1
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Tian Z, Shao D, Tang L, Li Z, Chen Q, Song Y, Li T, Simmel FC, Song J. Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems. Nat Commun 2024; 15:4635. [PMID: 38821953 PMCID: PMC11143192 DOI: 10.1038/s41467-024-49021-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
Cell-free protein expression (CFE) systems have emerged as a critical platform for synthetic biology research. The vectors for protein expression in CFE systems mainly rely on double-stranded DNA and single-stranded RNA for transcription and translation processing. Here, we introduce a programmable vector - circular single-stranded DNA (CssDNA), which is shown to be processed by DNA and RNA polymerases for gene expression in a yeast-based CFE system. CssDNA is already widely employed in DNA nanotechnology due to its addressability and programmability. To apply above methods in the context of synthetic biology, CssDNA can not only be engineered for gene regulation via the different pathways of sense CssDNA and antisense CssDNA, but also be constructed into several gene regulatory logic gates in CFE systems. Our findings advance the understanding of how CssDNA can be utilized in gene expression and gene regulation, and thus enrich the synthetic biology toolbox.
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Affiliation(s)
- Zhijin Tian
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Dandan Shao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhen Li
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Chen
- College of Forestry, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Yongxiu Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Ningbo institute of Dalian University of Technology, Ningbo, 315016, China
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
| | - Friedrich C Simmel
- Department of Bioscience, School of Natural Sciences, Technische Universität München, Garching, Germany
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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2
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Sorrentino D, Ranallo S, Nakamura E, Franco E, Ricci F. Synthetic Genes For Dynamic Regulation Of DNA-Based Receptors. Angew Chem Int Ed Engl 2024; 63:e202319382. [PMID: 38457363 DOI: 10.1002/anie.202319382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/10/2024]
Abstract
We present a strategy to control dynamically the loading and release of molecular ligands from synthetic nucleic acid receptors using in vitro transcription. We demonstrate this by engineering three model synthetic DNA-based receptors: a triplex-forming DNA complex, an ATP-binding aptamer, and a hairpin strand, whose ability to bind their specific ligands can be cotranscriptionally regulated (activated or inhibited) through specific RNA molecules produced by rationally designed synthetic genes. The kinetics of our DNA sensors and their genetically generated inputs can be captured using differential equation models, corroborating the predictability of the approach used. This approach shows that highly programmable nucleic acid receptors can be controlled with molecular instructions provided by dynamic transcriptional systems, illustrating their promise in the context of coupling DNA nanotechnology with biological signaling.
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Affiliation(s)
- Daniela Sorrentino
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Simona Ranallo
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Eiji Nakamura
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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3
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Hong F, Zhao Y, Pan S, Ren L, Jiang F, Wu L, Chen Y. Click Reaction-Mediated Fluorescent Immunosensor Based on Cu-MOF Nanoparticles for Ultrasensitive and High-Throughput Detection of Aflatoxin B 1 in Food Samples. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5975-5982. [PMID: 38462975 DOI: 10.1021/acs.jafc.3c09730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Due to the high toxicity of aflatoxin B1 and its risks to human health, we developed a click reaction-mediated automated fluorescent immunosensor (CAFI) for sensitive detection of aflatoxin B1 based on the Cu(I)-catalyzed click reaction. With its large specific surface area, a copper-based metal-organic framework (Cu-MOF) was synthesized to adsorb and enrich the copper ion (Cu(II)) and then load the complete antigen (BSA-AFB1). After the immunoreaction, Cu(II) inside the Cu-MOF-Antigen conjugate would be reduced to Cu(I) in the presence of sodium ascorbate, which triggered the click reaction between the fluorescent donor-modified DNA and the receptor-modified complementary DNA to lead to a fluorescence signal readout. The whole reaction steps were finished by the self-developed automated immunoreaction device. This CAFI method showed a limit of detection (LOD) of 0.48 pg/mL as well as a 670-fold enhancement in sensitivity compared to conventional ELISA, revealing its great potential in practical applications and automated detection.
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Affiliation(s)
- Feng Hong
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongkun Zhao
- College of Engineering, Huazhong Agricultural University, Wuhan 430070, China
| | - Shixing Pan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangqiong Ren
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Jiang
- Key Laboratory of Detection Technology of Focus Chemical Hazards in Animal-derived Food for State Market Regulation, Hubei Provincial Institute for Food Supervision and Test, Wuhan 430075, China
| | - Long Wu
- School of Food Science and Engineering, Key Laboratory of Tropical and Vegetables Quality and Safety for State Market Regulation, Hainan University, Haikou 570228, China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, Liaoning, China
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4
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Yu Y, Li Q, Shi W, Yang Y, He H, Dai J, Mao G, Ma Y. Programmable Aptasensor for Regulating CRISPR/Cas12a Activity. ACS Sens 2024; 9:244-250. [PMID: 38085648 DOI: 10.1021/acssensors.3c01881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
CRISPR-mediated aptasensors have gained prevalence for detecting non-nucleic acid targets. However, there is an urgent need to develop an easily customizable design to improve the signal-to-noise ratio, enhance universality, and expand the detection range. In this article, we report a CRISPR-mediated programmable aptasensor (CPAS) platform. The platform includes single-stranded DNA comprising the aptamer sequence, locker DNA, and a crRNA recognition region, forming a hairpin structure through complementary hybridization. With T4 DNA polymerase, the crRNA recognition region was transformed into a complete double-stranded DNA through stem-loop extension, thereby activating the trans-cleavage activity of Cas 12a and generating fluorescence signals. The specific binding between the target molecule and aptamer disrupted the formation of the hairpin structure, altering the fluorescence signals. Notably, the CPAS platform allows for easy customization by simply changing the aptamer sequence and locker DNA, without entailing adjustments to the crRNA. The optimal number of bases in the locker DNA was determined to be seven nucleotides for the SARS-CoV-2 spike (S) protein and four nucleotides for ATP. The CPAS platform exhibited high sensitivity for S protein and ATP detection. Integration with a lateral flow assay enabled sensitive detection within 1 h, revealing its excellent potential for portable analysis.
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Affiliation(s)
- Yao Yu
- College of Chemistry & Pharmacy, Northwest A&F University Yangling, Shaanxi 712100, China
| | - Qiaoyu Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wen Shi
- College of Chemistry & Pharmacy, Northwest A&F University Yangling, Shaanxi 712100, China
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuxin Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hongpeng He
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Junbiao Dai
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Guobin Mao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingxin Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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5
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Díaz-Fernández A, Ranallo S, Ricci F. Enzyme-Linked DNA Displacement (ELIDIS) Assay for Ultrasensitive Electrochemical Detection of Antibodies. Angew Chem Int Ed Engl 2024; 63:e202314818. [PMID: 37994381 DOI: 10.1002/anie.202314818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023]
Abstract
Here we report the development of a method for the electrochemical ultrasensitive detection of antibodies that couples the programmability and versatility of DNA-based systems with the sensitivity provided by enzymatic amplification. The platform, termed Enzyme-Linked DNA Displacement (ELIDIS), is based on the use of antigen-DNA conjugates that, upon the bivalent binding of a specific target antibody, induce the release of an enzyme-DNA hybrid strand from a preformed duplex. Such enzyme-DNA hybrid strand can then be electrochemically detected with a disposable electrode with high sensitivity. We applied ELIDIS to demonstrate the sensitive (limit of detection in the picomolar range), specific and multiplexed detection of five different antibodies including three clinically relevant ones. ELIDIS is also rapid (it only requires two reaction steps), works well in complex media (serum) and is cost-effective. A direct comparison with a commercial ELISA kit for the detection of Cetuximab demonstrates the promising features of ELIDIS as a point-of-care platform for antibodies detection.
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Affiliation(s)
- Ana Díaz-Fernández
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | - Simona Ranallo
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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6
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Li HD, Fang GH, Ye BC, Yin BC. RNase H-Driven crRNA Switch Circuits for Rapid and Sensitive Detection of Various Analytical Targets. Anal Chem 2023; 95:18549-18556. [PMID: 38073045 DOI: 10.1021/acs.analchem.3c04267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR/Cas12a) system has exhibited great promise in the rapid and sensitive molecular diagnostics for its trans-cleavage property. However, most CRISPR/Cas system-based detection methods are designed for nucleic acids and require target preamplification to improve sensitivity and detection limits. Here, we propose a generic crRNA switch circuit-regulated CRISPR/Cas sensor for the sensitive detection of various targets. The crRNA switch is engineered and designed in a blocked state but can be activated in the presence of triggers, which are target-induced association DNA to initiate the trans-cleavage activity of Cas12a for signal reporting. Additionally, RNase H is introduced to specifically hydrolyze RNA duplexed with the DNA trigger, resulting in the regeneration of the trigger to activate more crRNA switches. Such a combination provides a generic and sensitive strategy for the effective sensing of the p53 sequence, thrombin, and adenosine triphosphate. The design is incorporated with nucleic acid nanotechnology and extensively broadens the application scope of the CRISPR technology in biosensing.
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Affiliation(s)
- Hua-Dong Li
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Guan-Hua Fang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang 832000, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang 832000, China
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7
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Wang H, Zhang X, Liu Y, Zhou S. A nicking enzyme-assisted allosteric strategy for self-resetting DNA switching circuits. Analyst 2023; 149:169-179. [PMID: 37999719 DOI: 10.1039/d3an01677c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
The self-regulation of biochemical reaction networks is crucial for maintaining balance, stability, and adaptability within biological systems. DNA switching circuits, serving as basic units, play essential roles in regulating pathways, facilitating signal transduction, and processing biochemical reaction networks. However, the non-reusability of DNA switching circuits hinders its application in current complex information processing. Herein, we proposed a nicking enzyme-assisted allosteric strategy for constructing self-resetting DNA switching circuits to realize complex information processing. This strategy utilizes the unique cleavage ability of the nicking enzyme to achieve the automatic restoration of states. Based on this strategy, we implemented a self-resetting DNA switch. By leveraging the reusability of the DNA switch, we constructed a DNA switching circuit with selective activation characteristics and further extended its functionality to include fan-out and fan-in processes by expanding the number of functional modules and connection modes. Furthermore, we demonstrated the complex information processing capabilities of these switching circuits by integrating recognition, translation, and decision functional modules, which could analyze and transmit multiple input signals and realize parallel logic operations. This strategy simplifies the design of switching circuits and promotes the future development of biosensing, molecular computing, and nanomachines.
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Affiliation(s)
- Haoliang Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China.
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China.
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8
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Song YL, He XL, Li Y, Wang M, Jiang M, Xu L, Yu X. Homogeneous detection of viral nucleic acid via selective recognition proximity ligation and signal amplification with T7 transcription and CRISPR/Cas12a system. Anal Chim Acta 2023; 1280:341881. [PMID: 37858564 DOI: 10.1016/j.aca.2023.341881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/23/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023]
Abstract
The synthetic biology has employed the synthetic gene networks through engineering to construct various functions in biological systems. However, the use of gene circuits to create sensors for detecting low-abundance targets has been limited due to the lack of signal amplification strategies beyond direct output of detection signals. To address this issue, we introduce a novel method utilizing Selective Recognition Proximity Ligation and signal amplification with T7 Transcription and CRISPR/Cas12a system (SRPL-TraCs), which permits the incorporation of cell-free gene circuits with signal amplification and enables the construction of high-order cascade signal amplification strategy to detect biomarkers in homogeneous systems. Specifically, the SRPL-TraCs utilizes selective recognition proximity ligation with high-fidelity T4 DNA ligase and generates a unique crRNA via T7 transcription, along with target-activated Cas12a/crRNA system to achieve excellent specificity for HIV-1 DNA. With this straightforward synthetic biology-based method, the proposed SRPL-TraCs has the potential to detect numerous other interesting targets beyond the nucleic acids.
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Affiliation(s)
- Yong-Li Song
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiang-Lan He
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yong Li
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ming Jiang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Xu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China.
| | - Xu Yu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China.
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9
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Zhang R, Wang Y, Deng H, Zhou S, Wu Y, Li Y. Fast and bioluminescent detection of antibiotic contaminants by on-demand transcription of RNA scaffold arrays. Anal Chim Acta 2023; 1273:341538. [PMID: 37423654 DOI: 10.1016/j.aca.2023.341538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/11/2023] [Accepted: 06/16/2023] [Indexed: 07/11/2023]
Abstract
Cell-free biosensors have inspired low-cost and field-applicable methods to detect antibiotic contaminants. However, the satisfactory sensitivity of current cell-free biosensors is mostly achieved by sacrificing the rapidity, which prolongs turnaround time by hours. Additionally, the software-based result interpretation provides an obstacle for delivering these biosensors to untrained individuals. Here, we present a bioluminescence-based cell-free biosensor, termed enhanced Bioluminescence sensing of Ligand-Unleashed RNA Expression (eBLUE). The eBLUE leveraged antibiotic-responsive transcription factors to regulate the transcription of RNA arrays that can serve as scaffolds for reassembling and activating multiple luciferase fragments. This process converted target recognition into an amplified bioluminescence response, enabling smartphone-based quantification of tetracycline and erythromycin directly in milk within 15 min. Moreover, the detection threshold of eBLUE can be easily tuned according to the maximum residue limits (MRLs) established by government agencies. Owing to this tunable nature, the eBLUE was further repurposed as an on-demand semi-quantification platform, allowing for fast (∼20 min) and software-free identification of safe and MRL-exceeding milk samples only by glancing over the smartphone photographs. Overall, the sensitivity, rapidity and user-friendliness of eBLUE demonstrate its potentials for practical applications, especially in resource-limited and household settings.
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Affiliation(s)
- Rui Zhang
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, PR China
| | - Yu Wang
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, PR China
| | - Haifeng Deng
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, PR China
| | - Shiwen Zhou
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, PR China
| | - Yunhua Wu
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, PR China
| | - Yong Li
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, PR China; Hubei Jiangxia Laboratory, Wuhan, 430200, PR China.
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10
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Dong J, Willner I. Transient Transcription Machineries Modulate Dynamic Functions of G-Quadruplexes: Temporal Regulation of Biocatalytic Circuits, Gene Replication and Transcription. Angew Chem Int Ed Engl 2023; 62:e202307898. [PMID: 37380611 DOI: 10.1002/anie.202307898] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
Native G-quadruplex-regulated temporal biocatalytic circuits, gene polymerization, and transcription processes are emulated by biomimetic, synthetically engineered transcription machineries coupled to reconfigurable G-quadruplex nanostructures. These are addressed by the following example: (i) A reaction module demonstrates the fuel-triggered transcription machinery-guided transient synthesis of G-quadruplex nanostructures. (ii) A dynamically triggered and modulated transcription machinery that guides the temporal separation and reassembly of the anti-thrombin G-quadruplex aptamer/thrombin complex is introduced, and the transient thrombin-catalyzed coagulation of fibrinogen is demonstrated. (iii) A dynamically fueled transient transcription machinery for the temporal activation of G-quadruplex-topologically blocked gene polymerization circuits is introduced. (iv) Transcription circuits revealing G-quadruplex-promoted or G-quadruplex-inhibited cascaded transcription machineries are presented. Beyond advancing the rapidly developing field of dynamically modulated G-quadruplex DNA nanostructures, the systems introduce potential therapeutic applications.
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Affiliation(s)
- Jiantong Dong
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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11
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Ranallo S, Bracaglia S, Sorrentino D, Ricci F. Synthetic Antigen-Conjugated DNA Systems for Antibody Detection and Characterization. ACS Sens 2023. [PMID: 37463359 PMCID: PMC10391708 DOI: 10.1021/acssensors.3c00564] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Antibodies are among the most relevant biomolecular targets for diagnostic and clinical applications. In this Perspective, we provide a critical overview of recent research efforts focused on the development and characterization of devices, switches, and reactions based on the use of synthetic antigen-conjugated DNA strands designed to be responsive to specific antibodies. These systems can find applications in sensing, drug-delivery, and antibody-antigen binding characterization. The examples described here demonstrate how the programmability and chemical versatility of synthetic nucleic acids can be used to create innovative analytical tools and target-responsive systems with promising potentials.
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Affiliation(s)
- Simona Ranallo
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Sara Bracaglia
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Daniela Sorrentino
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
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12
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Liu B, Wang F, Chao J. Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing. SENSORS (BASEL, SWITZERLAND) 2023; 23:3313. [PMID: 36992023 PMCID: PMC10051322 DOI: 10.3390/s23063313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.
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Affiliation(s)
- Bing Liu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Fan Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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13
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Kieffer C, Genot AJ, Rondelez Y, Gines G. Molecular Computation for Molecular Classification. Adv Biol (Weinh) 2023; 7:e2200203. [PMID: 36709492 DOI: 10.1002/adbi.202200203] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/28/2022] [Indexed: 01/30/2023]
Abstract
DNA as an informational polymer has, for the past 30 years, progressively become an essential molecule to rationally build chemical reaction networks endowed with powerful signal-processing capabilities. Whether influenced by the silicon world or inspired by natural computation, molecular programming has gained attention for diagnosis applications. Of particular interest for this review, molecular classifiers have shown promising results for disease pattern recognition and sample classification. Because both input integration and computation are performed in a single tube, at the molecular level, this low-cost approach may come as a complementary tool to molecular profiling strategies, where all biomarkers are quantified independently using high-tech instrumentation. After introducing the elementary components of molecular classifiers, some of their experimental implementations are discussed either using digital Boolean logic or analog neural network architectures.
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Affiliation(s)
- Coline Kieffer
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Anthony J Genot
- LIMMS, CNRS-Institute of Industrial Science, IRL 2820, University of Tokyo, Tokyo, 153-8505, Japan
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Guillaume Gines
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
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14
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Zhao F, Zou M, Wu H, Yao Y, Zhou M, Ma S, Xiao F, Abudushalamu G, Chen Y, Cai S, Yuan C, Fan X, Jiang X, Wu G. A simple and programmable dual-mode aptasensor for the ultrasensitive detection of multidrug-resistant bacteria. Biomater Sci 2023; 11:1754-1764. [PMID: 36648428 DOI: 10.1039/d2bm01771g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Accurately identifying multidrug-resistant (MDR) bacteria from clinical samples has long been a challenge. Herein, we report a simple and programmable dual-mode aptasensor called DAPT to reliably detect MDR bacteria. The DAPT method comprises two elements, namely the mode of dynamic light scattering (Mode-DLS) for ultrasensitive detection and the mode of fluorescence (Mode-Flu) for reliable quantification as a potent complement. Benefiting from the states of aptamer-modified gold nanoparticles (AptGNPs) sensitively changing from dispersion to aggregation, the proposed Mode-DLS achieved the rapid, specific, and ultrasensitive detection of methicillin-resistant Staphylococcus aureus (MRSA) at the limit of detection (LOD) of 4.63 CFU mL-1 in a proof-of-concept experiment. Simultaneously, the Mode-Flu ensured the accuracy of the detection, especially at a high concentration of bacteria. Moreover, the feasibility and universality of the DAPT platform was validated with four other superbugs by simply reprogramming the corresponding sequence. Overall, the proposed DAPT method based on a dual-mode aptasensor can provide a universal platform for the rapid and ultrasensitive detection of pathogenic bacteria due to its superior programmability.
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Affiliation(s)
- Fengfeng Zhao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - Mingyuan Zou
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - Huina Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - Yuming Yao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - Meiling Zhou
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - Shuo Ma
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - Feng Xiao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - GuliNazhaer Abudushalamu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - Yaya Chen
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - Shijie Cai
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - Chenyan Yuan
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China.
| | - Xiaobo Fan
- Diagnostics Department, Medical School of Southeast University, Nanjing 210009, People's Republic of China
| | - Xinglu Jiang
- Clinical Laboratory Medicine Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, People's Republic of China.
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People's Republic of China. .,Diagnostics Department, Medical School of Southeast University, Nanjing 210009, People's Republic of China.,Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing 210009, People's Republic of China
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15
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Zhang M, Sun Y. DNA-based customized functional modules for signal transformation. Front Chem 2023; 11:1140022. [PMID: 36864900 PMCID: PMC9971431 DOI: 10.3389/fchem.2023.1140022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/03/2023] [Indexed: 02/16/2023] Open
Abstract
Information on the temporal and spatial scale of cellular molecules in biological systems is crucial for estimating life processes and may be conducive to an improved understanding of disease progression. This intracellular and extracellular information is often difficult to obtain at the same time due to the limitations of accessibility and sensing throughput. DNA is an excellent material for in vivo and in vitro applications, and can be used to build functional modules that can transform bio-information (input) into ATCG sequence information (output). Due to their small volume and highly amenable programming, DNA-based functional modules provide an opportunity to monitor a range of information, from transient molecular events to dynamic biological processes. Over the past two decades, with the advent of customized strategies, a series of functional modules based on DNA networks have been designed to gather different information about molecules, including the identity, concentration, order, duration, location, and potential interactions; the action of these modules are based on the principle of kinetics or thermodynamics. This paper summarizes the available DNA-based functional modules that can be used for biomolecular signal sensing and transformation, reviews the available designs and applications of these modules, and assesses current challenges and prospects.
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Affiliation(s)
- Mingzhi Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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16
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Bracaglia S, Ranallo S, Ricci F. Electrochemical Cell-Free Biosensors for Antibody Detection. Angew Chem Int Ed Engl 2023; 62:e202216512. [PMID: 36533529 DOI: 10.1002/anie.202216512] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/07/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
We report here the development of an electrochemical cell-free biosensor for antibody detection directly in complex sample matrices with high sensitivity and specificity that is particularly suitable for point-of-care applications. The approach is based on the use of programmable antigen-conjugated gene circuits that, upon recognition of a specific target antibody, trigger the cell-free transcription of an RNA sequence that can be consequently detected using a redox-modified probe strand immobilized to a disposable electrode. The platform couples the features of high sensitivity and specificity of cell-free systems and the strength of cost-effectiveness and possible miniaturization provided by the electrochemical detection. We demonstrate the sensitive, specific, selective, and multiplexed detection of three different antibodies, including the clinically-relevant Anti-HA antibody.
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Affiliation(s)
- Sara Bracaglia
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Simona Ranallo
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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17
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Lin X, Huang Q. Editorial: Smart nanomaterials for biosensing and therapy applications. Front Bioeng Biotechnol 2023; 11:1137508. [PMID: 36733966 PMCID: PMC9887176 DOI: 10.3389/fbioe.2023.1137508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Affiliation(s)
- Xiaofeng Lin
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Key Laboratory of Biomedical Sensors of Ganzhou, School of Medical and Information Engineering, Science Research Center, Gannan Medical University, Ganzhou, China,*Correspondence: Xiaofeng Lin, ; Qitong Huang,
| | - Qitong Huang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Key Laboratory of Biomedical Sensors of Ganzhou, School of Medical and Information Engineering, Science Research Center, Gannan Medical University, Ganzhou, China,Oil-Tea in Medical Healthcare and Functional Product Development Engineering Research Center in Jiangxi, Gannan Medical University, Ganzhou, China,*Correspondence: Xiaofeng Lin, ; Qitong Huang,
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18
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Li N, Li M, Li M. A programmable catalytic molecular nanomachine for highly sensitive protein and small molecule detection. Analyst 2023; 148:328-336. [PMID: 36484518 DOI: 10.1039/d2an01798a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we report the construction of a programmable catalytic molecular nanomachine based on a cross-linked catalytic hairpin assembly (CCHA) reaction for the one-step highly sensitive detection of proteins and small molecules. In this system, when the recognition elements attached on split initiators bind to the target proteins, it can trigger the cascade of the CCHA reaction, resulting in the formation of many macromolecular fluorescent products for signaling. This platform couples the advantages of highly efficient DNA-based nanotechnology with specific protein-small molecule interactions. We demonstrated the sensitive detection of streptavidin and anti-digoxigenin antibody with detection limits as low as 48.8 pM and 0.85 nM, respectively. This nanomachine also demonstrated its flexibility in the nanomolar detection of corresponding small molecules, such as biotin and digoxigenin, using a competitive method. In addition, the nanomachine was robust enough to perform well with human serum samples. Overall, this programmable catalytic molecular nanomachine provides a versatile platform for the detection of proteins and small molecules by replacing the recognition elements, which can promote the development of DNA nanotechnology in disease diagnosis and therapeutic drug monitoring.
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Affiliation(s)
- Na Li
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Higher Education, School of Pharmacy, Guangxi Medical University, Nanning 530021, China.
| | - Minhui Li
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Higher Education, School of Pharmacy, Guangxi Medical University, Nanning 530021, China.
| | - Mei Li
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Higher Education, School of Pharmacy, Guangxi Medical University, Nanning 530021, China.
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19
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Hu X, Qin W, Yuan R, Zhang L, Wang L, Ding K, Liu R, Huang W, Zhang H, Luo Y. Programmable molecular circuit discriminates multidrug-resistant bacteria. Mater Today Bio 2022; 16:100379. [PMID: 36042850 PMCID: PMC9420371 DOI: 10.1016/j.mtbio.2022.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 10/31/2022] Open
Abstract
Recognizing multidrug-resistant (MDR) bacteria with high accuracy and precision from clinical samples has long been a difficulty. For reliable detection of MDR bacteria, we investigated a programmable molecular circuit called the Background-free isothermal circuital kit (BRICK). The BRICK method provides a near-zero background signal by integrating four inherent modules equivalent to the conversion, amplification, separation, and reading modules. Interference elimination is largely owing to a molybdenum disulfide nanosheets-based fluorescence nanoswitch and non-specific suppression mediated by molecular inhibitors. In less than 70 min, an accurate distinction of various MDR bacteria was achieved without bacterial lysis. The BRICK technique detected 6.73 CFU/mL of methicillin-resistant Staphylococcus aureus in clinical samples in a proof-of-concept trial. By simply reprogramming the sequence panel, such a high signal-to-noise characteristic has been proven in the four other superbugs. The proposed BRICK method can provide a universal platform for infection surveillance and environmental management thanks to its superior programmability.
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Affiliation(s)
- Xiaolin Hu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Weichao Qin
- Department of Clinical Laboratory, Jiangjin Hospital, Chongqing University, 725 Jiangzhou Road, Jiangjin District, Chongqing, 402260, China
| | - Rui Yuan
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Liangliang Zhang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Liangting Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Ke Ding
- Department of Oncology, Jiangjin Hospital, Chongqing University, 725 Jiangzhou Road, Jiangjin District, Chongqing, 402260, China
| | - Ruining Liu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Wanyun Huang
- Life Science Laboratories, Biology Department, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA, 01002, USA
| | - Hong Zhang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, Shandong, 250033, China
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
- Department of Clinical Laboratory, Jiangjin Hospital, Chongqing University, 725 Jiangzhou Road, Jiangjin District, Chongqing, 402260, China
- Department of Clinical Laboratory, Fuling Hospital, Chongqing University, 2 Gaosuntang Road, Fuling District, Chongqing, 408099, China
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