1
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Rilievo G, Cecconello A, Fouladi Ghareshiran N, Magro M, Simmel FC, Vianello F. Integration of DNA-RNA-triplex-based regulation of transcription into molecular logic gates. FEBS Lett 2023; 597:2461-2472. [PMID: 37591635 DOI: 10.1002/1873-3468.14721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
In recent years, increasing numbers of noncoding RNA molecules were identified as possible components of endogenous DNA-RNA hybrid triplexes involved in gene regulation. Triplexes are potentially involved in complex molecular signaling networks that, if understood, would allow the engineering of biological computing components. Here, by making use of the enhancing and inhibiting effects of such triplexes, we demonstrate in vitro the construction of triplex-based molecular gates: 'exclusive OR' (XOR), 'exclusive NOT-OR' (XNOR), and a threshold gate, via transcription of a fluorogenic RNA aptamer. Precise modulation was displayed by the biomolecular-integrated systems over a wide interval of transcriptional outputs, ranging from drastic inhibition to significant enhancement. The present contribution represents a first example of molecular gates developed using DNA-RNA triplex nanostructures.
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Affiliation(s)
- Graziano Rilievo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Alessandro Cecconello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | | | - Massimiliano Magro
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Friedrich C Simmel
- Physik Department, Technische Universitat München, Garching bei München, Germany
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
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2
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Wei Q, Huang H, Wang S, Liu F, Xu J, Luo Z. A Novel Fluorescent Aptamer Sensor with DNAzyme Signal Amplification for the Detection of CEA in Blood. SENSORS (BASEL, SWITZERLAND) 2023; 23:1317. [PMID: 36772357 PMCID: PMC9920513 DOI: 10.3390/s23031317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Carcinoembryonic antigen (CEA) is a tumor-specific biomarker; however, its low levels in the early stages of cancer make it difficult to detect. To address the need for analysis of ultra-low-level substances, we designed and synthesized a fluorescent aptamer sensor with DNAzyme signal amplification and used it for the detection of CEA in blood. In the presence of the target protein, the aptamer sequence in the recognition probe binds to the target protein and opens the hairpin structure, hybridizes with the primer and triggers a polymerization reaction in the presence of polymerase to generate double-stranded DNA with two restriction endonuclease Nb.BbvCl cleavage sites. At the same time, the target protein is displaced and continues to bind to another recognition probe, triggering a new round of polymerization reaction, forming a cyclic signal amplification triggered by the target. The experimental results show that the blood detection with CEA has a high sensitivity and a wide detection range. The detection range: 10 fg/mL~10 ng/mL, with a detection limit of 5.2 fg/mL. In addition, the sensor can be used for the analysis of complex biological samples such as blood.
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Affiliation(s)
- Qingmin Wei
- Guangxi Key Lab of Agricultural Resources Chemistry and Biotechnology, College of Chemistry and Food Science, Yulin Normal University, 1303 Jiaoyudong Road, Yulin 537000, China
| | - Huakui Huang
- Yulin Campus, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Shulong Wang
- Guangxi Key Lab of Agricultural Resources Chemistry and Biotechnology, College of Chemistry and Food Science, Yulin Normal University, 1303 Jiaoyudong Road, Yulin 537000, China
| | - Fa Liu
- Guangxi Key Lab of Agricultural Resources Chemistry and Biotechnology, College of Chemistry and Food Science, Yulin Normal University, 1303 Jiaoyudong Road, Yulin 537000, China
| | - Jiayao Xu
- Guangxi Key Lab of Agricultural Resources Chemistry and Biotechnology, College of Chemistry and Food Science, Yulin Normal University, 1303 Jiaoyudong Road, Yulin 537000, China
| | - Zhihui Luo
- Guangxi Key Lab of Agricultural Resources Chemistry and Biotechnology, College of Chemistry and Food Science, Yulin Normal University, 1303 Jiaoyudong Road, Yulin 537000, China
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3
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Wang B, Wang M, Peng F, Fu X, Wen M, Shi Y, Chen M, Ke G, Zhang XB. Construction and Application of DNAzyme-based Nanodevices. Chem Res Chin Univ 2023; 39:42-60. [PMID: 36687211 PMCID: PMC9841151 DOI: 10.1007/s40242-023-2334-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023]
Abstract
The development of stimuli-responsive nanodevices with high efficiency and specificity is very important in biosensing, drug delivery, and so on. DNAzymes are a class of DNA molecules with the specific catalytic activity. Owing to their unique catalytic activity and easy design and synthesis, the construction and application of DNAzymes-based nanodevices have attracted much attention in recent years. In this review, the classification and properties of DNAzyme are first introduced. The construction of several common kinds of DNAzyme-based nanodevices, such as DNA motors, signal amplifiers, and logic gates, is then systematically summarized. We also introduce the application of DNAzyme-based nanodevices in sensing and therapeutic fields. In addition, current limitations and future directions are discussed.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Menghui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiaoyi Fu
- Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, 310022 P. R. China
| | - Mei Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Yuyan Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Mei Chen
- College of Materials Science and Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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4
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Zhong X, Li Y, Chang Y, Yuan R, Chai Y. A highly-efficient 3D DNAzyme motor for sensitive biosensing analysis. Talanta 2022; 250:123683. [PMID: 35777344 DOI: 10.1016/j.talanta.2022.123683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 11/19/2022]
Abstract
Herein, driven by the need of highly-efficient DNAzyme-amplified detection strategy, a novel 3D DNAzyme motor was designed as a biosensor platform for realizing sensitive detection of target DNA. The 3D DNAzyme motor was composed of target-activated DNAzyme nanowires and substrates H1-Fc that co-immobilized on Au@Fe3O4 nanoparticles (Au@Fe3O4NPS) surface, possessing high local concentration of DNA reactants and shortened distance between DNAzyme and substrates for enhancing electrochemical signal. Compared with traditional DNAzyme-powered machines, the target-activated DNAzyme nanowires of 3D DNAzyme motor had greater flexibility and more powerful cleavage capability without troublesome sequence optimization, which overcame the space limitation and simultaneously interacted with adjacent and distant substrates H1-Fc to output a large amount of cleavage products with high signal response. Therefore, on account of the above-mentioned merits of nanoparticles localization DNA design and DNAzyme nanowires, the reported 3D DNAzyme motor ingeniously overcame many defects existing in traditional DNAzyme-amplified detection strategies such as low reactants concentration, limited flexibility of DNAzyme and small DNAzyme swing range, realizing the sensitive detection of target DNA with a detection limit of 1.7 fM ranging from 5 fM to 50 nM. Impressively, the 3D DNAzyme motor here presented a new strategy to achieve effective DNAzyme signal amplification and provided a reference for the assembly of various and functional 3D DNA machines in the future.
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Affiliation(s)
- Xia Zhong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yunrui Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yuanyuan Chang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
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5
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Chen C, Wu R, Wang B. Development of a neuron model based on DNAzyme regulation. RSC Adv 2021; 11:9985-9994. [PMID: 35423534 PMCID: PMC8695483 DOI: 10.1039/d0ra10515e] [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: 12/14/2020] [Accepted: 03/02/2021] [Indexed: 12/25/2022] Open
Abstract
Neural networks based on DNA molecular circuits play an important role in molecular information processing and artificial intelligence systems. In fact, some DNA molecular systems can become dynamic units with the assistance of DNAzymes. The complex DNA circuits can spontaneously induce corresponding feedback behaviors when their inputs changed. However, most of the reported DNA neural networks have been implemented by the toehold-mediated strand displacement (TMSD) method. Therefore, it was important to develop a method to build a neural network utilizing the TMSD mechanism and adding a mechanism to account for modulation by DNAzymes. In this study, we designed a model of a DNA neuron controlled by DNAzymes. We proposed an approach based on the DNAzyme modulation of neuronal function, combing two reaction mechanisms: DNAzyme digestion and TMSD. Using the DNAzyme adjustment, each component simulating the characteristics of neurons was constructed. By altering the input and weight of the neuron model, we verified the correctness of the computational function of the neurons. Furthermore, in order to verify the application potential of the neurons in specific functions, a voting machine was successfully implemented. The proposed neuron model regulated by DNAzymes was simple to construct and possesses strong scalability, having great potential for use in the construction of large neural networks.
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Affiliation(s)
- Cong Chen
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University Dalian 116622 China
| | - Ranfeng Wu
- 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 China
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6
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Pan J, He Y, Liu Z, Chen J. Dual recognition element-controlled logic DNA circuit for COVID-19 detection based on exonuclease III and DNAzyme. Chem Commun (Camb) 2021; 57:1125-1128. [PMID: 33410447 DOI: 10.1039/d0cc06799g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two fragments of the COVID-19 genome (specific and homologous) were used as two inputs to construct an AND logic gate for COVID-19 detection based on exonuclease III and DNAzyme. The detection sensitivity of the assay can reach fM levels. Satisfactory recovery values were obtained in real sample analysis.
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Affiliation(s)
- Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, 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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7
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Chen J, Pan J, Liu C. Versatile Sensing Platform for Cd 2+ Detection in Rice Samples and Its Applications in Logic Gate Computation. Anal Chem 2020; 92:6173-6180. [PMID: 32208648 DOI: 10.1021/acs.analchem.0c01022] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A versatile sensing platform was designed for Cd2+ detection utilizing Mg2+-dependent DNAzyme as the biocatalyst and toehold-mediated strand replacement as the reaction mechanism. The Cd2+-aptamer interaction brings the split subunits of the Mg2+-dependent DNAzyme into close-enough proximity, which generates an active DNAzyme that can catalyze the cleavage reaction toward the hairpin substrate strand (H1). The trigger DNA fragment in H1 can open another hairpin probe (H2) to activate the cyclic signal amplification process. The generated numerous G-quadruplex DNAzyme structures will produce a high fluorescence response after incubation with the fluorescence dye N-methyl mesoporphyrin IX (NMM). This detection platform is ultrasensitive and the detection limit (LOD) is 2.5 pM (S/N = 3). The sensing system is robust and can work effectively even in a complex sample matrix, enabling the quantitative analysis of Cd2+ content in rice samples with good reliability. Showing the unique features of simple operation, label-free and enzyme-free format, high sensitivity and selectivity, and universal signal amplification mode, our proposed sensing protocol holds great promise for becoming a competitive alternative for the routine monitoring of Cd2+ pollution. Importantly, this flexible and versatile sensing platform was used to construct some exquisite logic gates, including AND, OR, INHIBIT, IMPLICATION, NOR, and NAND.
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Affiliation(s)
- Junhua Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Jiafeng Pan
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Chengshuai Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
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8
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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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9
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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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10
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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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11
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Harding BI, Pollak NM, Stefanovic D, Macdonald J. Repeated Reuse of Deoxyribozyme-Based Logic Gates. NANO LETTERS 2019; 19:7655-7661. [PMID: 31615207 DOI: 10.1021/acs.nanolett.9b02326] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Deoxyribozymes (DNAzymes) have demonstrated a significant capacity for biocomputing and hold promise for information processing within advanced biological devices if several key capabilities are developed. One required capability is reuse-having DNAzyme logic gates be cyclically, and controllably, activated and deactivated. We designed an oligonucleotide-based system for DNAzyme reuse that could (1) remove previously bound inputs by addition of complementary oligonucleotides via toe-hold mediated binding and (2) diminish output signal through the addition of quencher-labeled oligonucleotides complementary to the fluorophore-bound substrate. Our system demonstrated, for the first time, the ability for DNAzymes to have their activity toggled, with activity returning to 90-125% of original activity. This toggling could be performed multiple times with control being exerted over when the toggling occurs, with three clear cycles observed before the variability in activity became too great. Our data also demonstrated that fluorescent output of the DNAzyme activity could be actively removed and regenerated. This reuse system can increase the efficiency of DNAzyme-based logic circuits by reducing the number of redundant oligonucleotides and is critical for future development of reusable biodevices controlled by logical operations.
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Affiliation(s)
- Bradley I Harding
- Genecology Research Centre, School of Science and Engineering , University of the Sunshine Coast , Sippy Downs , QLD 4556 , Australia
| | - Nina M Pollak
- Genecology Research Centre, School of Science and Engineering , University of the Sunshine Coast , Sippy Downs , QLD 4556 , Australia
- CSIRO Synthetic Biology Future Science Platform , GPO Box 1700, Canberra , ACT 2601 , Australia
| | - Darko Stefanovic
- Department of Computer Science , University of New Mexico , Albuquerque , New Mexico 87131 , United States
- Center for Biomedical Engineering , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Joanne Macdonald
- Genecology Research Centre, School of Science and Engineering , University of the Sunshine Coast , Sippy Downs , QLD 4556 , Australia
- Division of Experimental Therapeutics, Department of Medicine , Columbia University , New York , New York 10032 , United States
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12
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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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13
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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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14
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Huang W, Wang J, Du J, Deng Y, He Y. Contrary logic pairs and circuits using a visually and colorimetrically detectable redox system consisting of MoO3-x nanodots and 3,3′-diaminobenzidine. Mikrochim Acta 2019; 186:79. [DOI: 10.1007/s00604-018-3190-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/14/2018] [Indexed: 12/11/2022]
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15
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Wang K, Zhai FH, He MQ, Wang J, Yu YL, He RH. A simple enzyme-assisted cascade amplification strategy for ultrasensitive and label-free detection of DNA. Anal Bioanal Chem 2018; 411:4569-4576. [DOI: 10.1007/s00216-018-1422-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 02/07/2023]
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Wang H, Zheng J, Sun Y, Li T. Cellular environment-responsive intelligent DNA logic circuits for controllable molecular sensing. Biosens Bioelectron 2018; 117:729-735. [DOI: 10.1016/j.bios.2018.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/12/2018] [Accepted: 07/05/2018] [Indexed: 12/31/2022]
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17
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Ying YL, Li ZY, Hu ZL, Zhang J, Meng FN, Cao C, Long YT, Tian H. A Time-Resolved Single-Molecular Train Based on Aerolysin Nanopore. Chem 2018. [DOI: 10.1016/j.chempr.2018.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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18
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Abstract
Invited by the editorial committee of the Annual Review of Physical Chemistry to "contribute my autobiography," I present it here, as I understand the term. It is about my parents, my mentors, my coworkers, and my friends in learning and the scientific problems that we tried to address. Courtesy of the editorial assistance of Annual Reviews, some of the science is in the figure captions and sidebars. I am by no means done: I am currently trying to fuse the quantitative rigor of physical chemistry with systems biology while also dealing with a post-Born-Oppenheimer regime in electronic dynamics and am attempting to instruct molecules to perform advanced logic.
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Affiliation(s)
- Raphael D Levine
- The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; .,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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19
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Chen J, Pan J, Chen S. A label-free and enzyme-free platform with a visible output for constructing versatile logic gates using caged G-quadruplex as the signal transducer. Chem Sci 2017; 9:300-306. [PMID: 29629099 PMCID: PMC5868315 DOI: 10.1039/c7sc04007e] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/18/2017] [Indexed: 01/02/2023] Open
Abstract
A complete set of binary basic logic gates (OR, AND, NOR, NAND, INHIBT, IMPLICATION, XOR and XNOR) is realized on a label-free and enzyme-free sensing platform using caged G-quadruplex as the signal transducer. In the presence of an appropriate input, the temporarily blocked G-rich sequence in the hairpin DNA is released through cleavage by the synergetically-stabilized Mg2+-dependent DNAzyme which can be made to function via the input-guided cooperative conjunction of the DNAzyme subunits. In the presence of hemin, the unblocked G-quadruplex DNAzyme catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by H2O2 to generate a colored readout signal which can be readily distinguished by the naked eye. This strategy is quite versatile and straightforward for logic operations. Two combinatorial gates (XOR + AND and XOR + NOR) are also successfully fabricated to demonstrate the modularity and scalability of the computing elements. The distinctive advantage of this logic system is that molecular events in aqueous solution could be translated into a color change which can be directly observed by the naked eye without resorting to any analytical instrumentation. Moreover, this work reveals a new route for the design of molecular logic gates that can be executed without any labeling and immobilization procedure or separation and washing step, which holds great promise for intelligent point-of-care diagnostics and in-field applications.
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Affiliation(s)
- Junhua Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management , Guangdong Institute of Eco-environmental Science & Technology , Guangzhou 510650 , China .
| | - Jiafeng Pan
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management , Guangdong Institute of Eco-environmental Science & Technology , Guangzhou 510650 , China .
| | - Shu Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management , Guangdong Institute of Eco-environmental Science & Technology , Guangzhou 510650 , China .
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20
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Xie H, Chai Y, Yuan Y, Yuan R. Highly effective molecule converting strategy based on enzyme-free dual recycling amplification for ultrasensitive electrochemical detection of ATP. Chem Commun (Camb) 2017; 53:8368-8371. [DOI: 10.1039/c7cc03497k] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An enzyme-free and highly effective molecule converting strategy was described for the sensitive electrochemical detection of ATP based on target-driven catalytic hairpin assembly and Mg2+-dependent DNAzymes.
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Affiliation(s)
- Hua Xie
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yali Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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