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12 pages, 10600 KiB

Open AccessArticle

A DNA Finite-State Machine Based on the Programmable Allosteric Strategy of DNAzyme

by Jun Wang, Xiaokang Zhang, Peijun Shi, Ben Cao and Bin Wang

Int. J. Mol. Sci. 2023, 24(4), 3588; https://doi.org/10.3390/ijms24043588 - 10 Feb 2023

Cited by 3 | Viewed by 2558

Living organisms can produce corresponding functions by responding to external and internal stimuli, and this irritability plays a pivotal role in nature. Inspired by such natural temporal responses, the development and design of nanodevices with the ability to process time-related information could facilitate the development of molecular information processing systems. Here, we proposed a DNA finite-state machine that can dynamically respond to sequential stimuli signals. To build this state machine, a programmable allosteric strategy of DNAzyme was developed. This strategy performs the programmable control of DNAzyme conformation using a reconfigurable DNA hairpin. Based on this strategy, we first implemented a finite-state machine with two states. Through the modular design of the strategy, we further realized the finite-state machine with five states. The DNA finite-state machine endows molecular information systems with the ability of reversible logic control and order detection, which can be extended to more complex DNA computing and nanomachines to promote the development of dynamic nanotechnology. Full article

(This article belongs to the Section Molecular Nanoscience)

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16 pages, 22609 KiB

Open AccessArticle

Construction of Multiple Logic Circuits Based on Allosteric DNAzymes

by Xin Liu, Qiang Zhang, Xun Zhang, Yuan Liu, Yao Yao and Nikola Kasabov

Biomolecules 2022, 12(4), 495; https://doi.org/10.3390/biom12040495 - 24 Mar 2022

Cited by 3 | Viewed by 3070

Abstract

In DNA computing, the implementation of complex and stable logic operations in a universal system is a critical challenge. It is necessary to develop a system with complex logic functions based on a simple mechanism. Here, the strategy to control the secondary structure of assembled DNAzymes’ conserved domain is adopted to regulate the activity of DNAzymes and avoid the generation of four-way junctions, and makes it possible to implement basic logic gates and their cascade circuits in the same system. In addition, the purpose of threshold control achieved by the allosteric secondary structure implements a three-input DNA voter with one-vote veto function. The scalability of the system can be remarkably improved by adjusting the threshold to implement a DNA voter with 2n + 1 inputs. The proposed strategy provides a feasible idea for constructing more complex DNA circuits and a highly integrated computing system. Full article

(This article belongs to the Special Issue Algorithmic Themes in Bioinformatics and Computational Biology)

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16 pages, 2847 KiB

Open AccessArticle

Constructing Controllable Logic Circuits Based on DNAzyme Activity

by Fengjie Yang, Yuan Liu, Bin Wang, Changjun Zhou and Qiang Zhang

Molecules 2019, 24(22), 4134; https://doi.org/10.3390/molecules24224134 - 15 Nov 2019

Cited by 9 | Viewed by 4258

Abstract

Recently, DNA molecules have been widely used to construct advanced logic devices due to their unique properties, such as a simple structure and predictable behavior. In fact, there are still many challenges in the process of building logic circuits. Among them, the scalability of the logic circuit and the elimination of the crosstalk of the cascade circuit have become the focus of research. Inspired by biological allosteric regulation, we developed a controllable molecular logic circuit strategy based on the activity of DNAzyme. The E6 DNAzyme sequence was temporarily blocked by hairpin DNA and activated under appropriate input trigger conditions. Using a substrate with ribonucleobase (rA) modification as the detection strand, a series of binary basic logic gates (YES, AND, and INHIBIT) were implemented on the computational component platform. At the same time, we demonstrate a parallel demultiplexer and two multi-level cascade circuits (YES-YES and YES-Three input AND (YES-TAND)). In addition, the leakage of the cascade process was reduced by exploring factors such as concentration and DNA structure. The proposed DNAzyme activity regulation strategy provides great potential for the expansion of logic circuits in the future. Full article

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