1
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Liu Y, Zhai Y, Hu H, Liao Y, Liu H, Liu X, He J, Wang L, Wang H, Li L, Zhou X, Xiao X. Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400011. [PMID: 38698560 PMCID: PMC11234411 DOI: 10.1002/advs.202400011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/09/2024] [Indexed: 05/05/2024]
Abstract
DNA is commonly employed as a substrate for the building of artificial logic networks due to its excellent biocompatibility and programmability. Till now, DNA logic circuits are rapidly evolving to accomplish advanced operations. Nonetheless, nowadays, most DNA circuits remain to be disposable and lack of field programmability and thereby limits their practicability. Herein, inspired by the Configurable Logic Block (CLB), the CLB-based erasable field-programmable DNA circuit that uses clip strands as its operation-controlling signals is presented. It enables users to realize diverse functions with limited hardware. CLB-based basic logic gates (OR and AND) are first constructed and demonstrated their erasability and field programmability. Furthermore, by adding the appropriate operation-controlling strands, multiple rounds of programming are achieved among five different logic operations on a two-layer circuit. Subsequently, a circuit is successfully built to implement two fundamental binary calculators: half-adder and half-subtractor, proving that the design can imitate silicon-based binary circuits. Finally, a comprehensive CLB-based circuit is built that enables multiple rounds of switch among seven different logic operations including half-adding and half-subtracting. Overall, the CLB-based erasable field-programmable circuit immensely enhances their practicability. It is believed that design can be widely used in DNA logic networks due to its efficiency and convenience.
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Affiliation(s)
- Yizhou Liu
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Yuxuan Zhai
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Hao Hu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Yuheng Liao
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Huan Liu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Xiao Liu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Jiachen He
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Limei Wang
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Hongxun Wang
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Longjie Li
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Xiaoyu Zhou
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000China
| | - Xianjin Xiao
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
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Zhang X, Liu X, Zhang X, Cui S, Yao Y, Wang B, Zhang Q. Arbitrary Digital DNA Computing: A Programmable Molecular Perceptron Driven by Lambda Exonuclease for Lighting up Concatenated Circuits. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38688864 DOI: 10.1021/acsami.4c03486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
DNA circuits, as a type of biochemical system, have the capability to synchronize the perception of molecular information with a chemical reaction response and directly process the molecular characteristic information in biological activities, making them a crucial area in molecular digital computing and smart bioanalytical applications. Instead of cascading logic gates, the traditional research approach achieves multiple logic operations which limits the scalability of DNA circuits and increases the development costs. Based on the interface reaction mechanism of Lambda exonuclease, the molecular perceptron proposed in this study, with the need for only adjusting weight and bias parameters to alter the corresponding logic expressions, enhances the versatility of the molecular circuits. We also establish a mathematical model and an improved heuristic algorithm for solving weights and bias parameters for arbitrary logic operations. The simulation and FRET experiment results of a series of logic operations demonstrate the universality of molecular perceptron. We hope the proposed molecular perceptron can introduce a new design paradigm for molecular circuits, fostering innovation and development in biomedical research related to biosensing, targeted therapy, and nanomachines.
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Affiliation(s)
- Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Shuang Cui
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
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3
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Zou C. A novel activation function based on DNA enzyme-free hybridization reaction and its implementation on nonlinear molecular learning systems. Phys Chem Chem Phys 2024; 26:11854-11866. [PMID: 38567416 DOI: 10.1039/d3cp02811a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
With the advent of the post-Moore's Law era, the development of traditional silicon-based computers has reached its limit, and there is an urgent need to develop new computing technologies to meet the needs of science, technology, and daily life. Due to its super-strong parallel computing capability and outstanding data storage capacity, DNA computing has become an important branch and hot research topic of new computer technology. DNA enzyme-free hybridization reaction technology is widely used in DNA computing, showing excellent performance in computing power and information processing. Studies have shown that DNA molecules not only have the computing function of electronic devices, but also exhibit certain human brain-like functions. In the field of artificial intelligence, activation functions play an important role as they enable artificial intelligence systems to fit and predict non-linear and complex variable relationships. Due to the difficulty of implementing activation functions in DNA computing, DNA circuits cannot easily achieve all the functions of artificial intelligence. DNA circuits need to rely on electronic computers to complete the training and learning process. Based on the parallel computing characteristics of DNA computing and the kinetic features of DNA molecule displacement reactions, this paper proposes a new activation function. This activation function can not only be easily implemented by DNA enzyme-free hybridization reaction reactions, but also has good nesting properties in DNA circuits, and can be cascaded with other DNA reactions to form a complete DNA circuit. This paper not only provides the mathematical analysis of the proposed activation function, but also provides a detailed analysis of its kinetic features. The activation function is then nested into a nonlinear neural network for DNA computing. This system is capable of fitting and predicting a certain nonlinear function.
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Affiliation(s)
- Chengye Zou
- College of Information Science and Engineering, Yanshan University, Qinhuangdao 066004, China.
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4
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Lv H, Xie N, Li M, Dong M, Sun C, Zhang Q, Zhao L, Li J, Zuo X, Chen H, Wang F, Fan C. DNA-based programmable gate arrays for general-purpose DNA computing. Nature 2023; 622:292-300. [PMID: 37704731 DOI: 10.1038/s41586-023-06484-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 07/26/2023] [Indexed: 09/15/2023]
Abstract
The past decades have witnessed the evolution of electronic and photonic integrated circuits, from application specific to programmable1,2. Although liquid-phase DNA circuitry holds the potential for massive parallelism in the encoding and execution of algorithms3,4, the development of general-purpose DNA integrated circuits (DICs) has yet to be explored. Here we demonstrate a DIC system by integration of multilayer DNA-based programmable gate arrays (DPGAs). We find that the use of generic single-stranded oligonucleotides as a uniform transmission signal can reliably integrate large-scale DICs with minimal leakage and high fidelity for general-purpose computing. Reconfiguration of a single DPGA with 24 addressable dual-rail gates can be programmed with wiring instructions to implement over 100 billion distinct circuits. Furthermore, to control the intrinsically random collision of molecules, we designed DNA origami registers to provide the directionality for asynchronous execution of cascaded DPGAs. We exemplify this by a quadratic equation-solving DIC assembled with three layers of cascade DPGAs comprising 30 logic gates with around 500 DNA strands. We further show that integration of a DPGA with an analog-to-digital converter can classify disease-related microRNAs. The ability to integrate large-scale DPGA networks without apparent signal attenuation marks a key step towards general-purpose DNA computing.
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Affiliation(s)
- Hui Lv
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Laboratory, Shanghai, China
| | - Nuli Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingkai Dong
- Institute of Parallel and Distributed Systems, Shanghai Jiao Tong University, Shanghai, China
| | - Chenyun Sun
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Zhang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Zhao
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- Xiangfu Laboratory, Jiashan, China
| | - Jiang Li
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai, China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haibo Chen
- Institute of Parallel and Distributed Systems, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
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5
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Liu J, Zhang C, Song J, Zhang Q, Zhang R, Zhang M, Han D, Tan W. Unlocking Genetic Profiles with a Programmable DNA-Powered Decoding Circuit. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2206343. [PMID: 37116171 PMCID: PMC10369254 DOI: 10.1002/advs.202206343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Human genetic architecture provides remarkable insights into disease risk prediction and personalized medication. Advances in genomics have boosted the fine-mapping of disease-associated genetic variants across human genome. In healthcare practice, interpreting intricate genetic profiles into actionable medical decisions can improve health outcomes but remains challenging. Here an intelligent genetic decoder is engineered with programmable DNA computation to automate clinical analyses and interpretations. The DNA-based decoder recognizes multiplex genetic information by one-pot ligase-dependent reactions and interprets implicit genetic profiles into explicit decision reports. It is shown that the DNA decoder implements intended computation on genetic profiles and outputs a corresponding answer within hours. Effectiveness in 30 human genomic samples is validated and it is shown that it achieves desirable performance on the interpretation of CYP2C19 genetic profiles into drug responses, with accuracy equivalent to that of Sanger sequencing. Circuit modules of the DNA decoder can also be readily reprogrammed to interpret another pharmacogenetics genes, provide drug dosing recommendations, and implement reliable molecular calculation of polygenic risk score (PRS) and PRS-informed cancer risk assessment. The DNA-powered intelligent decoder provides a general solution to the translation of complex genetic profiles into actionable healthcare decisions and will facilitate personalized healthcare in primary care.
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Affiliation(s)
- Junlan Liu
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chao Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinxing Song
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qing Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rongjun Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mingzhi Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
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6
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Abstract
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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7
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Xie N, Li M, Wang Y, Lv H, Shi J, Li J, Li Q, Wang F, Fan C. Scaling Up Multi-bit DNA Full Adder Circuits with Minimal Strand Displacement Reactions. J Am Chem Soc 2022; 144:9479-9488. [DOI: 10.1021/jacs.2c03258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nuli Xie
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yue Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Hui Lv
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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8
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Zou C, Zhang Q, Zhou C, Cao W. A nonlinear neural network based on an analog DNA toehold mediated strand displacement reaction circuit. NANOSCALE 2022; 14:6585-6599. [PMID: 35421885 DOI: 10.1039/d1nr06861j] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The DNA toehold mediated strand displacement reaction is one of the semi-synthetic biology technologies for next-generation computers. In this article, we present a framework for a novel nonlinear neural network based on an engineered biochemical circuit, which is constructed by several reaction modules including catalysis, degradation and adjustment reaction modules. The proposed neural network possesses an architecture that is similar to that of an error back propagation neural network, and is built of an input layer, hidden layer and output layer. As a proof of concept, we utilize this nonlinear neural network based on an analog DNA toehold mediated strand displacement reaction circuit to learn the standard quadratic form function and analyze the robustness of the nonlinear neural network toward DNA strand concentration detection, DNA strand displacement reaction rate and noise. Unlike in error back propagation neural networks, the adaptive behavior of this DNA molecular neural network system endows it with supervised learning capability. This investigation will highlight the potential of analog DNA displacement reaction circuits for implementing artificial intelligence.
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Affiliation(s)
- Chengye Zou
- School of Mathematics and Statistics, Anyang Normal University, Anyang 455000, China
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China.
- Informedia Electronic Co., Ltd, Dalian University of Technology, Dalian 116024, China
| | - Qiang Zhang
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Changjun Zhou
- College of Mathematics and Computer Science, Zhejiang Normal University, Jinhua 321000, China.
| | - Wenyu Cao
- Institution of Information Management and Information system, Dalian University of Technology, Dalian 116024, China
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9
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Zou C, Wei X, Zhang Q, Zhou C. A Novel Adaptive Linear Neuron Based on DNA Strand Displacement Reaction Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1424-1434. [PMID: 33347411 DOI: 10.1109/tcbb.2020.3045567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Analog DNA strand displacement circuits can be used to build artificial neural network due to the continuity of dynamic behavior. In this study, DNA implementations of novel catalysis, novel degradation and adjustment reaction modules are designed and used to build an analog DNA strand displacement reaction network. A novel adaptive linear neuron (ADALINE) is constructed by the ordinary differential equations of an ideal formal chemical reaction network, which is built by reaction modules. When reaction network approaches equilibrium, the weights of the ADALINE are updated without learning algorithm. Simulation results indicate that, ADALINE based on the analog DNA strand displacement circuit has ability to implement the learning function of the ADALINE based on the ideal formal chemical reaction networks, and fit a class of linear function.
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10
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Visual Construction of Logical AND and NAND Gates. J CHEM-NY 2022. [DOI: 10.1155/2022/1319762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA logic gates are an important branch of DNA computing and have a wide range of applications in DNA computing. In this study, logic circuits of AND gate and NAND gate are built on origami substrate. The realization of AND gate uses polymerase strand displacement (PSD) reaction and hybridization chain reaction (HCR). If there is a fluorescent band “1” displayed, the result is true. The realization of the NAND gate requires a cyclic reaction. If there is a fluorescent band “A” or “T” displayed, the result is true; if no fluorescent band is displayed, the result is false.
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11
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Cui X, Liu Y, Zhang Q. DNA tile self-assembly driven by antibody-mediated four-way branch migration. Analyst 2022; 147:2223-2230. [DOI: 10.1039/d1an02273c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antibody-mediated four-way branch migration mechanism provides a novel idea for realizing the assembly of nanostructures, simply by attaching structures such as tiles, proteins, quantum dots, etc. to the ends of the four-way branches.
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Affiliation(s)
- Xingdi Cui
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
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12
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Pan J, He Y, Liu Z, Chen J. Tetrahedron-Based Constitutional Dynamic Network for COVID-19 or Other Coronaviruses Diagnostics and Its Logic Gate Applications. Anal Chem 2021; 94:714-722. [PMID: 34935362 DOI: 10.1021/acs.analchem.1c03051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Considering the large-scale outbreak of the coronavirus, it is essential to develop a versatile sensing system for different coronaviruses diagnostics, such as COVID-19, severe acute respiratory syndrome-related coronavirus (SARS-CoV), and bat SARS-like coronavirus (Bat-SL-CoVZC45). In this work, a tetrahedron-based constitutional dynamic network was built as the sensing platform for coronavirus detection. Four different DNA probes were used to construct the tetrahedron structure. DNAzyme and the fluorophore modified substrate strand were used to generate different fluorescence signals, which can be used to distinguish different coronaviruses. The coronavirus biosensor shows a high sensitivity for COVID-19, Bat-SL-CoVZC45, and SARS-CoV detection, with detection limits of 2.5, 3.1, and 2.9 fM, respectively. Also, the platform is robust, and the possible interference from clinical samples was negligible. Using different coronaviruses as inputs, we have fabricated several concatenated logic gates, such as "AND-OR", "INHIBIT-AND", "AND-AND-AND", and "AND-INHIBIT". Importantly, our logic system can also be used to identify SARS-CoV-2 Delta and Lambda variants in the logic operations. Due to the unique advantages of high sensitivity and selectivity, multiple logic biocomputing capabilities, and multireadout mode, this flexible sensing system provides a versatile sensing strategy for intelligent diagnostics of different coronaviruses with low false-negative rates.
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Affiliation(s)
- Jiafeng Pan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Ying He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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13
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Xu S, Liu Y, Zhou S, Zhang Q, Kasabov NK. DNA Matrix Operation Based on the Mechanism of the DNAzyme Binding to Auxiliary Strands to Cleave the Substrate. Biomolecules 2021; 11:1797. [PMID: 34944442 PMCID: PMC8698824 DOI: 10.3390/biom11121797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/21/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
Numerical computation is a focus of DNA computing, and matrix operations are among the most basic and frequently used operations in numerical computation. As an important computing tool, matrix operations are often used to deal with intensive computing tasks. During calculation, the speed and accuracy of matrix operations directly affect the performance of the entire computing system. Therefore, it is important to find a way to perform matrix calculations that can ensure the speed of calculations and improve the accuracy. This paper proposes a DNA matrix operation method based on the mechanism of the DNAzyme binding to auxiliary strands to cleave the substrate. In this mechanism, the DNAzyme binding substrate requires the connection of two auxiliary strands. Without any of the two auxiliary strands, the DNAzyme does not cleave the substrate. Based on this mechanism, the multiplication operation of two matrices is realized; the two types of auxiliary strands are used as elements of the two matrices, to participate in the operation, and then are combined with the DNAzyme to cut the substrate and output the result of the matrix operation. This research provides a new method of matrix operations and provides ideas for more complex computing systems.
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Affiliation(s)
- Shaoxia Xu
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China;
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China;
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China;
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China;
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China;
| | - Nikola K. Kasabov
- Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, Auckland 1010, New Zealand;
- Intelligent Systems Research Center, Ulster University, Londonderry BT52 1SA, UK
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14
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Chen L, Chen W, Liu G, Li J, Lu C, Li J, Tan W, Yang H. Nucleic acid-based molecular computation heads towards cellular applications. Chem Soc Rev 2021; 50:12551-12575. [PMID: 34604889 DOI: 10.1039/d0cs01508c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids, with the advantages of programmability and biocompatibility, have been widely used to design different kinds of novel biocomputing devices. Recently, nucleic acid-based molecular computing has shown promise in making the leap from the test tube to the cell. Such molecular computing can perform logic analysis within the confines of the cellular milieu with programmable modulation of biological functions at the molecular level. In this review, we summarize the development of nucleic acid-based biocomputing devices that are rationally designed and chemically synthesized, highlighting the ability of nucleic acid-based molecular computing to achieve cellular applications in sensing, imaging, biomedicine, and bioengineering. Then we discuss the future challenges and opportunities for cellular and in vivo applications. We expect this review to inspire innovative work on constructing nucleic acid-based biocomputing to achieve the goal of precisely rewiring, even reconstructing cellular signal networks in a prescribed way.
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Affiliation(s)
- Lanlan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Wanzhen Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Guo Liu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Jingying Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, P. R. China
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China. .,Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
| | - Weihong Tan
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
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15
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Development of Synthetic DNA Circuit and Networks for Molecular Information Processing. NANOMATERIALS 2021; 11:nano11112955. [PMID: 34835719 PMCID: PMC8625377 DOI: 10.3390/nano11112955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/23/2022]
Abstract
Deoxyribonucleic acid (DNA), a genetic material, encodes all living information and living characteristics, e.g., in cell, DNA signaling circuits control the transcription activities of specific genes. In recent years, various DNA circuits have been developed to implement a wide range of signaling and for regulating gene network functions. In particular, a synthetic DNA circuit, with a programmable design and easy construction, has become a crucial method through which to simulate and regulate DNA signaling networks. Importantly, the construction of a hierarchical DNA circuit provides a useful tool for regulating gene networks and for processing molecular information. Moreover, via their robust and modular properties, DNA circuits can amplify weak signals and establish programmable cascade systems, which are particularly suitable for the applications of biosensing and detecting. Furthermore, a biological enzyme can also be used to provide diverse circuit regulation elements. Currently, studies regarding the mechanisms and applications of synthetic DNA circuit are important for the establishment of more advanced artificial gene regulation systems and intelligent molecular sensing tools. We therefore summarize recent relevant research progress, contributing to the development of nanotechnology-based synthetic DNA circuits. By summarizing the current highlights and the development of synthetic DNA circuits, this paper provides additional insights for future DNA circuit development and provides a foundation for the construction of more advanced DNA circuits.
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16
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Wang L, Hu M, Wang Y, Xi S, Cheng M, Niu L, Dong Y. Developing a three-input cascade DNA logic gate based on the biological characteristics of metal ion-GO, combined with analysis and verification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:4955-4963. [PMID: 34633006 DOI: 10.1039/d1ay01309b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Due to the limitation of technology, electronic computing is approaching the limit of technology, and new computing tools need to be developed. Here, we build a three-input cascade logic gate based on the advantages of biomolecules, particularly DNA, in the construction of computational logic systems, combined with metal ions and graphene oxide (GO). It is worth mentioning that this study uses a variety of research methods. In addition to the commonly used biological experiments, NUPACK and visual DSD simulation methods are used for analysis, and orthogonal, standardized and other statistical means are used to simplify the experimental process and make the results intuitive. Finally, the designed three-input logic gate is successfully constructed, and it is found that it may have the potential to realize complex computing.
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Affiliation(s)
- Luhui Wang
- Department of Life Science, Shaanxi Normal University, Xi'an 710119, China.
| | - Mengyang Hu
- Department of Computer Science, Shaanxi Normal University, Xi'an 710119, China
| | - Yue Wang
- Department of Computer Science, Shaanxi Normal University, Xi'an 710119, China
| | - Sunfan Xi
- Department of Life Science, Shaanxi Normal University, Xi'an 710119, China.
| | - Meng Cheng
- Department of Life Science, Shaanxi Normal University, Xi'an 710119, China.
| | - Li Niu
- Basic Medical College, Shanxi Medical University, Taiyuan 030001, China
| | - Yafei Dong
- Department of Life Science, Shaanxi Normal University, Xi'an 710119, China.
- Department of Computer Science, Shaanxi Normal University, Xi'an 710119, China
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17
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Tang Z, Yin Z, Wang L, Cui J, Yang J, Wang R. Solving 0-1 Integer Programming Problem Based on DNA Strand Displacement Reaction Network. ACS Synth Biol 2021; 10:2318-2330. [PMID: 34431290 DOI: 10.1021/acssynbio.1c00244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chemical reaction networks (CRNs) based on DNA strand displacement (DSD) can be used as an effective programming language for solving various mathematical problems. In this paper, we design three chemical reaction modules by using the DNA strand displacement reaction as the basic principle, with a weighted reaction module, sum reaction module, and threshold reaction module. These modules are used as basic elements to form chemical reaction networks that can be used to solve 0-1 integer programming problems. The problem can be solved through the three steps of weighting, sum, and threshold, and then the results of the operations can be expressed through a single-stranded DNA output with fluorescent molecules. Finally, we use biochemical experiments and Visual DSD simulation software to verify and evaluate the chemical reaction networks. The results have shown that the DSD-based chemical reaction networks constructed in this paper have good feasibility and stability.
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Affiliation(s)
- Zhen Tang
- School of Mathematics and Big Data, Anhui University of Science & Technology, Huainan, Anhui 232001, China
| | - Zhixiang Yin
- School of Mathematics and Big Data, Anhui University of Science & Technology, Huainan, Anhui 232001, China
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Luhui Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Jianzhong Cui
- Department of Computer, Huainan Union University, Huainan, Anhui 232001, China
| | - Jing Yang
- School of Mathematics and Big Data, Anhui University of Science & Technology, Huainan, Anhui 232001, China
| | - Risheng Wang
- School of Mathematics and Big Data, Anhui University of Science & Technology, Huainan, Anhui 232001, China
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18
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Zhu L, Yu L, Yang X. Electrochemical-Based DNA Logic Devices Regulated by the Diffusion and Intercalation of Electroactive Dyes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:42250-42257. [PMID: 34452580 DOI: 10.1021/acsami.1c12650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Electrochemical-based logic gates are simple to operate, sensitive, controllable, and easy to integrate with silicon-based semiconductor logic devices, showing great application prospects and remaining largely unexplored. Herein, an immobilization-free dual-output electrochemical molecular logic system based on the different diffusivity of electroactive dyes ferrocene (Fc) and methylene blue (MB) toward an indium tin oxide (ITO) electrode under different DNA hybridization reactions was developed. In this system, the hybridization of the catalytic strand IN1 with Fc-modified hairpin DNA H1 triggered an exonuclease III (Exo III) cleavage cycle to obtain free Fc and produce a large number of long double-stranded DNAs via the hybridization chain reaction for intercalating MB, which was previously in the free state. Such a hybridization reaction caused a significant change in the diffusion capacity of MB and Fc toward the ITO electrode, resulting in two electrochemical signals with opposite changes. On this basis, a contrary logic pair library, a parity generator/checker system for differentiating the erroneous bits during data transmission, a parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits for meeting the needs of computational complexity were developed. The proposed electrochemical-based molecular logic system greatly expanded the application of the electrochemical method in the construction of logic circuits and provided a conceptual prototype for the development of more advanced and complicated logic devices.
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Affiliation(s)
- Liping Zhu
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Linying Yu
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Xiurong Yang
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
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19
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Lv H, Li Q, Shi J, Fan C, Wang F. Biocomputing Based on DNA Strand Displacement Reactions. Chemphyschem 2021; 22:1151-1166. [PMID: 33871136 DOI: 10.1002/cphc.202100140] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/10/2021] [Indexed: 11/12/2022]
Abstract
The high sequence specificity and precise base complementary pairing principle of DNA provides a rich orthogonal molecular library for molecular programming, making it one of the most promising materials for developing bio-compatible intelligence. In recent years, DNA has been extensively studied and applied in the field of biological computing. Among them, the toehold-mediated strand displacement reaction (SDR) with properties including enzyme free, flexible design and precise control, have been extensively used to construct biological computing circuits. This review provides a systemic overview of SDR design principles and the applications. Strategies for designing DNA-only, enzymes-assisted, other molecules-involved and external stimuli-controlled SDRs are described. The recently realized computing functions and the application of DNA computing in other fields are introduced. Finally, the advantages and challenges of SDR-based computing are discussed.
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Affiliation(s)
- Hui Lv
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China
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20
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Zhao S, Yu L, Yang S, Tang X, Chang K, Chen M. Boolean logic gate based on DNA strand displacement for biosensing: current and emerging strategies. NANOSCALE HORIZONS 2021; 6:298-310. [PMID: 33877218 DOI: 10.1039/d0nh00587h] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA computers are considered one of the most prominent next-generation molecular computers that perform Boolean logic using DNA elements. DNA-based Boolean logic gates, especially DNA strand displacement-based logic gates (SDLGs), have shown tremendous potential in biosensing since they can perform the logic analysis of multi-targets simultaneously. Moreover, SDLG biosensors generate a unique output in the form of YES/NO, which is contrary to the quantitative measurement used in common biosensors. In this review, the recent achievements of SDLG biosensing strategies are summarized. Initially, the development and mechanisms of Boolean logic gates, strand-displacement reaction, and SDLGs are introduced. Afterwards, the diversified input and output of SDLG biosensors are elaborated. Then, the state-of-the-art SDLG biosensors are reviewed in the classification of different signal-amplification methods, such as rolling circle amplification, catalytic hairpin assembly, strand-displacement amplification, DNA molecular machines, and DNAzymes. Most importantly, limitations and future trends are discussed. The technology reviewed here is a promising tool for multi-input analysis and lays a foundation for intelligent diagnostics.
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Affiliation(s)
- Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
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21
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Zou C, Wei X, Zhang Q, Zhou C, Zhou S. Encryption Algorithm Based on DNA Strand Displacement and DNA Sequence Operation. IEEE Trans Nanobioscience 2021; 20:223-234. [PMID: 33577453 DOI: 10.1109/tnb.2021.3058399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
DNA strand displacement is introduced in this study and used to construct an analog DNA strand displacement chaotic system based on six reaction modules in nanoscale size. The DNA strand displacement circuit is employed in encryption as a chaotic generator to produce chaotic sequences. In the encryption algorithm, we convert chaotic sequences to binary ones by comparing the concentration of signal DNA strand. Simulation results show that the encryption scheme is sensitive to the keys, and key space is large enough to resist the brute-force attacks, furthermore algorithm has a high capacity to resist statistic attack. Based on robustness analysis, our proposed encryption scheme is robust to the DNA strand displacement reaction rate control, noise and concentration detection to a certain extent.
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22
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Luo T, Fan S, Liu Y, Song J. Information processing based on DNA toehold-mediated strand displacement (TMSD) reaction. NANOSCALE 2021; 13:2100-2112. [PMID: 33475669 DOI: 10.1039/d0nr07865d] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
SemiSynBio is an emerging topic toward the construction of platforms for next-generation information processing. Recent research has indicated its promising prospect toward information processing including algorithm design and pattern manipulation with the DNA TMSD reaction, which is one of the cores of the SemiSynBio technology route. The DNA TMSD reaction is the process in which an invader strand displaces the incumbent strand from the gate strand through initiation at the exposed toehold domain. Also, the DNA TMSD reaction generally involves three processes: toehold association, branch migration and strand disassociation. Herein, we review the recent progress on information processing with the DNA TMSD reaction. We highlight the diverse developments on information processing with the logic circuit, analog circuit, combinational circuit and information relay with the DNA origami structure. Additionally, we explore the current challenges and various trends toward the design and application of the DNA TMSD reaction in future information processing.
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Affiliation(s)
- Tao Luo
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Sisi Fan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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23
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Fan D, Wang J, Wang E, Dong S. Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001766. [PMID: 33344121 PMCID: PMC7740092 DOI: 10.1002/advs.202001766] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/30/2020] [Indexed: 05/11/2023]
Abstract
DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- Present address:
Institute of ChemistryThe Hebrew University of JerusalemJerusalem91904Israel
| | - Juan Wang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
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24
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Liu C, Liu Y, Zhu E, Zhang Q, Wei X, Wang B. Cross-Inhibitor: a time-sensitive molecular circuit based on DNA strand displacement. Nucleic Acids Res 2020; 48:10691-10701. [PMID: 33045746 PMCID: PMC7641751 DOI: 10.1093/nar/gkaa835] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 01/19/2023] Open
Abstract
Designing biochemical systems that can be effectively used in diverse fields, including diagnostics, molecular computing and nanomachines, has long been recognized as an important goal of molecular programming and DNA nanotechnology. A key issue in the development of such practical devices on the nanoscale lies in the development of biochemical components with information-processing capacity. In this article, we propose a molecular device that utilizes DNA strand displacement networks and allows interactive inhibition between two input signals; thus, it is termed a cross-inhibitor. More specifically, the device supplies each input signal with a processor such that the processing of one input signal will interdict the signal of the other. Biochemical experiments are conducted to analyze the interdiction performance with regard to effectiveness, stability and controllability. To illustrate its feasibility, a biochemical framework grounded in this mechanism is presented to determine the winner of a tic-tac-toe game. Our results highlight the potential for DNA strand displacement cascades to act as signal controllers and event triggers to endow molecular systems with the capability of controlling and detecting events and signals.
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Affiliation(s)
- Chanjuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Enqiang Zhu
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou 510006, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
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25
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Biocomputing label-free security system based on homogenous ligation chain reaction-induced dramatic change in melting temperature for screening single nucleotide polymorphisms. Talanta 2020; 218:121141. [PMID: 32797898 DOI: 10.1016/j.talanta.2020.121141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022]
Abstract
The development of smart platform with accurate, inexpensive and reliable detection of single-nucleotide polymorphisms (SNPs) has long been concerned in the fields of medical diagnosis and basic research. Here, we present a ligation chain reaction (LCR)-based sensing system for the cost-effective screening of SNPs by simply conducting DNA melting analysis. No chemical modification is required and the signaling operation is accomplished in homogeneous solution, circumventing the complex modification process and possibly compromised enzymatic activity associated with heterogeneous materials, such as quantum dot (QD) and gold nanoparticle (GNP). Due to the enzymatic catalysis and high fidelity of ligase, the system is capable of executing signal amplification, providing a high sensitivity and selectivity. KRAS gene is easily recognized and the site-specific mutation of guanine (G) to adenine (A), thymine (T) or cytosine (C) is accurately screened. Moreover, the excellent reliability was demonstrated by blind test and recovery test. LCR-based signaling mechanism was further used to develop the biocomputing security system, and two logic gates consisting of four single-stranded DNAs (ssDNAs) offer a double insurance to protect the information against illegal invasion, guaranteeing the reliability of output information. Once in the absence of one essential factor, the security system was always locked regardless of target key, serving as a novel strategy to ensure the safety of output information at molecular level. As a proof-of-concept scheme, this contribution introduces new insight into the development of DNA security systems and the exploitation of powerful signal transduction strategy suitable for rapid and convenient disease diagnosis.
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27
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A molecular device: A DNA molecular lock driven by the nicking enzymes. Comput Struct Biotechnol J 2020; 18:2107-2116. [PMID: 32913580 PMCID: PMC7451616 DOI: 10.1016/j.csbj.2020.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/28/2020] [Accepted: 08/01/2020] [Indexed: 11/22/2022] Open
Abstract
As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molecular lock is still a serious challenge. Therefore, taking advantage of the DNA strand displacement and enzyme control technology, we constructed a molecular lock with a self-destructive mechanism. This molecular lock is mainly composed of logic circuits and takes nicking enzymes as inputs. To build this molecular lock, we first constructed a series of cascade circuits, including a YES–YES cascade circuit and a YES–AND cascade circuit. Then, an Inhibit logic gate was constructed to explore the inhibitory properties between different combinations of two nicking enzymes. Finally, using the characteristics of mutual inhibition between several enzymes, a DNA molecular lock driven by three nicking enzymes was constructed. In this molecular device, only the correct sequence of nicking enzymes can be input to ensure the normal operation of the molecular lock. Once the wrong password is entered, the device will be destroyed and cannot be recovered, which effectively prevents intruders from cracking the lock through exhaustive methods. The molecular lock has the function of simulating an electronic keyboard, which can realize the protection of information at the molecular level, and provides a new implementation method for building more advanced and complex molecular devices.
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28
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Wang Y, Li Z, Sun J. Three-Variable Chaotic Oscillatory System Based on DNA Strand Displacement and Its Coupling Combination Synchronization. IEEE Trans Nanobioscience 2020; 19:434-445. [PMID: 32324559 DOI: 10.1109/tnb.2020.2989577] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The synchronization control of two chaotic oscillatory systems is designed based on DNA strand displacement in the present work. Thus, combination synchronization of three 3-variable chaotic oscillatory systems is proposed based on DNA strand displacement. Firstly, five chemical reaction modules of double, displacement, adjustment, catalysis and degradation are designed. Based on these five modules, a 3-variable chaotic oscillatory system is designed. Secondly, based on the design principle of coupling terms and theory of stability, synchronization modules and coupling terms are added to three chaotic oscillatory systems to design combination synchronization of three 3-variable chaotic oscillatory systems based on DNA strand displacement. Modules and systems are implemented and tested using visual DSD and Matlab, and the simulation results are presented to demonstrate the effectiveness and correctness of the chemical reaction modules and systems. The combination synchronization of three 3-variable chaotic oscillatory systems is proposed based on DNA strand displacement, which may be extended to the reaction networks of DNA strand displacement and to the combination synchronization of multivariable chaotic oscillatory systems based on DNA strand displacement.
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29
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Sun X, Zheng X, Zhao S, Liu Y, Wang B. DNA circuits driven by conformational changes in DNAzyme recognition arms. RSC Adv 2020; 10:7956-7966. [PMID: 35492184 PMCID: PMC9049901 DOI: 10.1039/d0ra00115e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
DNA computing plays an important role in nanotechnology due to the unique programmability and parallelism of DNA molecules. As an important tool to realize DNA computation, various logic computing devices have great application potential. The application of DNAzyme makes the achievements in the field of logical computing more diverse. In order to improve the efficiency of the logical units run by DNAzyme, we proposed a strategy to regulate the DNA circuit by the conformational change of the E6-type DNAzyme recognition arms driven by Mg2+. This strategy changes the single mode of DNAzyme signal transmission, extends the functions of E6-type DNAzyme, and saves the time of signal transmission in the molecular scale. To verify the feasibility of this strategy, first, we constructed DNA logic gates (YES, OR, and AND). Second, we cascade different logic gates (YES-YES, YES-AND) to prove the scalability. Finally, a self-catalytic DNA circuit is established. Through the experimental results, we verified that this DNAzyme regulation strategy relatively reduces the cost of logic circuits to some extent and significantly increases the reaction rate, and can also be used to indicate the range of Mg2+ concentrations. This research strategy provides new thinking for logical computing and explores new directions for detection and biosensors.
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Affiliation(s)
- Xinyi Sun
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University Dalian 116622 China
| | - Xuedong Zheng
- College of Computer Science, Shenyang Aerospace University Shenyang 110136 China
| | - Sue Zhao
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University Dalian 116622 China
| | - Yuan Liu
- School of Computer Scicence and Technology, Dalian University of Technology Dalian 116024 China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University Dalian 116622 China
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30
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Implementing digital computing with DNA-based switching circuits. Nat Commun 2020; 11:121. [PMID: 31913309 PMCID: PMC6949259 DOI: 10.1038/s41467-019-13980-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/09/2019] [Indexed: 11/30/2022] Open
Abstract
DNA strand displacement reactions (SDRs) provide a set of intelligent toolboxes for developing molecular computation. Whereas SDR-based logic gate circuits have achieved a high level of complexity, the scale-up for practical achievable computational tasks remains a hurdle. Switching circuits that were originally proposed by Shannon in 1938 and nowadays widely used in telecommunication represent an alternative and efficient means to realize fast-speed and high-bandwidth communication. Here we develop SDR-based DNA switching circuits (DSCs) for implementing digital computing. Using a routing strategy on a programmable DNA switch canvas, we show that arbitrary Boolean functions can be represented by DSCs and implemented with molecular switches with high computing speed. We further demonstrate the implementation of full-adder and square-rooting functions using DSCs, which only uses down to 1/4 DNA strands as compared with a dual-rail logic expression-based design. We expect that DSCs provide a design paradigm for digital computation with biomolecules. DNA strand displacement reactions can be difficult to scale up for computational tasks. Here the authors develop DNA switching circuits that achieve high-speed computing with fewer molecules.
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31
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Zhao S, Liu Y, Wang B, Zhou C, Zhang Q. DNA logic circuits based on FokI enzyme regulation. NEW J CHEM 2020. [DOI: 10.1039/c9nj05510j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A series of DNA logic devices was constructed based on the allosteric strategy of the enzyme-assisted cleavage regulation system, which are simple in scale, modular, and work efficiently.
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Affiliation(s)
- Sue Zhao
- Key Laboratory of Advanced Design and Intelligent Computing
- Ministry of Education
- School of Software Engineering
- Dalian University
- Dalian 116622
| | - Yuan Liu
- School of Computer Science and Technology
- Dalian University of Technology
- Dalian 116024
- China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing
- Ministry of Education
- School of Software Engineering
- Dalian University
- Dalian 116622
| | - Changjun Zhou
- College of Computer Science and Engineering
- Dalian Minzu University
- Dalian
- China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing
- Ministry of Education
- School of Software Engineering
- Dalian University
- Dalian 116622
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32
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Su H, Xu J, Wang Q, Wang F, Zhou X. High-efficiency and integrable DNA arithmetic and logic system based on strand displacement synthesis. Nat Commun 2019; 10:5390. [PMID: 31772166 PMCID: PMC6879481 DOI: 10.1038/s41467-019-13310-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022] Open
Abstract
Powerful information processing and ubiquitous computing are crucial for all machines and living organisms. The Watson-Crick base-pairing principle endows DNA with excellent recognition and assembly abilities, which facilitates the design of DNA computers for achieving intelligent systems. However, current DNA computational systems are always constrained by poor integration efficiency, complicated device structures or limited computational functions. Here, we show a DNA arithmetic logic unit (ALU) consisting of elemental DNA logic gates using polymerase-mediated strand displacement. The use of an enzyme resulted in highly efficient logic gates suitable for multiple and cascaded computation. Based on our basic single-rail DNA configuration, additional combined logic gates (e.g., a full adder and a 4:1 multiplexer) have been constructed. Finally, we integrate the gates and assemble the crucial ALU. Our strategy provides a facile strategy for assembling a large-scale complex DNA computer system, highlighting the great potential for programming the molecular behaviors of complicated biosystems. Current DNA computational systems are constrained by integration efficiency, device structures and limited functions. Here the authors design a DNA arithmetic logic unit that uses polymerase-mediated strand displacement.
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Affiliation(s)
- Haomiao Su
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Jinglei Xu
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China.,The Institute of Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Qi Wang
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China. .,The Institute of Advanced Studies, Wuhan University, Wuhan, 430072, China.
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33
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Constructing Controllable Logic Circuits Based on DNAzyme Activity. Molecules 2019; 24:molecules24224134. [PMID: 31731630 PMCID: PMC6891523 DOI: 10.3390/molecules24224134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022] Open
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.
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Zheng X, Yang J, Zhou C, Zhang C, Zhang Q, Wei X. Allosteric DNAzyme-based DNA logic circuit: operations and dynamic analysis. Nucleic Acids Res 2019; 47:1097-1109. [PMID: 30541100 PMCID: PMC6379719 DOI: 10.1093/nar/gky1245] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/29/2022] Open
Abstract
Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers. However, those regulations required to change the sequences of whole DNAzyme, as separating parts and inserting extra DNA sequence. Inspired by the allosteric regulation of proteins in nature, a new allosteric strategy is proposed to regulate the activity of DNAzyme without DNA sequences changes. In this strategy, DNA strand displacement was used to regulate the DNAzyme structure, through which the activity of DNAzyme was well controlled. The strategy was applied to E6-type DNAzymes, and the operations of DNA logic circuit (YES, OR, AND, cascading and feedback) were established and simulated with the dynamic analyses. The allosteric regulation has potential to construct more complicated molecular systems, which can be applied to bio-sensing and detection.
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Affiliation(s)
- Xuedong Zheng
- College of Computer Science, Shenyang Aerospace University, Shenyang 110136, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Changjun Zhou
- College of Mathematics and Computer sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Key laboratory of High Confidence Software Technologies, Ministry of Education, Beijing 100871, China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
- School of Computer Scicence and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaopeng Wei
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
- School of Computer Scicence and Technology, Dalian University of Technology, Dalian 116024, China
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35
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Zou C, Wei X, Zhang Q, Liu C, Liu Y. Solution of Equations Based on Analog DNA Strand Displacement Circuits. IEEE Trans Nanobioscience 2019; 18:191-204. [PMID: 30716045 DOI: 10.1109/tnb.2019.2897116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Deoxyribonucleic acid (DNA) strand displacement can be used to build complex functional circuits due to its highly modular and programmable properties. While DNA strand displacement is most often used to solve logic problems, it can also be used to compute the roots of equations. In this paper, we present the design of novel architectures for catalysis, degradation, and annihilation in ideal formal reaction modules, and we translate these reaction modules to DNA networks. These ideal formal or DNA reaction modules are suitable for building analog circuits for solving tasks. The computing analog DNA circuits are assessed by solving a linear equation, a one-variable quadratic equation, and a set of two simultaneous linear equations. The results were evaluated by simulation.
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36
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Yang S, Yang C, Huang D, Song L, Chen J, Yang Q. Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits. Chemistry 2019; 25:5389-5405. [PMID: 30328639 DOI: 10.1002/chem.201804420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/16/2018] [Indexed: 01/06/2023]
Abstract
DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA's advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.
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Affiliation(s)
- Shu Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Chunrong Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Dan Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Lingbo Song
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jianchi Chen
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
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37
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Zhong W, Tang W, Tan Y, Fan J, Huang Q, Zhou D, Hong W, Liu Y. A DNA arithmetic logic unit for implementing data backtracking operations. Chem Commun (Camb) 2019; 55:842-845. [DOI: 10.1039/c8cc08441f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A data backtracking operation was successfully realized by adding redundant modules to the circuit, greatly improving the system reliability.
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Affiliation(s)
- Weiye Zhong
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Weiyang Tang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Yun Tan
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Jin Fan
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Qichen Huang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Danli Zhou
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Weimin Hong
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
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38
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Xue C, Xiao S, Ouyang CH, Li CC, Gao ZH, Shen ZF, Wu ZS. Inverted mirror image molecular beacon-based three concatenated logic gates to detect p53 tumor suppressor gene. Anal Chim Acta 2018; 1051:179-186. [PMID: 30661615 DOI: 10.1016/j.aca.2018.11.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
Mutation of p53 tumor suppressor gene represents one of the early molecular events in tumor initiation and progression. Although molecular computing holds tremendous potential with important applications in diagnosis, prognosis and treatment of human diseases at the molecular level, designing molecular logic gates to implement cascade amplification via operating autonomously for the detection of point mutations still remains challenging. In this contribution, we developed a three concatenated logic gates (TCLG) to perform multiple strand displacement amplification (m-SDA) for screening the cancer-related point mutations only via designing an innovative molecular beacon (MB). Specifically, using p53 gene as model target, extending the two ends of a MB via adding two fragments with the same sequence achieves two unique terminal single-stranded (ss) overhangs. After self-folding of MB into hairpin structure, the two overhangs exhibit a near inverted mirror image (IM) relationship if taking the base nature and direction into account. For this, the probe is called IM-MB. Because cascade SDAs can occur on IM-MB and promote each other, the target gene can be detected down to 10 pM. Along this line, the TCLG circuit was proposed, and two primers and target gene serve as the indispensable input signals. Utilizing this logic circuit, the point mutation or absence of target gene can be sensitively screened. Moreover, its potential application in the recognition of point mutations in complex biomatrix has been demonstrated via blind test. The proof-of-concept scheme is expected to provide new insight into the development of DNA-based molecular logic gates and their applications in basic research, medical diagnosis and precise treatment and treatment of genetic diseases.
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Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Shuai Xiao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, China
| | - Chang-He Ouyang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Cong-Cong Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Zhi-Hua Gao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zhi-Fa Shen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China.
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39
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Yang T, Fu J, Zheng S, Yao H, Jin Y, Lu Y, Liu H. Biomolecular logic devices based on stimuli-responsive PNIPAM-DNA film electrodes and bioelectrocatalysis of natural DNA with Ru(bpy)32+ as mediator. Biosens Bioelectron 2018; 108:62-68. [DOI: 10.1016/j.bios.2018.02.048] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 11/16/2022]
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40
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Zou C, Wei X, Zhang Q. Visual synchronization of two 3-variable Lotka–Volterra oscillators based on DNA strand displacement. RSC Adv 2018; 8:20941-20951. [PMID: 35542339 PMCID: PMC9080848 DOI: 10.1039/c8ra01393d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/21/2018] [Indexed: 01/30/2023] Open
Abstract
DNA strand displacement as a theoretic foundation is helpful in constructing reaction networks and DNA circuits.
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Affiliation(s)
- Chengye Zou
- School of Computer Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
| | - Xiaopeng Wei
- School of Computer Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
| | - Qiang Zhang
- School of Computer Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
- Key Laboratory of Advanced and Intelligent Computing
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41
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Pan L, Wang Z, Li Y, Xu F, Zhang Q, Zhang C. Nicking enzyme-controlled toehold regulation for DNA logic circuits. NANOSCALE 2017; 9:18223-18228. [PMID: 29164226 DOI: 10.1039/c7nr06484e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA strand displacement is widely used in DNA-related nanoengineering for its remarkable specificity and predictability. We report a nicking enzyme-assisted mechanism to regulate strand displacement, where DNA toeholds are dynamically controlled. To demonstrate the strategy, a protein/DNA-based Boolean operation system is constructed and based on it a two-channel multiplexer controlled by three different nicking enzymes is realized. The proposed regulatory mechanism can be used for switch logic statement and bridges protein and DNA logic circuits.
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Affiliation(s)
- Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Automation, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
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42
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Zou C, Wei X, Zhang Q, Liu C, Zhou C, Liu Y. Four-Analog Computation Based on DNA Strand Displacement. ACS OMEGA 2017; 2:4143-4160. [PMID: 30023715 PMCID: PMC6044888 DOI: 10.1021/acsomega.7b00572] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/05/2017] [Indexed: 05/13/2023]
Abstract
DNA strand displacement plays an important role in biological computations. The inherent advantages of parallelism, high storability, and cascading have resulted in increased functional circuit realization of DNA strand displacement on the nanoscale. Herein, we propose an analog computation with minus based on DNA strand displacement. The addition, subtraction, multiplication, and division gates as elementary gates could realize analog computation with minus. The advantages of this proposal are the analog computation with negative value and division computation. In this article, we provide the designs and principles of these elementary gates and demonstrate gate performance by simulation. Furthermore, to show the cascade property of gates, we computed a polynomial as an example by these gates.
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Affiliation(s)
- Chengye Zou
- Faculty of Electronic
Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Xiaopeng Wei
- Faculty of Electronic
Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China
- E-mail: (X.W.)
| | - Qiang Zhang
- Faculty of Electronic
Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China
- E-mail: (Q.Z.)
| | - Chanjuan Liu
- Faculty of Electronic
Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Changjun Zhou
- Key Laboratory of Advanced and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
| | - Yuan Liu
- Faculty of Electronic
Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China
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43
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Zhang S, Wang K, Li KB, Chen F, Shi W, Jia WP, Zhang J, Han DM. A label-free and universal platform for the construction of an odd/even detector for decimal numbers based on graphene oxide and DNA-stabilized silver nanoclusters. NANOSCALE 2017; 9:11912-11919. [PMID: 28786459 DOI: 10.1039/c7nr03670a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular logic devices with different functions can perform various tasks in the areas of biological molecule detection, disease diagnosis, multivariate analysis, and bioimaging. Herein, a series of logic circuits based on silver nanoclusters (AgNCs)/graphene oxide (GO) are constructed to execute nonarithmetic functions, including 3-, 4-, and 5-bit odd/even checking. The resulting devices can differentiate between even and odd decimal numbers in the range from 0 to 31. Moreover, the devices can be expanded to operate with wider ranges of numbers when more inputs are added. The signal reporter is structured using AgNCs and GO, preventing laborious modification of biomolecules. The designed DNA-based logic nanodevices share the same DNA platform and a constant threshold value, showing great potential for application in information processing at the molecular level. Additionally, these devices can stably carry out their logic operations in a biological matrix, indicating that the AgNC/GO-based system can operate in a complicated biological environment. Given the biocompatibility and design flexibility of DNA, this study provides novel outcomes towards the development of label-free intelligent nanodevices. This may open a new path for the application of AgNCs/GO in molecular logic circuits and fluorescence imaging.
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Affiliation(s)
- Siqi Zhang
- Department of Chemistry, Taizhou University, Jiaojiang, 318000, China.
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44
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Ohara M, Takinoue M, Kawano R. Nanopore Logic Operation with DNA to RNA Transcription in a Droplet System. ACS Synth Biol 2017; 6:1427-1432. [PMID: 28414903 DOI: 10.1021/acssynbio.7b00101] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This paper describes an AND logic operation with amplification and transcription from DNA to RNA, using T7 RNA polymerase. All four operations, (0 0) to (1 1), with an enzyme reaction can be performed simultaneously, using four-droplet devices that are directly connected to a patch-clamp amplifier. The output RNA molecule is detected using a biological nanopore with single-molecule translocation. Channel current recordings can be obtained using the enzyme solution. The integration of DNA logic gates into electrochemical devices is necessary to obtain output information in a human-recognizable form. Our method will be useful for rapid and confined DNA computing applications, including the development of programmable diagnostic devices.
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Affiliation(s)
- Masayuki Ohara
- Department of Biotechnology
and Life Science, Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
| | - Masahiro Takinoue
- Department
of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Yokohama, Kanagawa 226-8502, Japan
| | - Ryuji Kawano
- Department of Biotechnology
and Life Science, Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
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45
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Gao RR, Yao TM, Lv XY, Zhu YY, Zhang YW, Shi S. Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing. Chem Sci 2017; 8:4211-4222. [PMID: 28626564 PMCID: PMC5469004 DOI: 10.1039/c7sc00361g] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/05/2017] [Indexed: 11/30/2022] Open
Abstract
To create sophisticated molecular logic circuits from scratch, you may not believe how common the building blocks can be and how diverse and powerful such circuits can be when scaled up. Using the two simple building blocks of G-quadruplex and silver nanoclusters (Ag NCs), we experimentally construct a series of multifunctional, label-free, and multi-output logic circuits to perform nonarithmetic functions: a 1-to-2 decoder, a 4-to-2 encoder, an 8-to-3 encoder, dual transfer gates, a 2 : 1 multiplexer, and a 1 : 2 demultiplexer. Moreover, a parity checker which is capable of identifying odd and even numbers from natural numbers is constructed conceptually. Finally, a multi-valued logic gate (ternary inhibit gate) is readily achieved by taking this DNA/Ag NC system as a universal platform. All of the above logic circuits share the same building blocks, indicating the great prospects of the assembly of nanomaterials and DNA for biochemical logic devices. Considering its biocompatibility, the novel prototypes developed here may have potential applications in the fields of biological computers and medical diagnosis and serve as a promising proof of principle in the not-too-distant future.
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Affiliation(s)
- Ru-Ru Gao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Tian-Ming Yao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Xiao-Yan Lv
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Yan-Yan Zhu
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Yi-Wei Zhang
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Shuo Shi
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
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46
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McKinney BOF, Daly B, Yao C, Schroeder M, de Silva AP. Consolidating Molecular Logic with New Solid-Bound YES and PASS 1 Gates and Their Combinations. Chemphyschem 2017; 18:1760-1766. [DOI: 10.1002/cphc.201700120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Indexed: 01/05/2023]
Affiliation(s)
| | - Brian Daly
- School of Chemistry and Chemical Engineering; Queen's University; Belfast BT9 5AG UK
| | - Chaoyi Yao
- School of Chemistry and Chemical Engineering; Queen's University; Belfast BT9 5AG UK
| | - Marc Schroeder
- School of Chemistry and Chemical Engineering; Queen's University; Belfast BT9 5AG UK
| | - A. Prasanna de Silva
- School of Chemistry and Chemical Engineering; Queen's University; Belfast BT9 5AG UK
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47
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Song T, Wang X, Liang H. Engineering chemical reaction modules via programming the assembly of DNA hairpins. J Mater Chem B 2017; 5:2297-2301. [PMID: 32263620 DOI: 10.1039/c6tb03098j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The architect of enzyme-free chemical reaction modules, working as building blocks in implementing complex computing tasks, was achieved by modulating the assembly of DNA hairpins, including non-catalytic and catalytic systems. The performance of heterogeneous outputted sequences, which were programmed on different hairpins for triggering the downstream reaction, was asymmetric in the non-catalytic system, whereas symmetric in the catalytic system. Furthermore, complicated DNA-only chemical modules possessing controllable species of inputs or outputs were constructed based on our strategy. The kinetic studies revealed that the performance of the chemical modules was toehold length correlated; on the basis of which, a DNA concentration monitor was constructed.
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Affiliation(s)
- Tingjie Song
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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48
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Song X, Eshra A, Dwyer C, Reif J. Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement. RSC Adv 2017. [DOI: 10.1039/c7ra02607b] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We propose a scalable design and verifications for photoregulated renewable DNA seesaw logic circuits, which can be repeatedly reset to reliably process new inputs. Synchronized control of complex DNA reaction networks could be achieved efficiently.
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Affiliation(s)
- Xin Song
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
| | - Abeer Eshra
- Department of Computer Science
- Duke University
- Durham
- USA
- Department of Computer Science and Engineering
| | - Chris Dwyer
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
- Department of Computer Science
| | - John Reif
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
- Department of Computer Science
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49
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Wang M, Huang H, Zhang Z, Xiao SJ. 2D DNA lattices constructed from two-tile DAE-O systems possessing circular central strands. NANOSCALE 2016; 8:18870-18875. [PMID: 27812582 DOI: 10.1039/c6nr06745j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We reported a classical two-tile system of DAE-O (doublecrossover, antiparallel, and even half-turns tiles with odd half-turns connection) to construct regular single crystalline 2D (two dimensional) DNA lattices, using pre-circularised oligonucleotides of 42-, 64-, and 84-nt (nucleotides) as the central looped strands in DAE tiles respectively. DAE tiles with 42- and 64-nt as central strands, either in circular form or in linear form, grew regular single crystalline lattices well. However DAE tiles including a circular 84-nt as the central strand grew single crystalline lattices, those including a linear 84-nt as the central strand grew polycrystalline 2D lattices. A subtle difference in the lateral rigidity of DAE tiles with regard to the duplex axis was suggested to be the cause of the morphological difference.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China.
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50
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In Vitro Implementation of a Stack Data Structure Based on DNA Strand Displacement. UNCONVENTIONAL COMPUTATION AND NATURAL COMPUTATION 2016. [DOI: 10.1007/978-3-319-41312-9_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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