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Han J, Lv X, Zhang Y, Wang J, Fan D, Dong S. Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits. Anal Chem 2023; 95:16725-16732. [PMID: 37906527 DOI: 10.1021/acs.analchem.3c03793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
DNA logic nanodevices are powerful tools for both molecular computing tasks and smart bioanalytical applications. Nevertheless, the hour-level operation time and high cost caused by the frequent redesign/reconstruction of gates, tedious strand-displacement reaction, and expensive labeled probes (or tool enzymes) in previous works are ineluctable drawbacks. Herein, we report an ultrafast and cost-effective system for engineering concurrent DNA logic nanodevices (CDLNs) by combining polythymine CuNCs with SYBR Green I (SG I) as universal dual-output producers. Particularly, benefiting from the concomitant minute-level quick response of both unlabeled illuminators and the exquisite strand-displacement-free design, all CDLNs including contrary logic pairs (YES∧NOT, OR∧NOR, and Even∧Odd number classifier), noncontrary ones (IDE∧IMP, OR∧NAND), and concatenated circuits are implemented in just 10 min via a "one-stone-two-birds" method, resulting in only 1/12 the operation time and 1/4 the cost needed in previous works, respectively. Moreover, all of them share the same threshold value, and the dual output can be easily visualized by the naked eye under a portable UV lamp, indicating the universality and practicality of this system. Furthermore, by exploiting the "positive/negative cross-verification" advantages of concurrent contrary logic, the smart in vitro analysis of the polyadenine strand and its polymerase is realized, providing novel molecular tools for the early diagnosis of cancer-related diseases.
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Affiliation(s)
- Jiawen Han
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Xujuan Lv
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Yuwei Zhang
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Juan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Intelligent Wearable Engineering Research Center of Qingdao, Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China
| | - Daoqing Fan
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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2
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Han J, Ding Y, Lv X, Zhang Y, Fan D. Integration of G-Quadruplex and Pyrene as a Simple and Efficient Ratiometric Fluorescent Platform That Programmed by Contrary Logic Pair for Highly Sensitive and Selective Coralyne (COR) Detection. BIOSENSORS 2023; 13:bios13040489. [PMID: 37185564 PMCID: PMC10136222 DOI: 10.3390/bios13040489] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023]
Abstract
The effective and accurate detection of the anticancer drug coralyne (COR) is highly significant for drug quality control, medication safety and good health. Although various COR sensors have been reported in recent years, previous ones can only exhibit single-signal output (turn ON or turn OFF) with poor reliability and anti-interference ability. Therefore, exploring novel platform with dual-signal response for COR detection is urgently needed. Herein, we reported the first ratiometric fluorescent platform for highly sensitive and selective COR detection by integrating G-quadruplex (G4) and Pyrene (Py) as signal probes and harnessing A-COR-A interaction. In the absence of COR, the platform shows a low fluorescence signal of PPIX (F642) and a high one of Py monomer (F383). With the addition of COR, two delicately designed poly-A ssDNAs will hybridize with each other via A-COR-A coordination to form complete G4, yielding the increased fluorescence signal of PPIX and the decreased one of Py due to the formation of Py excimer. Based on the above mechanism, we constructed a simple and efficient sensor that could realize the ratiometric fluorescent detection of COR with high sensitivity and selectivity. A linear relationship between F642/F383 and COR's concentration is obtained in the range from 1 nM to 8 μM. And the limit of detection of COR could reach to as low as 0.63 nM without any amplification, which is much lower than that of most COR sensors reported so far. Notably, the logical analysis of COR can be carried out under the control of a "YES-NOT" contrary logic pair, enabling the smart dual-channel response with an adequate S/N ratio and improved reliability and anti-interference ability. Moreover, this system also presents satisfactory performance in fetal bovine serum (FBS) samples.
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Affiliation(s)
- Jiawen Han
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yaru Ding
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Xujuan Lv
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yuwei Zhang
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Daoqing Fan
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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Han J, Wang J, Wang J, Fan D, Dong S. Recent advancements in coralyne (COR)-based biosensors: Basic principles, various strategies and future perspectives. Biosens Bioelectron 2022; 210:114343. [PMID: 35561578 DOI: 10.1016/j.bios.2022.114343] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 11/02/2022]
Abstract
As a kind of protoberberine alkaloid heterocyclic analogues, coralyne (COR) has been reported to exhibit superior antileukemic ability and used as anticancer drug agent. While, the severe hazards and side effects caused by unreasonable use have made its accurate detection more and more important. Although scientists have explored various methods to sense COR and other related targets, a systematical review which could not only elaborate recent developments and analyze current challenges of COR-based biosensors, but also present future perspective has not been reported and is urgently needed. In this review, we attempt to summarize latest advancements in COR-based biosensors in recent decade. Firstly, the operating principles, advantages and disadvantages of various strategies for COR detection (colorimetric, fluorescent, electrochemical and other ones) are comprehensively demonstrated and reviewed. Secondly, COR-assisted biosensors for detection of different non-COR targets (heparin, toxins, nucleic acids and other small molecules) are further discussed. Finally, we analyze current challenges and also suggest potential perspectives for this area.
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Affiliation(s)
- Jiawen Han
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Juan Wang
- Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, Qingdao University, Qingdao, Shandong, 266071, China
| | - Jun Wang
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Daoqing Fan
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China.
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
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4
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Xie T, Deng Y, Zhang J, Zhang Z, Hu Z, Wu T. DNA circuits compatible encoder and demultiplexer based on a single biomolecular platform with DNA strands as outputs. Nucleic Acids Res 2022; 50:8431-8440. [PMID: 35904810 PMCID: PMC9410916 DOI: 10.1093/nar/gkac650] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022] Open
Abstract
A series of multiple logic circuits based on a single biomolecular platform is constructed to perform nonarithmetic and arithmetic functions, including 4-to-2 encoder, 1-to-2 demultiplexer, 1-to-4 demultiplexer, and multi-input OR gate. The encoder to a DNA circuit is the equivalent of a sensory receptor to a reflex arc. They all function to encode information from outside the pathway (DNA circuit or reflex arc) into a form that subsequent pathways can recognize and utilize. Current molecular encoders are based on optical or electrical signals as outputs, while DNA circuits are based on DNA strands as transmission signals. The output of existing encoders cannot be recognized by subsequent DNA circuits. It is the first time the DNA-based encoder with DNA strands as outputs can be truly applied to the DNA circuit, enabling the application of DNA circuits in non-binary biological environments. Another novel feature of the designed system is that the developed nanodevices all have a simple structure, low leakage and low crosstalk, which allows them to implement higher-level encoders and demultiplexers easily. Our work is based on the idea of complex functionality in a simple form, which will also provide a new route for developing advanced molecular logic circuits.
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Affiliation(s)
- Tianci Xie
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuhan Deng
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiarui Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhen Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhe Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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5
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Liu X, Zhang Q, Zhang X, Liu Y, Yao Y, Kasabov N. Construction of Multiple Logic Circuits Based on Allosteric DNAzymes. Biomolecules 2022; 12:biom12040495. [PMID: 35454084 PMCID: PMC9032175 DOI: 10.3390/biom12040495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
In DNA computing, the implementation of complex and stable logic operations in a universal system is a critical challenge. It is necessary to develop a system with complex logic functions based on a simple mechanism. Here, the strategy to control the secondary structure of assembled DNAzymes’ conserved domain is adopted to regulate the activity of DNAzymes and avoid the generation of four-way junctions, and makes it possible to implement basic logic gates and their cascade circuits in the same system. In addition, the purpose of threshold control achieved by the allosteric secondary structure implements a three-input DNA voter with one-vote veto function. The scalability of the system can be remarkably improved by adjusting the threshold to implement a DNA voter with 2n + 1 inputs. The proposed strategy provides a feasible idea for constructing more complex DNA circuits and a highly integrated computing system.
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Affiliation(s)
- Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
- Correspondence: ; Tel.: +86-0411-84708470
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Nikola 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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He S, Cui R, Zhang Y, Yang Y, Xu Z, Wang S, Dang P, Dang K, Ye Q, Liu Y. Design and Realization of Triple dsDNA Nanocomputing Circuits in Microfluidic Chips. ACS APPLIED MATERIALS & INTERFACES 2022; 14:10721-10728. [PMID: 35188362 DOI: 10.1021/acsami.1c24220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
DNA logic gates, nanocomputing circuits, have already implemented basic computations and shown great signal potential for nano logic material application. However, the reaction temperature and computing speed still limit its development. Performing complicated computations requires a more stable component and a better computing platform. We proposed a more stable design of logic gates based on a triple, double-stranded, DNA (T-dsDNA) structure. We demonstrated a half adder and a full adder using these DNA nanocircuits and performed the computations in a microfluidic chip device at room temperature. When the solutions were mixed in the device, we obtained the expected results in real time, which suggested that the T-dsDNA combined microfluidic chip provides a concise strategy for large DNA nanocircuits.
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Affiliation(s)
- Songlin He
- School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
- Institute of Orthopedics, the First Medical Center, Chinese PLA General Hospital; Beijing Key Lab of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma & War Injuries PLA; No. 28 Fuxing Road, Haidian District, Beijing 100853, People's Republic of China
| | - Ruiming Cui
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, People's Republic of China
| | - Yao Zhang
- School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Yongkang Yang
- School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Ziheng Xu
- School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Shuoyu Wang
- School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Pingxiu Dang
- School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Kexin Dang
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, People's Republic of China
| | - Qing Ye
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, People's Republic of China
- Nankai University Eye Institute, Nankai University, Tianjin 300071, People's Republic of China
| | - Yin Liu
- School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
- Nankai University Eye Institute, Nankai University, Tianjin 300071, People's Republic of China
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7
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Cheng W, Xiang L, Adeel K, Zhang J, Sun Y, Zhang Z, Li J. Ultrasensitive fluorescent detection of telomerase activity based on tetrahedral DNA nanostructures as carriers for DNA-templated silver nanoclusters. Anal Bioanal Chem 2022; 414:2431-2438. [PMID: 35037986 DOI: 10.1007/s00216-022-03883-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/27/2021] [Accepted: 01/06/2022] [Indexed: 12/17/2022]
Abstract
Precise evaluation of telomerase activity is essential for the clinical diagnosis of early tumors. Herein, we have ingeniously designed a tetrahedral DNA nanostructure, with hairpin-shaped DNA probes rich in cytosine bases at four vertices for telomerase detection. The DNA-templated silver nanoclusters can be formed after the addition of Ag. Then the introduction of telomerase adds the single-strand TTAGGG extension, which can "turn on" the fluorescence of silver nanoclusters quickly by the proximity of the resulting guanine-rich sequences to silver nanoclusters and realize accurate detection of telomerase activity. In this study, integration of high stability tetrahedral DNA nanostructure and fluorescence signal amplification of four DNA-templated silver nanoclusters offers the advantage of high sensitivity, with a low detection limit of 1 cell. More than that, this method is low-cost, facile, and feasible for practical clinical applications.
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Affiliation(s)
- Wenting Cheng
- Department of Clinical Laboratory, Gaochun People's Hospital, Nanjing, 211300, China
| | - Liangliang Xiang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, China
| | - Khan Adeel
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jianchun Zhang
- Department of Clinical Laboratory, Gaochun People's Hospital, Nanjing, 211300, China
| | - Ying Sun
- Department of Clinical Laboratory, Gaochun People's Hospital, Nanjing, 211300, China
| | - Zhaoli Zhang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, China
| | - Jinlong Li
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, China.
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8
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Fan D, Wang J, Han J, Wang E, Dong S. Engineering DNA logic systems with non-canonical DNA-nanostructures: basic principles, recent developments and bio-applications. Sci China Chem 2021. [DOI: 10.1007/s11426-021-1131-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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9
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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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10
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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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11
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Huang D, Han H, Guo C, Lin X, Chen D, Yang S, Yang Q, Li F. Information processing using an integrated DNA reaction network. NANOSCALE 2021; 13:5706-5713. [PMID: 33683263 DOI: 10.1039/d0nr09148k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Living organisms use interconnected chemical reaction networks (CRNs) to exchange information with the surrounding environment and respond to diverse external stimuli. Inspired by nature, numerous artificial CRNs with a complex information processing function have been recently introduced, with DNA as one of the most attractive engineering materials. Although much progress has been made in DNA-based CRNs in terms of controllable reaction dynamics and molecular computation, the effective integration of signal translation with information processing in a single CRN remains to be difficult. In this work, we introduced a stimuli-responsive DNA reaction network capable of integrated information translation and processing in a stepwise manner. This network is designed to integrate sensing, translation, and decision-making operations by independent modules, in which various logic units capable of performing different functions were realized, including information identification (YES and OR gates), integration (AND and AND-AND gates), integration-filtration (AND-AND-NOT gate), comparison (Comparator), and map-to-map analysis (Feynman gate). Benefitting from the modular and programmable design, continuous and parallel processing operations are also possible. With the innovative functions, we show that the DNA network is a highly useful addition to the current DNA-based CRNs by offering a bottom-up strategy to design devices capable of cascaded information processing with high efficiency.
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Affiliation(s)
- Dan Huang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China.
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12
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Wang HB, Mao AL, Tao BB, Zhang HD, Liu YM. Fabrication of multiple molecular logic gates made of fluorescent DNA-templated Au nanoclusters. NEW J CHEM 2021. [DOI: 10.1039/d0nj06192a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A universal platform of label-free multiple molecular logic gates have been constructed by taking the advantage of DNA-AuNCs.
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Affiliation(s)
- Hai-Bo Wang
- College of Chemistry and Chemical Engineering
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains
- Xinyang Normal University
- Xinyang 464000
- China
| | - An-Li Mao
- College of Chemistry and Chemical Engineering
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains
- Xinyang Normal University
- Xinyang 464000
- China
| | - Bei-Bei Tao
- College of Chemistry and Chemical Engineering
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains
- Xinyang Normal University
- Xinyang 464000
- China
| | - Hong-Ding Zhang
- College of Chemistry and Chemical Engineering
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains
- Xinyang Normal University
- Xinyang 464000
- China
| | - Yan-Ming Liu
- College of Chemistry and Chemical Engineering
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains
- Xinyang Normal University
- Xinyang 464000
- China
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13
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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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14
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Wang Y, Wei Y, Zhang Y, Wang L, Dong Y. Enzyme-free and DNA-based universal platform for the construction of various logic devices based on graphene oxide and G-quadruplex. Comput Biol Chem 2020; 89:107374. [PMID: 32987286 DOI: 10.1016/j.compbiolchem.2020.107374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/22/2020] [Accepted: 09/10/2020] [Indexed: 11/16/2022]
Abstract
In the fields of biocomputing and biomolecular, DNA molecules are applicable to be regarded as data of logical computing platform that uses elaborate logic gates to perform a variety of tasks. Graphene oxide (GO) is a type of novel nanomaterial, which brings new research focus to materials science and biosensors due to its special selectivity and excellent quenching ability. G-quadruplex as a unique DNA structure stimulates the intelligent application of DNA assembly on the strength of its exceptional binding activity. In this paper, we report a universal logic device assisted with GO and G-quadruplex under an enzyme-free condition. Integrated with the quenching ability of GO to the TAMRA (fluorophore, Carboxytetramethylrhodamine) and the enhancement of fluorescence intensity produced by the peculiar binding of G-quadruplex to the NMM (N-methylmesoporphyrin IX), a series of basic binary logic gates (AND. OR. INHIBIT. XOR) have been designed and verified through biological experiments. Given the modularity and programmability of this strategy, two advanced logic gates (half adder and half subtractor) were realized on the basis of the same work platform. The fluorescence signals generated from different input combinations possessed satisfactory results, which provided proof of feasibility. We believe that the proposed universal logical platform that operates at the nanoscale is expected to be utilized for future applications in molecular computing as well as disease diagnosis.
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Affiliation(s)
- Yue Wang
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Yani Wei
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yingying Zhang
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Luhui Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yafei Dong
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China; College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
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15
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Chen D, Wu Z, Xu X, Yang S. A Supramolecular Counter Circuit Based on Cyanine Dye Assembly. Chemistry 2020; 26:13235-13240. [PMID: 32337743 DOI: 10.1002/chem.202001240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/16/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Die Chen
- 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 P. R. China
| | - Zhiming Wu
- College of Computer Science Sichuan University Chengdu 610065 P. R. China
| | - Xiaoping Xu
- 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 P. R. China
| | - 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 P. R. China
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16
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Srivastava R. Nucleobase Pair-Metal Dimer/Dinuclear Metal Cation Interaction: A Theoretical Study. ACS OMEGA 2020; 5:18808-18817. [PMID: 32775882 PMCID: PMC7408194 DOI: 10.1021/acsomega.0c01931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Nucleobase pair-metal dimer/dinuclear metal cation interactions play an important role in biological applications because of their highly symmetrical structures and high stabilities. In this work, we have selected five adenine-adenine hydrogen bonding, adenine-thymine (AT), adenine-uracil, adenine-adenine stacking pairs, and Watson-Crick AT stacking pairs and studied their interaction with the coinage metal dimer M2 and M2 2+ metal cations, where M = Ag, Au, and Cu. Quantum chemical calculations have been carried out with density functional theory (DFT) and time-dependent DFT (TDDFT) methods. Electronic structures were analyzed by the partial density of states method. During interactions, we find that M-M distances are shorter than the sum of van der Waals radii of the corresponding two homocoinage metal atoms, which show the existence of significant metallophilic interactions. Results indicated that nucleobase-M2 2+ complexes are stronger as compared to nucleobase-M2 complexes. Also, the replacement of the hydrogen bond by the dinuclear metal cation-coordinated bond forms more stable alternative metallo-DNA sequences in AAST base pairs. TDDFT calculations reveal that nucleobase-Cu2 complexes and nucleobase-Ag2 2+/Au2 2+ complexes can be used for fluorescent markers and logic gate applications. Atom-in-molecules analysis predicted the noncovalent interaction in these complexes.
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Affiliation(s)
- Ruby Srivastava
- Bioinformatics, CSIR-Centre
for Cellular and Molecular Biology, Hyderabad 500607, India
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17
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Lv M, Zhou W, Fan D, Guo Y, Zhu X, Ren J, Wang E. Illuminating Diverse Concomitant DNA Logic Gates and Concatenated Circuits with Hairpin DNA-Templated Silver Nanoclusters as Universal Dual-Output Generators. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1908480. [PMID: 32196133 DOI: 10.1002/adma.201908480] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 05/21/2023]
Abstract
Exquisite administration of a new type of hairpin DNA-templated silver nanoclusters (H-AgNCs) as universal dual-output generators in DNA-based logic systems is reported. Diverse concomitant contrary logic gates (CCLGs) with opposite functions (YES^ NOT, OR^ NOR, INHIBIT^ IMPLICATION, XOR^ XNOR, and MAJORITY^ MINORITY) and extended concatenated logic circuits are presented and some of them perform specific functions, such as parity generators and checkers. The introduction of H-AgNCs as noncovalent signal reporters avoids tedious and high-cost labeling procedures. Of note, the concomitant feature of CCLGs attributed to the dual-emitter AgNCs conduces to reducing the time and cost to devise multiple logic gates. As compared to previous ones, this design eliminates numerous substances (e.g., organic dyes) and unstable components (hydrogen peroxide), which not only decreases the complexity of logic performs and improves repeatability of operation, but also makes it convenient to connect distinct DNA-based logic gates. It is worthy to anticipate that the cost-effective strategy will inspire researchers to develop much more complex logic systems and contribute to the field of molecular computing.
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Affiliation(s)
- Mengmeng Lv
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weijun Zhou
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Daoqing Fan
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Yuchun Guo
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- College of Chemistry, Jilin University, Changchun, Jilin, 130012, China
| | - Xiaoqing Zhu
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Jiangtao Ren
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Erkang Wang
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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Liang J, Wei W, Yao H, Shi K, Liu H. A biocomputing platform with electrochemical and fluorescent signal outputs based on multi-sensitive copolymer film electrodes with entrapped Au nanoclusters and tetraphenylethene and electrocatalysis of NADH. Phys Chem Chem Phys 2019; 21:24572-24583. [PMID: 31663551 DOI: 10.1039/c9cp03687c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this work, poly(N,N'-dimethylaminoethylmethacrylate-co-N-isopropylacrylamide) copolymer films were polymerized on the surface of Au electrodes with a facile one-step method, and Au nanoclusters (AuNCs) and tetraphenylethene (TPE) were synchronously embedded in the films, designated as P(DMA-co-NIPA)/AuNCs/TPE. Ferrocene dicarboxylic acid (FDA), an electroactive probe in solution displayed inverse pH- and SO42--sensitive on-off cyclic voltammetric (CV) behaviors at the film electrodes. The electrocatalytic oxidation of nicotinamide adenine dinucleotide (NADH) mediated by FDA in solution could substantially amplify the CV response difference between the on and off states. Moreover, the two fluorescence emission (FL) signals from the TPE constituent at 450 nm and AuNCs component at 660 nm in the films also demonstrated SO42-- and pH-sensitive behaviors. Based on the aforementioned results, a 4-input/9-output biomolecular logic circuit was constructed with pH, Na2SO4, FDA and NADH as the inputs, and the CV signals and the FL responses at 450 and 660 nm at different levels as the outputs. Additionally, some functional non-Boolean devices were elaborately designed on an identical platform, including a 1-to-2 decoder, a 2-to-1 encoder, a 1-to-2 demultiplexer and different types of keypad locks. This work combines copolymer films, bioelectrocatalysis, and fluorescence together so that more complicated biocomputing systems could be established. This work may pave a new way to develop advanced and sophisticated biocomputing logic circuits and functional devices in the future.
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Affiliation(s)
- Jiying Liang
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
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Huang D, Guo C, Miao J, Zhang Y, Lin X, Chen D, Yang S, Yang Q, Tang Y. Construction of a novel DNA-based comparator and its application in intelligent analysis. NANOSCALE 2019; 11:16241-16244. [PMID: 31454010 DOI: 10.1039/c9nr05270d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, a novel and general comparator was constructed based on cascaded strand displacement reactions and DNA hybridization and its potential in intelligently weighing the quantitative predominance of two targets was explored in a complex biological matrix, which not only enriches the information processing mode of DNA computation but also provides an instructive way to deal with quantitative analyzing tasks in further DNA-based logic sensors.
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Affiliation(s)
- Dan Huang
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Chen Guo
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Jiarong Miao
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Yi Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Xiao Lin
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Die Chen
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Shu Yang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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20
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Wang H, Wang H, Wu Q, Liang M, Liu X, Wang F. A DNAzyme-amplified DNA circuit for highly accurate microRNA detection and intracellular imaging. Chem Sci 2019; 10:9597-9604. [PMID: 32055333 PMCID: PMC7006504 DOI: 10.1039/c9sc03552d] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/25/2019] [Indexed: 12/27/2022] Open
Abstract
A rationally and modularly engineered CHA-HCR-DNAzyme circuit was constructed for amplified biosensing and bioimaging with high performance.
Biomolecular self-assembly circuits have been well developed for high-performance biosensing and bioengineering applications. Here we designed an isothermal concatenated nucleic acid amplification system which is composed of a lead-in catalyzed hairpin assembly (CHA), intermediate hybridization chain reaction (HCR) and ultimate DNAzyme amplifier units. The analyte initiates the self-assembly of hairpin reactants into dsDNA products in CHA, which generates numerous trigger sequences for activating the subsequent HCR-assembled long tandem DNAzyme nanowires. The as-acquired DNAzyme catalyzed the successive cleavage of its substrates, leading to an amplified fluorescence readout. The sophisticated design of our CHA-HCR-DNAzyme scheme was systematically investigated in vitro and showed dramatically enhanced detection performance. As a general sensing strategy, this CHA-HCR-DNAzyme method enables the amplified analysis of miRNA and its accurate intracellular imaging in living cells, originating from their synergistic signal amplifications. This method shows great potential for analyzing trace amounts of biomarkers in various clinical research studies.
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Affiliation(s)
- Hong Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Qiong Wu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Meijuan Liang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
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Fan D, Wang J, Wang E, Dong S. A Janus-inspired amphichromatic system that kills two birds with one stone for operating a "DNA Janus Logic Pair" (DJLP) library. Chem Sci 2019; 10:7290-7298. [PMID: 31588299 PMCID: PMC6686727 DOI: 10.1039/c9sc01865d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/12/2019] [Indexed: 12/27/2022] Open
Abstract
Although DNA computing has exhibited a magical power across diverse areas, current DNA logic gates with different functions are always separately operated and can only produce hard-to-visualize output. The fussy/obligatory gates' redesign/reconstruction and the non-intuitive output cause the wastage of time and costs, low efficiency and practicality. Herein, inspired by the ancient Roman mythical God Janus, for the first time, we propose the concept of "DNA Janus Logic Pair" (DJLP) to classify the DNA logic gates with contrary functions into "Positive + Negative" gates (DJLP = Pos + Neg). Based on the biocatalytic property of G-quadruplex DNAzyme (G4zyme) and the luminescence quenching ability of oxidized 3,3',5,5'-tetramethylbenzidine (OxTMB) towards the upconversion (UC) particles, we fabricated a universal amphichromatic platform that kills two birds with one stone for operating a versatile DJLP library. Different from the previous DNA logic systems, the "Pos + Neg" gates of each DJLP in this study were concomitantly achieved via the same one-time DNA reaction, which avoided the gates' redesign/reoperation and reduced the operating costs/time of the DNA gates by at least half. Besides, both the amphichromatic outputs (Visual-blue and UC luminescent-green) can be visualized under harmless-NIR, thus bringing greatly enhanced practicality to the method. Moreover, we constructed various concatenated logic circuits via logically modulating the G4zyme's biocatalytic property with glutathione, thus enabling the largely improved computing complexity. Furthermore, taking the circuit "YES-INH-1-2 decoder" as the "computing core", we designed an "antioxidant indicator" with ratiometric logical responses that could recognize the presence of antioxidants smartly (output changed from "10" to "01"), which provided a typical prototype for potential intelligent bio-applications.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Juan Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
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22
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Thioflavin T as luminescence biosensors for nucleic acid study and RNase A activity detection. Microchem J 2019. [DOI: 10.1016/j.microc.2019.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Fan Y, Zhang W, Liu Y, Zeng Z, Quan X, Zhao H. Three-Dimensional Branched Crystal Carbon Nitride with Enhanced Intrinsic Peroxidase-Like Activity: A Hypersensitive Platform for Colorimetric Detection. ACS APPLIED MATERIALS & INTERFACES 2019; 11:17467-17474. [PMID: 31021073 DOI: 10.1021/acsami.9b04320] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Graphitic carbon nitride (g-C3N4) as a metal-free nanozyme has attracted huge attention for catalytic applications. However, the catalytic activity of pure g-C3N4 causes very moderate H2O2 activation. Herein, a novel three-dimensional (3D) branched carbon nitride nanoneedle (3DBC-C3N4) nanozyme has been proposed to overcome such shortcoming. This unique 3D branched structure of 3DBC-C3N4 facilitated effective mass transfer during catalytic reaction and induced a lightning rodlike effect to accelerate electron collection at the tip area for H2O2 activation. With improved H2O2 activation for hydroxyl radical (•OH) generation, 3DBC-C3N4 showed excellent peroxidase-like activity toward 3,3',5,5'-tetramethylbenzidine oxidation in the presence of H2O2. As for H2O2, the Vmax value of 3DBC-C3N4 was found to be 20 times higher than that of natural horseradish peroxidase. Moreover, the 3D branched structure of 3DBC-C3N4 offered large interface for the reversible conjugation of single-stranded DNA, which enhanced the colorimetric sensitivity. Moreover, 3DBC-C3N4 exhibited high sensitivity toward oxytetracycline detection, with the detection limit and quantitative limit of 1 and 50 μg/L, respectively.
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Affiliation(s)
- Yaofang Fan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology , Dalian University of Technology , Dalian 116024 , China
| | - Weican Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology , Dalian University of Technology , Dalian 116024 , China
| | - Yanming Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology , Dalian University of Technology , Dalian 116024 , China
| | - Zhenxing Zeng
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology , Dalian University of Technology , Dalian 116024 , China
| | - Xie Quan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology , Dalian University of Technology , Dalian 116024 , China
| | - Huimin Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology , Dalian University of Technology , Dalian 116024 , China
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Huang D, Yang C, Yao Y, Li J, Guo C, Chen J, Zhang Y, Yang S, Yang Q, Tang Y. Versatile and Homogeneous DNA Tetraplex Platform for Constructing Label‐Free Logic Devices: From Design to Application. Chemistry 2019; 25:6996-7003. [PMID: 30933378 DOI: 10.1002/chem.201900734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Dan Huang
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Chunrong Yang
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Ye Yao
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Jicheng Li
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Chen Guo
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Jianchi Chen
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Yi Zhang
- Department West China School of PharmacySichuan University Chengdu 610064 P.R. China
| | - Shu Yang
- Department West China School of PharmacySichuan University Chengdu 610064 P.R. China
| | - Qianfan Yang
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Yalin Tang
- National Laboratory for Molecular SciencesCentre for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable, and Stable SpeciesInstitute of ChemistryChinese Academy of Sciences Beijing 100190 P.R. China
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25
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SERS detection of mercury (II)/lead (II): A new class of DNA logic gates. Talanta 2019; 195:497-505. [DOI: 10.1016/j.talanta.2018.11.089] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/07/2018] [Accepted: 11/24/2018] [Indexed: 11/21/2022]
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26
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Chen J, Yang S, Yang C, Li J, Huang D, Lin X, Guo C, Zhou Q, Yang Q, Tang Y. A Visibly Observable, Programmable Supramolecular Logic Platform and Its Application in Smart Thiols Sensing. Chemistry 2019; 25:5691-5697. [PMID: 30741458 DOI: 10.1002/chem.201900060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/31/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Jianchi Chen
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Shu Yang
- West China School of PharmacySichuan University Chengdu 610041 Sichuan P.R. China
| | - Chunrong Yang
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Jicheng Li
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Dan Huang
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Xiao Lin
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Chen Guo
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Qiuju Zhou
- Analysis & Testing CenterXinyang Normal University Xinyang 464000 Henan P.R. China
| | - Qianfan Yang
- College of ChemistrySichuan University Chengdu 610064 Sichuan P.R. China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of ChemistryChinese Academy of Sciences Beijing 100190 P.R. China
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27
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Zhang Y, Wang L, Dong Y. A Label-free and Universal Platform for the Construction of Various Logic Circuits Based on Graphene Oxide and G-Quadruplex Structure. ANAL SCI 2019; 35:181-187. [PMID: 30745511 DOI: 10.2116/analsci.18p349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Due to structual polymorphism, excellent binding activity and functional significances in biological regulation, G-quadruplex has become the focus of research as an innovated module for analytical chemistry and biomedicine. Meanwhile, in the biosensor fields, new nanomaterial graphene oxide (GO) has also received extensive attention due to its brilliant physical and chemical properties. Herein, we propose a non-label and enzyme-free logic operation platform based on G-quadruplex structure and GO instead of any expensive modification. Taking advantage of the quenching ability of GO to AgNCs and the fluorescence enhancement of NMM (N-methylmesoporphyrin IX) mediated by the split G-quadruplex, a series of binary logic gates (AND, OR, INHIBIT, XOR) have been constructed and verified by biological experiments. Subsequently, two combinatorial logic gates were successfully realized conceptually on the basis of the same BGG platform, including half adder and half subtractor. Taken together, such a universal platform has great potential in applications, such as biocomputing, bio-imaging and disease diagnosis, which cultivate a new view for future biological research.
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Affiliation(s)
| | - Luhui Wang
- College of Life Sciences, Shaanxi Normal University
| | - Yafei Dong
- College of Life Sciences, Shaanxi Normal University.,Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China
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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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29
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Li J, Ma J, Zhang Y, Zhang Z, He G. A fluorometric method for determination of the activity of T4 polynucleotide kinase by using a DNA-templated silver nanocluster probe. Mikrochim Acta 2019; 186:48. [DOI: 10.1007/s00604-018-3157-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/07/2018] [Indexed: 12/31/2022]
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Abstract
DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.
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Affiliation(s)
- Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering , Nanjing University , Nanjing 210023 , China.,ARNA Laboratory , Université de Bordeaux, Inserm U 1212, CNRS UMR5320, IECB , Pessac 33600 , France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135 , 612 65 Brno , Czech Republic
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
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31
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Zhong W, Tang W, Fan J, Zhang J, Zhou X, Liu Y. A domain-based DNA circuit for smart single-nucleotide variant identification. Chem Commun (Camb) 2018; 54:1311-1314. [PMID: 29177325 DOI: 10.1039/c7cc07733e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
According to the differential information of four homologous oligonucleotides, two domain-based encoders have been constructed with the molecular information as the input. Based on the one-to-one correspondence between the input and output, SNVs can be identified and their sites can be located at the domain level.
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Affiliation(s)
- Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, P. R. China.
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32
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Tregubov AA, Nikitin PI, Nikitin MP. Advanced Smart Nanomaterials with Integrated Logic-Gating and Biocomputing: Dawn of Theranostic Nanorobots. Chem Rev 2018; 118:10294-10348. [DOI: 10.1021/acs.chemrev.8b00198] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Andrey A. Tregubov
- Moscow Institute of Physics and Technology (State University), 1A Kerchenskaya St, Moscow 117303, Russia
| | - Petr I. Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, Moscow 119991, Russia
| | - Maxim P. Nikitin
- Moscow Institute of Physics and Technology (State University), 1A Kerchenskaya St, Moscow 117303, Russia
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33
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Fan D, Fan Y, Wang E, Dong S. A simple, label-free, electrochemical DNA parity generator/checker for error detection during data transmission based on "aptamer-nanoclaw"-modulated protein steric hindrance. Chem Sci 2018; 9:6981-6987. [PMID: 30210773 PMCID: PMC6124900 DOI: 10.1039/c8sc02482k] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/15/2018] [Indexed: 01/01/2023] Open
Abstract
The first electrochemical DNA parity generator/checker system for error detection during data transmission was constructed based on “aptamer-nanoclaw”-modulated protein steric hindrance.
Versatile DNA logic devices have exhibited magical power in molecular-level computing and data processing. During any type of data transmission, the appearance of erroneous bits (which have severe impacts on normal computing) is unavoidable. Luckily, the erroneous bits can be detected via placing a parity generator (pG) at the sending module and a parity checker (pC) at the receiving module. However, all current DNA pG/pC systems use optical signals as outputs. In comparison, sensitive, facilely operated, electric-powered electrochemical outputs possess inherent advantages in terms of potential practicability and future integration with semiconductor transistors. Herein, taking an even pG/pC as a model device, we construct the first electrochemical DNA pG/pC system so far. Innovatively, a thrombin aptamer is integrated into the input-strand and it functions as a “nanoclaw” to selectively capture thrombin; the electrochemical impedance changes induced by the “nanoclaw/thrombin” complex are used as label-free outputs. Notably, this system is simple and can be operated within 2 h, which is comparable with previous fluorescent ones, but avoids the high-cost labeled-fluorophore and tedious nanoquencher. Moreover, taking non-interfering poly-T strands as additional inputs, a cascade logic circuit (OR-2 to 1 encoder) and a parity checker that could distinguish even/odd numbers from natural numbers (0 to 9) is also achieved based on the same system. This work not only opens up inspiring horizons for the design of novel electrochemical functional devices and complicated logic circuits, but also lays a solid foundation for potential logic-programmed target detection.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electro Analytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . .,University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Yongchao Fan
- State Key Laboratory of Electro Analytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . .,University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Erkang Wang
- State Key Laboratory of Electro Analytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . .,University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Shaojun Dong
- State Key Laboratory of Electro Analytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . .,University of Chinese Academy of Sciences , Beijing , 100039 , China
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Lin X, Liu Y, Deng J, Lyu Y, Qian P, Li Y, Wang S. Multiple advanced logic gates made of DNA-Ag nanocluster and the application for intelligent detection of pathogenic bacterial genes. Chem Sci 2018; 9:1774-1781. [PMID: 29675221 PMCID: PMC5892130 DOI: 10.1039/c7sc05246d] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/05/2018] [Indexed: 12/19/2022] Open
Abstract
The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer. Under UV irradiation, all the logic functions could be instantly visualized, confirming an excellent repeatability. The logic operations were entirely based on DNA hybridization in an enzyme-free and label-free condition, avoiding waste accumulation and reducing cost consumption. Interestingly, a DNA-AgNCs-based multiplexer was, for the first time, used as an intelligent biosensor to identify pathogenic genes, E. coli and S. aureus genes, with a high sensitivity. The investigation provides a prototype for the wireless integration of multiple devices on even the simplest single-strand DNA platform to perform diverse complex functions in a straightforward and cost-effective way.
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Affiliation(s)
- Xiaodong Lin
- Key Laboratory of Food Nutrition and Safety (Ministry of Education) , College of Food Engineering and Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China .
| | - Yaqing Liu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education) , College of Food Engineering and Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China .
| | - Jiankang Deng
- Key Laboratory of Food Nutrition and Safety (Ministry of Education) , College of Food Engineering and Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China .
| | - Yanlong Lyu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education) , College of Food Engineering and Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China .
| | - Pengcheng Qian
- Key Laboratory of Food Nutrition and Safety (Ministry of Education) , College of Food Engineering and Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China .
| | - Yunfei Li
- Key Laboratory of Food Nutrition and Safety (Ministry of Education) , College of Food Engineering and Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China .
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health , School of Medicine , Nankai University , Tianjin 300071 , China .
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Leng X, Wang Y, Li R, Liu S, Yao J, Pei Q, Cui X, Tu Y, Tang D, Huang J. Circular exponential amplification of photoinduced electron transfer using hairpin probes, G-quadruplex DNAzyme and silver nanocluster-labeled DNA for ultrasensitive fluorometric determination of pathogenic bacteria. Mikrochim Acta 2018; 185:168. [PMID: 29594727 DOI: 10.1007/s00604-018-2698-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/20/2018] [Indexed: 01/17/2023]
Abstract
The authors describe a fluorometric strategy for the detection of pathogenic bacteria with ultrasensitivity and high specificity. This strategy relies on the combination of target-modulated photoinduced electron transfer (PET) between G-quadruplex DNAzyme and DNA (labeled with silver nanoclusters) along with hairpin probe-based circular exponential amplification. The reaction system involves three hairpin probes (H1, H2 and H3). Probe H1 contains an aptamer against S. Typhimurium and the recognition sequence for nicking endonuclease. It is used to recognize S. Typhimurium and participates in polymerase-catalyzed target recycle amplification and secondary-target recycle amplification. Probe H2 contains an aptamer against hemin and is used to form the G-quadruplex DNAzyme in the presence of hemin and potassium ion. It acts as the electron acceptor and quenches the fluorescence of the labeled DNA. Fluorescence is best measured at excitation/emission wavelengths of 567/650 nm. Probe H3 contains the template sequence for the synthesis of AgNCs and the H2-annealing sequence. Both H2 and H3 are utilized to perform a strand displacement reaction and to achieve PET between G-quadruplex DNAzyme and DNA/AgNCs. To the best of our knowledge, this is the first example of a PET between G-quadruplex DNAzyme and DNA/AgNCs coupled with circular exponential amplification. The assay has an ultra-low detection limit 8 cfu·mL-1 of S. Typhimurium. The assay is rapid, accurate, inexpensive and simple. Hence, the strategy may represent a useful platform for ultrasensitive and highly specific detection of pathogenic bacteria as encountered in food analysis and clinical diagnosis. Graphical abstract The reaction system includes three hairpin probes (H1, H2 and H3), primer probe (P), Phi 29 DNA ploymerase (Phi 29) and nicking endonuclease Nt.AlwI (Nt.AlwI). Phi 29 and Nt.AlwI -assisted signal amplification leads to the recycling of target and produces numerous single stranded-DNAs (S). Strand displacement amplification leads to photoinduced electron transfer (PET) between G-quadruplex DNAzyme and DNA/AgNCs. HAP-based circular exponential amplification of PET results in an ultrasensitive fluorometric assay.
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Affiliation(s)
- Xueqi Leng
- College of Resources and Environment, University of Jinan, Jinan, 250022, People's Republic of China
| | - Yu Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Rongguo Li
- Jinan Maternity and Child Care Hospital, Jinan, 250022, People's Republic of China
| | - Su Liu
- College of Resources and Environment, University of Jinan, Jinan, 250022, People's Republic of China.
| | - Jianzhuang Yao
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Qianqian Pei
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, College of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Xuejun Cui
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, College of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Yuqin Tu
- College of Resources and Environment, University of Jinan, Jinan, 250022, People's Republic of China
| | - Dan Tang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Jiadong Huang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, People's Republic of China.,Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, College of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
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36
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Yang C, Zou D, Chen J, Zhang L, Miao J, Huang D, Du Y, Yang S, Yang Q, Tang Y. A Novel Reconfigurable Logic Unit Based on the DNA-Templated Potassium-Concentration-Dependent Supramolecular Assembly. Chemistry 2018; 24:4019-4025. [PMID: 29226990 DOI: 10.1002/chem.201704824] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Chunrong Yang
- College of Chemistry; Sichuan University; Chengdu 610064, Sichuan P. R. China
| | - Dan Zou
- Key Laboratory of Drug Targeting and Drug Delivery SystemsWest China School of Pharmacy; Sichuan University; Chengdu 610041 P. R. China
| | - Jianchi Chen
- College of Chemistry; Sichuan University; Chengdu 610064, Sichuan P. R. China
| | - Linyan Zhang
- College of Chemistry; Sichuan University; Chengdu 610064, Sichuan P. R. China
| | - Jiarong Miao
- College of Chemistry; Sichuan University; Chengdu 610064, Sichuan P. R. China
| | - Dan Huang
- College of Chemistry; Sichuan University; Chengdu 610064, Sichuan P. R. China
| | - Yuanyuan Du
- West China School of Public Health, No.4 West Teaching Hospital; Sichuan University; Chengdu 610041 P. R. China
| | - Shu Yang
- Key Laboratory of Drug Targeting and Drug Delivery SystemsWest China School of Pharmacy; Sichuan University; Chengdu 610041 P. R. China
| | - Qianfan Yang
- College of Chemistry; Sichuan University; Chengdu 610064, Sichuan P. R. China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry, of Unstable and Stable Species, Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P. R. China
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37
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Deng J, Tao Z, Liu Y, Lin X, Qian P, Lyu Y, Li Y, Fu K, Wang S. A target-induced logically reversible logic gate for intelligent and rapid detection of pathogenic bacterial genes. Chem Commun (Camb) 2018. [DOI: 10.1039/c8cc00178b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A target-induced Feynman gate acts as an intelligent biosensor to distinguish all information of the targets from the output signal patterns.
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Affiliation(s)
- Jiankang Deng
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Zhanhui Tao
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Yaqing Liu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Xiaodong Lin
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Pengcheng Qian
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Yanlong Lyu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Yunfei Li
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Kejing Fu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
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38
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Filipov Y, Gamella M, Katz E. Nano-species Release System Activated by Enzyme-based XOR Logic Gate. ELECTROANAL 2017. [DOI: 10.1002/elan.201700742] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yaroslav Filipov
- Department of Chemistry and Biomolecular Science
- Department of Physics; Clarkson University; Potsdam, NY 13699 USA
| | | | - Evgeny Katz
- Department of Chemistry and Biomolecular Science
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Gao J, Liu Y, Lin X, Deng J, Yin J, Wang S. Implementation of cascade logic gates and majority logic gate on a simple and universal molecular platform. Sci Rep 2017; 7:14014. [PMID: 29070871 PMCID: PMC5656625 DOI: 10.1038/s41598-017-14416-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 10/11/2017] [Indexed: 12/18/2022] Open
Abstract
Wiring a series of simple logic gates to process complex data is significantly important and a large challenge for untraditional molecular computing systems. The programmable property of DNA endows its powerful application in molecular computing. In our investigation, it was found that DNA exhibits excellent peroxidase-like activity in a colorimetric system of TMB/H2O2/Hemin (TMB, 3,3′, 5,5′-Tetramethylbenzidine) in the presence of K+ and Cu2+, which is significantly inhibited by the addition of an antioxidant. According to the modulated catalytic activity of this DNA-based catalyst, three cascade logic gates including AND-OR-INH (INHIBIT), AND-INH and OR-INH were successfully constructed. Interestingly, by only modulating the concentration of Cu2+, a majority logic gate with a single-vote veto function was realized following the same threshold value as that of the cascade logic gates. The strategy is quite straightforward and versatile and provides an instructive method for constructing multiple logic gates on a simple platform to implement complex molecular computing.
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Affiliation(s)
- Jinting Gao
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Yaqing Liu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China.
| | - Xiaodong Lin
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Jiankang Deng
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Jinjin Yin
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China.
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40
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Hu X, Liu Y, Qu X, Sun Q. A quantum dot-labelled aptamer/graphene oxide system for the construction of a half-adder and half-subtractor with high resettability. Chem Commun (Camb) 2017; 53:11181-11184. [PMID: 28956037 DOI: 10.1039/c7cc05279k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
By a combination of quantum dot-labelled aptamers and graphene oxide, a hybrid molecular system was developed for the integration of multiple logic gates to implement half adder and half subtractor functions. On the merits of quantum dots, repetitious arithmetic operations and a reliable fluorescent switch were demonstrated.
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Affiliation(s)
- Xianyun Hu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, P. R. China.
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41
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Filipov Y, Domanskyi S, Wood ML, Gamella M, Privman V, Katz E. Experimental Realization of a High-Quality Biochemical XOR Gate. Chemphyschem 2017; 18:2908-2915. [PMID: 28745425 DOI: 10.1002/cphc.201700705] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 07/22/2017] [Indexed: 11/09/2022]
Abstract
We report an experimental realization of a biochemical XOR gate function that avoids many of the pitfalls of earlier realizations based on biocatalytic cascades. Inputs-represented by pairs of chemicals-cross-react to largely cancel out when both are nearly equal. The cross-reaction can be designed to also optimize gate functioning for noise handling. When not equal, the residual inputs are further processed to result in the output of the XOR type, by biocatalytic steps that allow for further gate-function optimization. The quality of the realized XOR gate is theoretically analyzed.
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Affiliation(s)
- Yaroslav Filipov
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA.,Department of Physics, Clarkson University, Potsdam, NY, 13699, USA
| | - Sergii Domanskyi
- Department of Physics, Clarkson University, Potsdam, NY, 13699, USA
| | - Mackenna L Wood
- Department of Physics, Clarkson University, Potsdam, NY, 13699, USA
| | - Maria Gamella
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, NY, 13699, USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
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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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Fan D, Shang C, Gu W, Wang E, Dong S. Introducing Ratiometric Fluorescence to MnO 2 Nanosheet-Based Biosensing: A Simple, Label-Free Ratiometric Fluorescent Sensor Programmed by Cascade Logic Circuit for Ultrasensitive GSH Detection. ACS APPLIED MATERIALS & INTERFACES 2017; 9:25870-25877. [PMID: 28696093 DOI: 10.1021/acsami.7b07369] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Glutathione (GSH) plays crucial roles in various biological functions, the level alterations of which have been linked to varieties of diseases. Herein, we for the first time expanded the application of oxidase-like property of MnO2 nanosheet (MnO2 NS) to fluorescent substrates of peroxidase. Different from previously reported fluorescent quenching phenomena, we found that MnO2 NS could not only largely quench the fluorescence of highly fluorescent Scopoletin (SC) but also surprisingly enhance that of nonfluorescent Amplex Red (AR) via oxidation reaction. If MnO2 NS is premixed with GSH, it will be reduced to Mn2+ and lose the oxidase-like property, accompanied by subsequent increase in SC's fluorescence and decrease in AR's. On the basis of the above mechanism, we construct the first MnO2 NS-based ratiometric fluorescent sensor for ultrasensitive and selective detection of GSH. Notably, this ratiometric sensor is programmed by the cascade logic circuit (an INHIBIT gate cascade with a 1 to 2 decoder). And a linear relationship between ratiometric fluorescent intensities of the two substrates and logarithmic values of GSH's concentrations is obtained. The detection limit of GSH is as low as 6.7 nM, which is much lower than previous ratiometric fluorescent sensors, and the lowest MnO2 NS-based fluorescent GSH sensor reported so far. Furthermore, this sensor is simple, label-free, and low-cost; it also presents excellent applicability in human serum samples.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100039, China
| | - Changshuai Shang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100039, China
| | - Wenling Gu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100039, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100039, China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100039, China
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Koklioti MA, Skaltsas T, Sato Y, Suenaga K, Stergiou A, Tagmatarchis N. Mechanistic insights into the photocatalytic properties of metal nanocluster/graphene ensembles. Examining the role of visible light in the reduction of 4-nitrophenol. NANOSCALE 2017; 9:9685-9692. [PMID: 28675211 DOI: 10.1039/c7nr02944f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Metal nanoclusters (MNCs) based on silver and gold, abbreviated as AgNCs and AuNCs, respectively, were synthesized and combined with functionalized graphene, abbreviated as f-G, forming novel MNC/f-G ensembles. The preparation of MNCs/f-G was achieved by employing attractive electrostatic interactions developed between negatively charged MNCs, attributed to the presence of carboxylates due to α-lipoic acid employed as a stabilizer, and positively charged f-G, attributed to the presence of ammonium units as addends. The realization of MNC/f-G ensembles was established via titration assays as evidenced by electronic absorption and photoluminescence spectroscopy as well as scanning transmission electron microscopy (STEM) and energy-dispersive X-ray (EDX) spectroscopy analyses. Photoinduced charge-transfer phenomena were inferred within MNCs/f-G, attributed to the suppression of MNC photoluminescence by the presence of f-G. Next, the MNC/f-G ensembles were successfully employed as proficient catalysts for the model reduction of 4-nitrophenol to the corresponding 4-aminophenol as proof for the photoinduced hydrogen production. Particularly, the reduction kinetics decelerated by half when bare MNCs were employed vs. the MNC/f-G ensembles, highlighting the beneficial role of MNCs/f-G in catalysing the process. Furthermore, AuNCs/f-G displayed exceptionally higher catalytic activity both in the dark and under visible light illumination conditions, which is ascribed to three synergistic mechanisms, namely, (a) hydride transfer from Au-H, (b) hydride transfer from photogenerated Au-H species, and (c) hydrogen produced by the photoreduction of water. Finally, recycling and re-employing MNCs/f-G in successive catalytic cycles without loss of activity toward the reduction of 4-nitrophenol was achieved, thereby highlighting their wider applicability.
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Affiliation(s)
- Malamatenia A Koklioti
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece.
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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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Hou T, Zhao T, Li W, Li F, Gai P. A label-free visual platform for self-correcting logic gate construction and sensitive biosensing based on enzyme-mimetic coordination polymer nanoparticles. J Mater Chem B 2017; 5:4607-4613. [PMID: 32264303 DOI: 10.1039/c7tb00791d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In molecular logic gates, the occurrence of erroneous procedures is a frequently encountered and critical problem in data transmission, and thus it is highly desirable to develop novel logic systems with self-correction abilities. Herein, based on the horseradish peroxidase (HRP)-like activity of the novel metal coordination polymer nanoparticles formed between Cu2+ and guanosine monophosphate (GMP), denoted as Cu-GMP CPNs, a label-free visual platform was constructed and successfully utilized for both self-correcting logic gate construction and sensitive biosensing. The HRP-mimicking ability of Cu-GMP CPNs was verified and utilized for the sensitive detection of both H2O2 and glucose. More importantly, a set of logic gates (AND, OR, NOR, INHIBIT, and XNOR) were fabricated, in which two intermediate outputs, i.e., color change and precipitate formation, were combined in an "AND" mode to produce the final output, and thus the as-proposed logic system exhibited the self-correction ability to automatically correct the erroneous intermediate outputs induced by interfering substances such as HRP. Moreover, in addition to the unique feature of self-correction, the as-proposed logic system also exhibited the advantages of simple operation, rapid response and easy detection of the visual outputs by the naked eye, thus expanding its practical applications to a variety of fields. Therefore, the label-free visual platform we have proposed here offers a promising strategy for logic gate fabrication and may pave the way for the development of novel molecular computing with self-correction abilities.
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Affiliation(s)
- Ting Hou
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China.
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Ravan H, Amandadi M, Esmaeili-Mahani S. DNA Domino-Based Nanoscale Logic Circuit: A Versatile Strategy for Ultrasensitive Multiplexed Analysis of Nucleic Acids. Anal Chem 2017; 89:6021-6028. [PMID: 28459545 DOI: 10.1021/acs.analchem.7b00607] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In recent years, the analytical application of logical nanodevices has attracted much attention for making accurate decisions on molecular diagnosis. Herein, a DNA domino-based nanoscale logic circuit has been constructed by integrating three logic gates (AND-AND-YES) for simultaneous analysis of multiple nucleic acid biomarkers. In the first AND gate, a chimeric target DNA comprising of four biomarkers was hybridized to three biomarker-specific oligonucleotides (TRs) via their 5'-end regions and to a capture probe-magnetic microparticle. After harvesting the complex, 3' overhang regions of the TRs were labeled with three distinct monolayer double-stranded (ds) DNA-gold nanoparticles (DNA-AuNPs). Upon gleaning the complex and addition of initiator oligonucleotide, a series of toehold-mediated strand displacement reactions, which are reminiscent of a domino chain, spontaneously occurred between the confined dsDNAs on the nanoparticles' surface in the second AND gate. The output of the second gate entered into the last gate and triggered an exponential hairpin assembly to form four-way junction nanostructures. The resulting nanostructures bear split parts of DNAzyme at each end of the four arms which, in the presence of hemin, form catalytic hemin/G-quadruplex DNAzymes with peroxidase activity. The smart biosensor has exhibited a turn-on signal when all biomarkers are present in the sample. In fact, should any of the biomarkers be nonexistent, the signal remains turned-off. The biosensor can detect the biomarkers with a LOD value of 100 aM and a noticeable capability to discriminate single-nucleotide substitutions.
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Affiliation(s)
- Hadi Ravan
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman , Kerman, Iran 7616914111
| | - Mojdeh Amandadi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman , Kerman, Iran 7616914111
| | - Saeed Esmaeili-Mahani
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman , Kerman, Iran 7616914111
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48
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Enzyme‐Based Logic Gates and Networks with Output Signals Analyzed by Various Methods. Chemphyschem 2017; 18:1688-1713. [DOI: 10.1002/cphc.201601402] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Indexed: 01/16/2023]
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49
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Campbell EA, Peterson E, Kolpashchikov DM. Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles. Chemphyschem 2017; 18:1730-1734. [PMID: 28234410 DOI: 10.1002/cphc.201700109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Indexed: 02/02/2023]
Abstract
DNA-based computational hardware has attracted ever-growing attention due to its potential to be useful in the analysis of complex mixtures of biological markers. Here we report the design of self-assembling logic gates that recognize DNA inputs and assemble into crossover tiles when the output signal is high; the crossover structures disassemble to form separate DNA stands when the output is low. The output signal can be conveniently detected by fluorescence using a molecular beacon probe as a reporter. AND, NOT, and OR logic gates were designed. We demonstrate that the gates can connect to each other to produce other logic functions.
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Affiliation(s)
- Eleanor A Campbell
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Evan Peterson
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, College of Medicine and National Center for Forensic Science, University of Central Florida, Orlando, FL, 32816, USA)An invited contribution to a Special Issue on Molecular Logic
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50
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Fan D, Wang E, Dong S. A DNA-based parity generator/checker for error detection through data transmission with visual readout and an output-correction function. Chem Sci 2017; 8:1888-1895. [PMID: 28553479 PMCID: PMC5424811 DOI: 10.1039/c6sc04056j] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 10/26/2016] [Indexed: 12/19/2022] Open
Abstract
During any type of binary data transmission, the occurrence of bit errors is an inevitable and frequent problem suffered. These errors, which have fatal effects on the correct logic computation, especially in sophisticated logic circuits, can be checked through insertion of a parity generator (pG) at the transmitting end and a parity checker (pC) at the receiving end. Herein, taking even pG/pC as a model device, we constructed the first DNA-based molecular parity generator/checker (pG/pC) for error detection through data transmission, on a universal single-strand platform according to solely DNA hybridization. Compared with previous pG/pC systems, the distinct advantage of this one is that it can present not only fluorescence signals but also visual outputs, which can be directly recognized by the naked eye, using DNA inputs modulated split-G-quadruplex and its DNAzyme as signal reporters, thus greatly extending its potential practical applications. More importantly, an "Output-Correction" function was introduced into the pC for the first time, in which all of the erroneous outputs can be adequately corrected to their normal states, guaranteeing the regular operation of subsequent logic devices. Furthermore, through negative logic conversion towards the constructed even pG/pC, the odd pG/pC with equal functions was obtained. Furthermore, this system can also execute multi-input triggered concatenated logic computations with dual output-modes, which largely fulfilled the requirements of complicated computing.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin , 130022 China .
- University of Chinese Academy of Sciences , Beijing , 100039 China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin , 130022 China .
- University of Chinese Academy of Sciences , Beijing , 100039 China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin , 130022 China .
- University of Chinese Academy of Sciences , Beijing , 100039 China
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