Boehr

2022

Catalysts

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“…Concepts inspired by Boolean logic were applied for the realization of neuronal networks, 15 anticancer drug releasing containers, 16 synthetic multicellular biological computers 17 and logic circuits. 18 The current study is focusing on the development of modular DNA logic gates that employ miRNA markers as input signals and nucleic acid substrate cleavage as output signals for further implementation into bio-computation, diagnostic or therapeutic systems.…”

Section: Introductionmentioning

confidence: 99%

“…24 RNA-cleaving Dzs 25 are attractive candidates for the development of DNA logic gates that can solve the aforementioned issues due to their (1) catalytic activity, (2) ability of multiple turnover reactions which lead to significant signal amplification, and (3) flexible sequence adaptation to interact with virtually any input and/or target nucleic acid sequence. 14,18…”

Section: Introductionmentioning

confidence: 99%

Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs

Smirnov,

Drozd,

Patra

et al. 2024

Analyst

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“…Bio-computing implies the construction of computations and logical operations based on biocomponents: DNA, RNA, enzymes and cells [ 2 ]. Thus, a lot of work has already been done to create logical operations involving DNA [ 3 , 4 ], RNA [ 5 ], DNAzymes [ 6 , 7 , 8 ] and enzymes [ 9 , 10 ]. These systems can perform basic arithmetic operations, such as addition and subtraction [ 11 , 12 ], calculate the square root [ 13 ], play logic games [ 14 , 15 ] and simulate keyboard lock [ 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Logic Gates Based on DNA Aptamers

Andrianova

Kuznetsov

2020

Pharmaceuticals

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DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.

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Implementing Molecular Logic Gates, Circuits, and Cascades Using DNAzymes

Cited by 3 publications

References 141 publications

Catalyst-Based Biomolecular Logic Gates

Catalyst-Based Biomolecular Logic Gates

Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs

Logic Gates Based on DNA Aptamers

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