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Yang Y, Mou Z, Liu Q, Wang B, Luo C, Xu Y, Huang Q, He B, Chang K, Wang G, You Z, Qian H. Sunflower Pollen-Derived Microspheres Selectively Absorb DNA for microRNA Detection. Chembiochem 2024:e202400249. [PMID: 38819725 DOI: 10.1002/cbic.202400249] [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: 03/19/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/01/2024]
Abstract
Herein, we report the finding that a naturally sunflower pollen-derived microspheres (HSECs) with hierarchical structures can selectively absorb polyC and polyA with high efficiency and affinity. HSECs exhibit the capability to selectively absorb polyC and polyA ssDNA under neutral and acidic conditions. It has been observed that the presence of metal cations, specifically Ca2+, enhances the absorption efficiency of HSECs. Mechanically, this absorption phenomenon can be attributed to both electrostatic interactions and cation-π interactions. Such an appealing property enables the functionalization of HSECs for broad potential biomedical applications, such as microRNA detection.
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Affiliation(s)
- Yao Yang
- Institute of Respiratory Diseases, Xinqiao Hospital, Chongqing Key Laboratory of Precision Medicine and Prevention of Major Respiratory Diseases, Third Military Medical University, Chongqing, 400037, China
| | - Ziye Mou
- Department of General Practice, Xinqiao Hospital, Third Military Medical University., Chongqing, 400037, China
| | - Qian Liu
- Laboratory of Pharmacy and Chemistry, Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, 400016, China
| | - Bin Wang
- Institute of Respiratory Diseases, Xinqiao Hospital, Chongqing Key Laboratory of Precision Medicine and Prevention of Major Respiratory Diseases, Third Military Medical University, Chongqing, 400037, China
| | - Chenjing Luo
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, 400037, China
| | - Yuhang Xu
- Institute of Respiratory Diseases, Xinqiao Hospital, Chongqing Key Laboratory of Precision Medicine and Prevention of Major Respiratory Diseases, Third Military Medical University, Chongqing, 400037, China
| | - Qiuhong Huang
- Department of General Practice, Xinqiao Hospital, Third Military Medical University., Chongqing, 400037, China
| | - Binfeng He
- Department of General Practice, Xinqiao Hospital, Third Military Medical University., Chongqing, 400037, China
| | - Kai Chang
- School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Guansong Wang
- Institute of Respiratory Diseases, Xinqiao Hospital, Chongqing Key Laboratory of Precision Medicine and Prevention of Major Respiratory Diseases, Third Military Medical University, Chongqing, 400037, China
| | - Zaichun You
- Department of General Practice, Xinqiao Hospital, Third Military Medical University., Chongqing, 400037, China
| | - Hang Qian
- Institute of Respiratory Diseases, Xinqiao Hospital, Chongqing Key Laboratory of Precision Medicine and Prevention of Major Respiratory Diseases, Third Military Medical University, Chongqing, 400037, China
- Department of General Practice, Xinqiao Hospital, Third Military Medical University., Chongqing, 400037, China
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Chen J, Shi G, Yan C. Portable biosensor for on-site detection of kanamycin in water samples based on CRISPR-Cas12a and an off-the-shelf glucometer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162279. [PMID: 36801336 DOI: 10.1016/j.scitotenv.2023.162279] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/05/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
On-site and cost-effective monitoring of antibiotic residue in water samples using a ubiquitous device that is readily available to the general public is a big challenge. Herein, we developed a portable biosensor for kanamycin (KAN) detection based on a glucometer and CRISPR-Cas12a. The aptamer-KAN interactions liberate the trigger C strand, which can initiate the hairpin assembly to produce numerous double-stranded DNA. After recognition by CRISPR-Cas12a, Cas12a can cleave the magnetic bead and invertase-modified single-stranded DNA. After magnetic separation, the invertase can convert sucrose into glucose, which can be quantified by a glucometer. The linear range of the glucometer biosensor is from 1 pM to 100 nM and the detection limit is 1 pM. The biosensor also exhibited high selectivity and the nontarget antibiotics had no significant interference with KAN detection. The sensing system is robust and can work in complex samples with excellent accuracy and reliability. The recovery values were in the range of 89-107.2 % for water samples and 86-106.5 % for milk samples. The relative standard deviation (RSD) was below 5 %. With the advantages of simple operation, low cost, and easy accessibility to the public, this portable pocket-sized sensor can realize the on-site detection of antibiotic residue in resource-limited settings.
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Affiliation(s)
- Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Chong Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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Pan J, Deng F, Zeng L, Liu Z, Chen J. Target-mediated competitive hybridization of hairpin probes for kanamycin detection based on exonuclease III cleavage and DNAzyme catalysis. Anal Bioanal Chem 2022; 414:8255-8261. [PMID: 36178489 DOI: 10.1007/s00216-022-04354-3] [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: 08/26/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/25/2022]
Abstract
Based on aptamer recognition and target-mediated competitive hybridization of hairpin probes, we developed a fluorescence sensor for kanamycin (KAN) detection. The aptamer and KAN binding will open hairpin H1 to release the trigger DNA fragment, which can initiate the competitive hybridization between hairpins H2 and H3. Then, exonuclease III (Exo III) can cleave H2 and H3 to produce numerous DNA3 and DNA4. Through the synergetic hybridization among DNA1, DNA2, DNA3, and DNA4, an active Mg2+-DNAzyme can be formed. The cleavage reaction toward FAM-BHQ-modified DNA2 will produce a high fluorescence signal for KAN assay. Through Exo III-guided cleavage and Mg2+-DNAzyme-based catalysis, the sensor exhibits high sensitivity, with a detection limit of 3.1 fM. This method is robust and has been applied to the detection of KAN in milk and water samples with good accuracy and reliability. Our developed fluorescence sensor exhibits the advantages of simple operation, high sensitivity, and good robustness, which are beneficial for KAN detection in food samples.
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Affiliation(s)
- Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Fang Deng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Lingwen Zeng
- Guangdong Langyuan Biotechnology Co., LTD, Foshan, 528313, China
- School of Food Science and Engineering, Foshan University, Foshan, 528231, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.
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Yuan H, Sun J, Zhang Q, Chu M, Cheng G, Li X, Xue Q. Spatially-extended 3D magnetic DNA nanodevice-based split-type photoelectrochemical strategy for sensitive and reliable miRNA detection in cancer cells. Analyst 2022; 147:3415-3419. [DOI: 10.1039/d2an00712f] [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
To improve the accuracy of PEC sensing. We developed a split-type “turn-off” PEC biosensor based on spatially-extended 3D magnetic DNA nanodevices with high-order DNA amplifiers for sensitive and reliable detection of miRNAs in cancer cells.
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Affiliation(s)
- Hui Yuan
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Jiuming Sun
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Qi Zhang
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Mingyue Chu
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Guiguang Cheng
- Faculty of Agriculture and Food, Kunming University of Science and Technology, Kunming, China
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Qingwang Xue
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China
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Xie Y, Wang H, Yuwen X, Lai G. Exo III-Catalyzed Release of a Zn 2+-Ligation DNAzyme to Drive the Strand Displacement Reaction and Gold Aggregation for the Homogeneous Bioassay of Kanamycin Antibiotics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10371-10378. [PMID: 34436884 DOI: 10.1021/acs.jafc.1c04030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Herein, we combine the exonuclease III (Exo III)-catalyzed release of a Zn2+-dependent ligation DNAzyme with the DNAzyme-driven strand displacement reaction (SDR) to develop a novel homogeneous colorimetric bioassay method for kanamycin (Kana) antibiotic detection. Upon the biorecognition reaction between Kana and a designed hairpin DNA, the DNAzyme-containing strand can be catalytically released by Exo III. Then, this DNAzyme will catalyze the ligation of two oligonucleotides to cause a SDR and the aggregation of gold nanoparticles (Au NPs) labeled by two linker DNA strands. Due to the aggregation of Au NPs for colorimetric signal transduction and the Exo III and SDR-assisted dual signal amplification, this method shows a wide linear range of 5 orders of magnitude and a very low detection limit down to 8.1 fg mL-1. Together with its excellent selectivity, repeatability, reliability, and convenient manipulation, the proposed method shows a great potential for the food quality monitoring application.
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Affiliation(s)
- Yiming Xie
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Haiyan Wang
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Xinyue Yuwen
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Guosong Lai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
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Wang D, Chen C, Liu Q, Zhao Q, Wu D, Yuan Y, Huang C, Sun X, Huang C, Leong DT, Wang G, Qian H. Functionalizing DNA nanostructures with natural cationic amino acids. Bioact Mater 2021; 6:2946-2955. [PMID: 33732965 PMCID: PMC7930363 DOI: 10.1016/j.bioactmat.2021.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 11/04/2022] Open
Abstract
Complexing self-assembled DNA nanostructures with various functional guest species is the key to unlocking new and exciting biomedical applications. Cationic guest species not only induce magnesium-free DNA to self-assemble into defined structures but also endow the final complex nanomaterials with new properties. Herein, we propose a novel strategy that employs naturally occurring cationic amino acids to induce DNA self-assembly into defined nanostructures. Natural l-arginine and l-lysine can readily induce the assembly of tile-based DNA nanotubes and DNA origami sheets in a magnesium-free manner. The self-assembly processes are demonstrated to be pH- and concentration-dependent and are achieved at constant temperatures. Moreover, the assembled DNA/amino acid complex nanomaterials are stable at a physiological temperature of 37 °C. Substituting l-arginine with its D form enhances its serum stability. Further preliminary examination of this complex nanomaterial platform for biomedical applications indicates that DNA/amino acids exhibit distinct cellular uptake behaviors compared with their magnesium-assembled counterparts. The nanomaterial mainly clusters around the cell membrane and might be utilized to manipulate molecular events on the membrane. Our study suggests that the properties of DNA nanostructures can be tuned by complexing them with customized guest molecules for a designed application. The strategy proposed herein might be promising to advance the biomedical applications of DNA nanostructures. A “noncanonical DNA self-assembly” strategy is proposed. Cationic amino acids can assemble DNA nanostructures in a magnesium-free system. The complex nanomaterial exhibited high structural and serum stability. DNA nanostructures can be engineered with customized guest molecules for multiple applications.
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Affiliation(s)
- Dong Wang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China.,Department of Respiratory Medicine, Jinling Hospital, Nanjing, Jiangsu, 210002, China
| | - Chunfa Chen
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Qian Liu
- Laboratory of Pharmacy and Chemistry, And Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, 400016, China
| | - Qianwen Zhao
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Di Wu
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Yue Yuan
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Chaowang Huang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Xiaorong Sun
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Chunji Huang
- Basic Medical College, Third Military Medical University, Chongqing, 400038, China
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Guansong Wang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Hang Qian
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
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7
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Affiliation(s)
- Fangfei Yin
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Fei Wang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Translational Medicine Shanghai Jiao Tong University Shanghai China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Translational Medicine Shanghai Jiao Tong University Shanghai China
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Translational Medicine Shanghai Jiao Tong University Shanghai China
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Translational Medicine Shanghai Jiao Tong University Shanghai China
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