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Hou X, Ga L, Zhang X, Ai J. Advances in the application of logic gates in nanozymes. Anal Bioanal Chem 2024:10.1007/s00216-024-05240-w. [PMID: 38488951 DOI: 10.1007/s00216-024-05240-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/17/2024]
Abstract
Nanozymes are a class of nanomaterials with biocatalytic function and enzyme-like activity, whose advantages include high stability, low cost, and mass production. They can catalyze the substrates of natural enzymes based on specific nanostructures and serve as substitutes for natural enzymes. Their applied research involves a wide range of fields such as biomedicine, environmental governance, agriculture, and food. Molecular logic gates are a new cross-disciplinary discipline, which can simulate the function of silicon circuits on a molecular scale, perform single or multiple input logic operations, and generate logic outputs. A molecular logic gate is a binary operation that converts an input signal into an output signal according to the rules of Boolean logic, generating two signals, a high level, and a low level. The high and low levels represent the "true" and "false" values of the logic gates, and their outputs correspond to "l" and "0" of the molecular logic gates, respectively. The combination of nanozymes and logic gates is a novel and attractive research direction, and the cross-application of the two brings new opportunities and ideas for various fields, such as the construction of efficient biocomputers, intelligent drug delivery systems, and the precise diagnosis of diseases. This review describes the application of logic gates based on nanozymes, which is expected to provide a certain theoretical foundation for researchers' subsequent studies.
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Affiliation(s)
- Xiangru Hou
- College of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 zhaowudalu, Hohhot, 010022, China
| | - Lu Ga
- College of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot, 010110, China
| | - Xin Zhang
- College of Chemical Engineering, Inner Mongolia University of Technology, 49 Aimin Road, Hohhot, 010051, China.
| | - Jun Ai
- College of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 zhaowudalu, Hohhot, 010022, China.
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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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Liu QY, Wu Y, Bu ZQ, Quan MX, Lu JY, Huang WT. Sequential-Dependent Synthesis of Bimetallic Silver-Chromium Nanoparticles for Multichannel Sensing, Logic Computing, and 3 in 1 Information Protection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2207436. [PMID: 37026417 DOI: 10.1002/smll.202207436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/12/2023] [Indexed: 06/19/2023]
Abstract
Bimetallic nanomaterials (BNMs) have been used in sensing, biomedicine, and environmental remediation, but their multipurpose and comprehensive applications in molecular logic computing and information security protection have received little attention. Herein, This synthesis method is achieved by sequentially adding reactants under ice bath conditions. Interestingly, Ag-Cr NPs can dynamically selectively sense anions and reductants in multiple channels. Especially, ClO- can be quantitatively detected by oxidizing Ag-Cr NPs with detection limits of 98.37 nM (at 270 nm) and 31.83 nM (at 394 nm). Based on sequential-dependent synthesis process of Ag-Cr NPs, Boolean logic gates and customizable molecular keypad locks are constructed by setting the reactants as the inputs, the states of the resulting solutions as the outputs. Furthermore, dynamically selective response patterns of the Ag-Cr NPs can be converted into binary strings to exploit molecular crypto-steganography to encode, store, and hide information. By integrating the three dimensions of authorization, encryption, and steganography, 3 in 1 advanced information protection based on Ag-Cr nanosensing system can be achieved, which can enhance the anti-cracking ability of information. This research will promote the development and application of nanocomposites in the field of information security and deepen the connection between molecular sensing and the information world.
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Affiliation(s)
- Qing Yu Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, P. R. China
| | - Ying Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, P. R. China
| | - Zhen Qi Bu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, P. R. China
| | - Min Xia Quan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, P. R. China
| | - Jiao Yang Lu
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Academician Workstation, Changsha Medical University, Changsha, 410219, P. R. China
| | - Wei Tao Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, P. R. China
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Zhu L, Yu L, Meng T, Peng Y, Yang X. Contrary Logic Pair Library, Parity Generator/Checker and Various Concatenated Logic Circuits Engineered by a Label-Free and Immobilization-Free Electrochemiluminescence Resonance Energy Transfer System. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102881. [PMID: 34792279 DOI: 10.1002/smll.202102881] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/24/2021] [Indexed: 06/13/2023]
Abstract
Herein, a label-free and immobilization-free electrochemiluminescence resonance energy transfer (ECL-RET) system based on graphitic carbon nitride nanosheets (GCNNs)/Ru(phen)32+ donor/acceptor pair is developed, in which the ECL-RET is regulated by regulating the diffusivity of Ru(phen)32+ molecules toward the negatively charged GCNNs through logically programmed DNA hybridization reactions. The two optical signals of GCNNs (445 nm) and Ru(phen)32+ (593 nm) show completely opposite changes through the same one-time DNA hybridization reaction. Based on this ECL-RET system, a contrary logic pair (CLP) library, a parity generator/checker system for differentiating the erroneous bits during data transmission, the parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits including a six-input logic gate capable of implementing of 64 input combinations for meeting the needs of computational complexity are developed. The ECL-RET-based molecular logic system avoids the time-consuming, costly and inefficient labeling procedures and the laborious processes of immobilization, presenting great potential for building more complicated and advanced logic gates, and providing a refreshing inspiration for the construction of combinatorial logic circuits based on ECL method.
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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
| | - Tian Meng
- 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
| | - Yao Peng
- University of Science and Technology of China, Hefei, Anhui, 230026, 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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5
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Abstract
DNA-based Boolean logic gates (for example, AND, OR, and NOT) can be assembled into complex computational circuits that generate an output signal in response to specific patterns of oligonucleotide inputs. However, the fundamental nature of NOT gates, which convert the absence of an input into an output, makes their implementation within DNA-based circuits difficult. Premature execution of a NOT gate before completion of its upstream computation introduces an irreversible error into the circuit. By utilizing photocaging groups, we developed a novel DNA gate design that prevents gate function until irradiation at a certain time point. Optical activation provides temporal control over circuit performance by preventing premature computation and is orthogonal to all other components of DNA computation devices. Using this approach, we designed NAND and NOR logic gates that respond to synthetic microRNA sequences. We further demonstrate the utility of the NOT gate within multilayer circuits in response to a specific pattern of four microRNAs.
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Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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6
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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: 58] [Impact Index Per Article: 14.5] [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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7
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Feng C, Chen T, Mao D, Zhang F, Tian B, Zhu X. Construction of a Ternary Complex Based DNA Logic Nanomachine for a Highly Accurate Imaging Analysis of Cancer Cells. ACS Sens 2020; 5:3116-3123. [PMID: 32799436 DOI: 10.1021/acssensors.0c01166] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Due to the complexity and variability of the cellular metabolic process and the physiological environment inside and outside the cell, higher requirements are needed on the application of DNA molecular logic gate in cell analysis. In addition, heterogeneity of tumor cells tends to lead to false positives in the clinical diagnosis of a single target, even those with the same cancer type. To address these issues above, we have developed a novel DNA molecular logic gate responsive nanomachine for bispecific recognition and computation of cell membranes. Only when two membrane proteins, MUC1 and EpCAM as model proteins, exist simultaneously, the DNA molecular logic gate can be activated to perform "AND" logic operation and generate amplified "ON" fluorescence signal from the cell membrane. Therefore, our proposed dual-specific "recognition-biocomputing" DNA molecular logic gate has achieved highly accurate imaging analysis of dual-target membrane proteins in situ. Furthermore, the logic gate responsive DNA nanomachine can also be used to analyze target cells in complex cell samples with excellent specificity, which will meet the needs of biomedicine and their application in clinical diagnosis and provide new tools for the biomedical application of DNA molecular logic gates in complex cell systems.
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Affiliation(s)
- Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- School of Medicine, Shanghai University, Shanghai 200444, P. R. China
| | - Tianshu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Dongsheng Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Fan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Bo Tian
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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8
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Integration of logic gates to CRISPR/Cas12a system for rapid and sensitive detection of pathogenic bacterial genes. Anal Chim Acta 2020; 1125:162-168. [DOI: 10.1016/j.aca.2020.05.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 12/26/2022]
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9
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Zhou C, Geng H, Wang P, Guo C. Ten-Input Cube Root Logic Computation with Rational Designed DNA Nanoswitches Coupled with DNA Strand Displacement Process. ACS APPLIED MATERIALS & INTERFACES 2020; 12:2601-2606. [PMID: 31867943 DOI: 10.1021/acsami.9b15180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The predictability of Watson-Crick base-pairing provides a unique structural programmability to DNAs, promoting a facile design of bimolecular reactions that perform computation. However, most of the current architectures could only implement limited logical circuits and are incapable of handling more complex mathematical operations, thus limiting computing devices from advancing to the next-stage functional complexity. Here, by designing a multifunctional DNA-based reaction platform coupled with multiple fluorescent substrates as output reporters, we construct, for the first time, a logic circuit that can compute the cube root of a 10-bit binary number (within the decimal number 1000). This relatively large-scale logic system with 10 inputs and four outputs showcases the power of DNAs in the field of biological computing and will potentially open up a new horizon for designing novel functional devices and complex computing circuits and bringing breakthroughs in biocomputing.
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Affiliation(s)
- Chunyang Zhou
- The Photonics Laboratory, Changchun Institute of Optics, Fine Mechanics and Physics , Chinese Academy of Sciences , Changchun , Jilin 130033 , China
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Hongmei Geng
- The Photonics Laboratory, Changchun Institute of Optics, Fine Mechanics and Physics , Chinese Academy of Sciences , Changchun , Jilin 130033 , China
| | - Pengfei Wang
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Chunlei Guo
- The Photonics Laboratory, Changchun Institute of Optics, Fine Mechanics and Physics , Chinese Academy of Sciences , Changchun , Jilin 130033 , China
- The Institute of Optics , University of Rochester , Rochester , New York 14627 , United States
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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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11
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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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12
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Chen RP, Blackstock D, Sun Q, Chen W. Dynamic protein assembly by programmable DNA strand displacement. Nat Chem 2018. [DOI: 10.1038/s41557-018-0016-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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13
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Bernardinelli G, Högberg B. Entirely enzymatic nanofabrication of DNA-protein conjugates. Nucleic Acids Res 2017; 45:e160. [PMID: 28977490 PMCID: PMC5737863 DOI: 10.1093/nar/gkx707] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/14/2017] [Indexed: 12/22/2022] Open
Abstract
While proteins are highly biochemically competent, DNA offers the ability to program, both reactions and the assembly of nanostructures, with a control that is unprecedented by any other molecule. Their joining: DNA–protein conjugates - offer the ability to combine the programmability of DNA with the competence of proteins to form novel tools enabling exquisite molecular control and the highest biological activity in one structure. However, in order for tools like these to become viable for biological applications, their production must be scalable, and an entirely enzymatic process is one way to achieve this. Here, we present a step in this direction: enzymatic production of DNA–protein conjugates using a new self-labeling tag derived from a truncated VirD2 protein of Agrobacterium tumefaciens. Using our previously reported MOSIC method for enzymatic ssDNA oligo production, we outline a pipeline for protein–DNA conjugates without the need for any synthetic chemistry in a one-pot reaction. Further, we validate HER2 staining using a completely enzymatically produced probe, enable the decoration of cell membranes and control of genetic expression. Establishing a method where protein–DNA conjugates can be made entirely using biological or enzymatic processing, opens a path to harvest these structures directly from bacteria and ultimately in-vivo assembly.
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Affiliation(s)
- Giulio Bernardinelli
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 177 Stockholm, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 177 Stockholm, Sweden
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14
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Hierarchical control of enzymatic actuators using DNA-based switchable memories. Nat Commun 2017; 8:1117. [PMID: 29061965 PMCID: PMC5714950 DOI: 10.1038/s41467-017-01127-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/18/2017] [Indexed: 12/30/2022] Open
Abstract
Inspired by signaling networks in living cells, DNA-based programming aims for the engineering of biochemical networks capable of advanced regulatory and computational functions under controlled cell-free conditions. While regulatory circuits in cells control downstream processes through hierarchical layers of signal processing, coupling of enzymatically driven DNA-based networks to downstream processes has rarely been reported. Here, we expand the scope of molecular programming by engineering hierarchical control of enzymatic actuators using feedback-controlled DNA-circuits capable of advanced regulatory dynamics. We developed a translator module that converts signaling molecules from the upstream network to unique DNA strands driving downstream actuators with minimal retroactivity and support these findings with a detailed computational analysis. We show our modular approach by coupling of a previously engineered switchable memories circuit to downstream actuators based on β-lactamase and luciferase. To the best of our knowledge, our work demonstrates one of the most advanced DNA-based circuits regarding complexity and versatility. Naturally evolved regulatory circuits have hierarchical layers of signal generation and processing. Here, the authors emulate these networks using feedback-controlled DNA circuits that convert upstream signaling to downstream enzyme activity in a switchable memories circuit.
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15
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Morihiro K, Ankenbruck N, Lukasak B, Deiters A. Small Molecule Release and Activation through DNA Computing. J Am Chem Soc 2017; 139:13909-13915. [DOI: 10.1021/jacs.7b07831] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kunihiko Morihiro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Bradley Lukasak
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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16
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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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17
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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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18
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Song T, Wang X, Liang H. Engineering chemical reaction modules via programming the assembly of DNA hairpins. J Mater Chem B 2017; 5:2297-2301. [PMID: 32263620 DOI: 10.1039/c6tb03098j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The architect of enzyme-free chemical reaction modules, working as building blocks in implementing complex computing tasks, was achieved by modulating the assembly of DNA hairpins, including non-catalytic and catalytic systems. The performance of heterogeneous outputted sequences, which were programmed on different hairpins for triggering the downstream reaction, was asymmetric in the non-catalytic system, whereas symmetric in the catalytic system. Furthermore, complicated DNA-only chemical modules possessing controllable species of inputs or outputs were constructed based on our strategy. The kinetic studies revealed that the performance of the chemical modules was toehold length correlated; on the basis of which, a DNA concentration monitor was constructed.
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Affiliation(s)
- Tingjie Song
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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19
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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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20
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Fan D, Zhu X, Dong S, Wang E. Tyramine Hydrochloride Based Label-Free System for Operating Various DNA Logic Gates and a DNA Caliper for Base Number Measurements. Chemphyschem 2017; 18:1767-1772. [DOI: 10.1002/cphc.201601291] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P.R. China
- University of Chinese Academy of Sciences; Beijing 100039 P.R. China
| | - Xiaoqing Zhu
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P.R. China
- University of Chinese Academy of Sciences; Beijing 100039 P.R. China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P.R. China
- University of Chinese Academy of Sciences; Beijing 100039 P.R. China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P.R. China
- University of Chinese Academy of Sciences; Beijing 100039 P.R. China
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21
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Fan D, Wang E, Dong S. Exploiting Polydopamine Nanospheres to DNA Computing: A Simple, Enzyme-Free and G-Quadruplex-Free DNA Parity Generator/Checker for Error Detection during Data Transmission. ACS APPLIED MATERIALS & INTERFACES 2017; 9:1322-1330. [PMID: 27990820 DOI: 10.1021/acsami.6b14317] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Molecular logic devices with various functions play an indispensable role in molecular data transmission/processing. However, during any kinds of data transmission, a constant and unavoidable circumstance is the appearance of bit errors, which have serious effects on the regular logic computation. Fortunately, these errors can be detected via plugging a parity generator (pG) at the transmitting terminal and a parity checker (pC) at the receiving terminal. Herein, taking advantage of the efficient adsorption/quenching ability of polydopamine nanospheres toward fluorophore-labeled single-stranded DNA, we explored this biocompatible nanomaterial to DNA logic computation and constructed the first simple, enzyme-free, and G-quadruplex-free DNA pG/pC for error detection through data transmission. Besides, graphene oxide (GO) was innovatively introduced as the "corrective element" to perform the output-correction function of pC. All the erroneous outputs were corrected to normal conditions completely, ensuring the regular operation of later logic computing. The total operation of this non-G4 pG/pC system (error checking/output-correction) could be completed within 1 h (about 1/3 of previous G4 platform) in a simpler and more efficient way. Notably, the odd pG/pC with analogous functions was also achieved through negative logic conversion to the fabricated even one. Furthermore, the same system could also perform three-input concatenated logic computation (XOR-INHIBIT), enriching the complexity of PDs-based logic computation.
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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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22
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Zhou C, Liu D, Wu C, Liu Y, Wang E. Integration of DNA and graphene oxide for the construction of various advanced logic circuits. NANOSCALE 2016; 8:17524-17531. [PMID: 27714033 DOI: 10.1039/c6nr01213b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Multiple advanced logic circuits including the full-adder, full-subtract and majority logic gate have been successfully realized on a DNA/GO platform for the first time. All the logic gates were implemented in an enzyme-free condition. The investigation provides a wider field of vision towards prototypical DNA-based algebra logical operations and promotes the development of advanced logic circuits.
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Affiliation(s)
- Chunyang Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. and Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, Tianjin, 300457, P. R. China. and State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Dali Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. and Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, Tianjin, 300457, P. R. China. and State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Changtong Wu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. and Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, Tianjin, 300457, P. R. China. and State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Yaqing Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. and Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, Tianjin, 300457, P. R. China. and State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. and Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, Tianjin, 300457, P. R. China. and State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
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23
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Xiao Z, Zhu H, Xin A, Li Y, Ling L. Triplex DNA logic gate based upon switching on/off their structure by Ag(+)/cysteine. Analyst 2016; 140:7322-6. [PMID: 26359516 DOI: 10.1039/c5an01371b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The formation of intramolecular triplex DNA can be regulated by Ag(+) and Cys (cysteine), which switch off/on the fluorescence of the oligonucleotides, 5'-TAMRA-TTC TCT TCC TCT TCC TTC TGA CGA CAG TTG ACT CTT CCT TCT CCT TCT CTT-BHQ-2-3' (Oligo 1) and 3'-GAA GGA AGA GGA AGA GAA-5' (Oligo 2). Based on this principle, sensors for Ag(+) and Cys are developed. The sensor for Ag(+) has a linear range of 2.5 nM-40 nM and a detection limit of 1.8 nM, whereas the sensor for Cys has a linear range of 10.0 nM-120.0 nM and a detection limit of 8.2 nM. Furthermore, the fluorescence is reversible with the alternate addition of Ag(+) and Cys. We constructed a DNA logic gate using Ag(+) and Cys as the input, and the fluorescence intensity as the output. The DNA logic gate is simple; moreover, it has a fast response and good reversibility.
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Affiliation(s)
- Zhiyou Xiao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
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24
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Engelen W, Janssen BMG, Merkx M. DNA-based control of protein activity. Chem Commun (Camb) 2016; 52:3598-610. [PMID: 26812623 PMCID: PMC4767025 DOI: 10.1039/c5cc09853j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA has emerged as a highly versatile construction material for nanometer-sized structures and sophisticated molecular machines and circuits. The successful application of nucleic acid based systems greatly relies on their ability to autonomously sense and act on their environment. In this feature article, the development of DNA-based strategies to dynamically control protein activity via oligonucleotide triggers is discussed. Depending on the desired application, protein activity can be controlled by directly conjugating them to an oligonucleotide handle, or expressing them as a fusion protein with DNA binding motifs. To control proteins without modifying them chemically or genetically, multivalent ligands and aptamers that reversibly inhibit their function provide valuable tools to regulate proteins in a noncovalent manner. The goal of this feature article is to give an overview of strategies developed to control protein activity via oligonucleotide-based triggers, as well as hurdles yet to be taken to obtain fully autonomous systems that interrogate, process and act on their environments by means of DNA-based protein control.
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Affiliation(s)
- W Engelen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
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25
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Zhou C, Wu C, Liu Y, Wang E. Effective construction of a AuNPs–DNA system for the implementation of various advanced logic gates. RSC Adv 2016. [DOI: 10.1039/c6ra21585h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Four advanced logic gates were successfully realized under enzyme-free conditions by integration of DNA and AuNPs.
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Affiliation(s)
- Chunyang Zhou
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Changtong Wu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Yaqing Liu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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26
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Janssen BMG, van Ommeren SPFI, Merkx M. Efficient Synthesis of Peptide and Protein Functionalized Pyrrole-Imidazole Polyamides Using Native Chemical Ligation. Int J Mol Sci 2015; 16:12631-47. [PMID: 26053396 PMCID: PMC4490465 DOI: 10.3390/ijms160612631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/25/2015] [Accepted: 05/28/2015] [Indexed: 01/02/2023] Open
Abstract
The advancement of DNA-based bionanotechnology requires efficient strategies to functionalize DNA nanostructures in a specific manner with other biomolecules, most importantly peptides and proteins. Common DNA-functionalization methods rely on laborious and covalent conjugation between DNA and proteins or peptides. Pyrrole-imidazole (Py-Im) polyamides, based on natural minor groove DNA-binding small molecules, can bind to DNA in a sequence specific fashion. In this study, we explore the use of Py-Im polyamides for addressing proteins and peptides to DNA in a sequence specific and non-covalent manner. A generic synthetic approach based on native chemical ligation was established that allows efficient conjugation of both peptides and recombinant proteins to Py-Im polyamides. The effect of Py-Im polyamide conjugation on DNA binding was investigated by Surface Plasmon Resonance (SPR). Although the synthesis of different protein-Py-Im-polyamide conjugates was successful, attenuation of DNA affinity was observed, in particular for the protein-Py-Im-polyamide conjugates. The practical use of protein-Py-Im-polyamide conjugates for addressing DNA structures in an orthogonal but non-covalent manner, therefore, remains to be established.
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Affiliation(s)
- Brian M G Janssen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
| | - Sven P F I van Ommeren
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
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27
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Leone L, Pezzella A, Crescenzi O, Napolitano A, Barone V, d’Ischia M. Trichocyanines: a Red-Hair-Inspired Modular Platform for Dye-Based One-Time-Pad Molecular Cryptography. ChemistryOpen 2015; 4:370-7. [PMID: 26246999 PMCID: PMC4522187 DOI: 10.1002/open.201402164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 12/24/2022] Open
Abstract
Current molecular cryptography (MoCryp) systems are almost exclusively based on DNA chemistry and reports of cryptography technologies based on other less complex chemical systems are lacking. We describe herein, as proof of concept, the prototype of the first asymmetric MoCryp system, based on an 8-compound set of a novel bioinspired class of cyanine-type dyes called trichocyanines. These novel acidichromic cyanine-type dyes inspired by red hair pigments were synthesized and characterized with the aid of density functional theory (DFT) calculations. Trichocyanines consist of a modular scaffold easily accessible via an expedient condensation of 3-phenyl- or 3-methyl-2H-1,4-benzothiazines with N-dimethyl- or o-methoxyhydroxy-substituted benzaldehyde or cinnamaldehyde derivatives. The eight representative members synthesized herein can be classified as belonging to two three-state systems tunable through four different control points. This versatile dye platform can generate an expandable palette of colors and appears to be specifically suited to implement an unprecedented single-use asymmetric molecular cryptography system. With this system, we intend to pioneer the translation of digital public-key cryptography into a chemical-coding one-time-pad-like system.
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Affiliation(s)
- Loredana Leone
- Department of Chemical Sciences, University of Naples Federico IIVia Cintia 4, 80126, Naples, Italy
| | - Alessandro Pezzella
- Department of Chemical Sciences, University of Naples Federico IIVia Cintia 4, 80126, Naples, Italy
| | - Orlando Crescenzi
- Department of Chemical Sciences, University of Naples Federico IIVia Cintia 4, 80126, Naples, Italy
| | - Alessandra Napolitano
- Department of Chemical Sciences, University of Naples Federico IIVia Cintia 4, 80126, Naples, Italy
| | - Vincenzo Barone
- Scuola Normale SuperiorePiazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Marco d’Ischia
- Department of Chemical Sciences, University of Naples Federico IIVia Cintia 4, 80126, Naples, Italy
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28
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Wu C, Wan S, Hou W, Zhang L, Xu J, Cui C, Wang Y, Hu J, Tan W. A survey of advancements in nucleic acid-based logic gates and computing for applications in biotechnology and biomedicine. Chem Commun (Camb) 2015; 51:3723-34. [PMID: 25597946 PMCID: PMC4442017 DOI: 10.1039/c4cc10047f] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nucleic acid-based logic devices were first introduced in 1994. Since then, science has seen the emergence of new logic systems for mimicking mathematical functions, diagnosing disease and even imitating biological systems. The unique features of nucleic acids, such as facile and high-throughput synthesis, Watson-Crick complementary base pairing, and predictable structures, together with the aid of programming design, have led to the widespread applications of nucleic acids (NA) for logic gate and computing in biotechnology and biomedicine. In this feature article, the development of in vitro NA logic systems will be discussed, as well as the expansion of such systems using various input molecules for potential cellular, or even in vivo, applications.
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Affiliation(s)
- Cuichen Wu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States, , Fax: +1-352-392-4651, Tel: +1-352-846-2410
| | - Shuo Wan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States, , Fax: +1-352-392-4651, Tel: +1-352-846-2410
| | - Weijia Hou
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States, , Fax: +1-352-392-4651, Tel: +1-352-846-2410
| | - Liqin Zhang
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States, , Fax: +1-352-392-4651, Tel: +1-352-846-2410
| | - Jiehua Xu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States, , Fax: +1-352-392-4651, Tel: +1-352-846-2410
- Department of Nuclear Medicine, the third affiliated hospital, Sun Yat-sen University, Guangzhou 510630, P. R. China
| | - Cheng Cui
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States, , Fax: +1-352-392-4651, Tel: +1-352-846-2410
| | - Yanyue Wang
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States, , Fax: +1-352-392-4651, Tel: +1-352-846-2410
| | - Jun Hu
- Hunan Tumor Hospital, Changsha 410082, P. R. China
| | - Weihong Tan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States, , Fax: +1-352-392-4651, Tel: +1-352-846-2410
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Janssen BMG, van Rosmalen M, van Beek L, Merkx M. Antibody activation using DNA-based logic gates. Angew Chem Int Ed Engl 2015; 54:2530-3. [PMID: 25573528 DOI: 10.1002/anie.201410779] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Indexed: 11/06/2022]
Abstract
Oligonucleotide-based molecular circuits offer the exciting possibility to introduce autonomous signal processing in biomedicine, synthetic biology, and molecular diagnostics. Here we introduce bivalent peptide-DNA conjugates as generic, noncovalent, and easily applicable molecular locks that allow the control of antibody activity using toehold-mediated strand displacement reactions. Employing yeast as a cellular model system, reversible control of antibody targeting is demonstrated with low nM concentrations of peptide-DNA locks and oligonucleotide displacer strands. Introduction of two different toehold strands on the peptide-DNA lock allowed signal integration of two different inputs, yielding logic OR- and AND-gates. The range of molecular inputs could be further extended to protein-based triggers by using protein-binding aptamers.
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Affiliation(s)
- Brian M G Janssen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, De Rondom 70, 5612 AP Eindhoven (The Netherlands)
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30
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Janssen BMG, van Rosmalen M, van Beek L, Merkx M. Antibody Activation using DNA-Based Logic Gates. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410779] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Ma L, Diao A. Design of enzyme-interfaced DNA logic operations (AND, OR and INHIBIT) with an assaying application for single-base mismatch. Chem Commun (Camb) 2015; 51:10233-5. [DOI: 10.1039/c5cc02835c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We devised AND, OR and INHIBIT logic gates.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
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