1
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Liang H, Mu Y, Yin M, He PP, Guo W. Solar-powered simultaneous highly efficient seawater desalination and highly specific target extraction with smart DNA hydrogels. SCIENCE ADVANCES 2023; 9:eadj1677. [PMID: 38134281 PMCID: PMC10745703 DOI: 10.1126/sciadv.adj1677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Obtaining freshwater and important minerals from seawater with solar power facilitates the sustainable development of human society. Hydrogels have demonstrated great solar-powered water evaporation potential, but highly efficient and specific target extraction remains to be expanded. Here, we report the simultaneous highly efficient seawater desalination and specific extraction of uranium with smart DNA hydrogels. The DNA hydrogel greatly promoted the evaporation of water, with the water evaporation rate reached a high level of 3.54 kilograms per square meter per hour (1 kilowatt per square meter). Simultaneously, uranyl-specific DNA hydrogel exhibited a high capture capacity of 5.7 milligrams per gram for uranium from natural seawater due to the rapid ion transport driven by the solar powered interfacial evaporation and the high selectivity (10.4 times over vanadium). With programmable functions and easy-to-use devices, the system is expected to play a role in future seawater treatment.
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Affiliation(s)
- Hanxue Liang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Yali Mu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Mengyuan Yin
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Ping-Ping He
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Weiwei Guo
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China
- Smart Sensing Interdisciplinary Science Center, School of Materials Science and Engineering, Nankai University, Tianjin 300350, China
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2
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Wu Y, Torabi SF, Lake RJ, Hong S, Yu Z, Wu P, Yang Z, Nelson K, Guo W, Pawel GT, Van Stappen J, Shao X, Mirica LM, Lu Y. Simultaneous Fe 2+/Fe 3+ imaging shows Fe 3+ over Fe 2+ enrichment in Alzheimer's disease mouse brain. SCIENCE ADVANCES 2023; 9:eade7622. [PMID: 37075105 PMCID: PMC10115418 DOI: 10.1126/sciadv.ade7622] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Visualizing redox-active metal ions, such as Fe2+ and Fe3+ ions, are essential for understanding their roles in biological processes and human diseases. Despite the development of imaging probes and techniques, imaging both Fe2+ and Fe3+ simultaneously in living cells with high selectivity and sensitivity has not been reported. Here, we selected and developed DNAzyme-based fluorescent turn-on sensors that are selective for either Fe2+ or Fe3+, revealing a decreased Fe3+/Fe2+ ratio during ferroptosis and an increased Fe3+/Fe2+ ratio in Alzheimer's disease mouse brain. The elevated Fe3+/Fe2+ ratio was mainly observed in amyloid plaque regions, suggesting a correlation between amyloid plaques and the accumulation of Fe3+ and/or conversion of Fe2+ to Fe3+. Our sensors can provide deep insights into the biological roles of labile iron redox cycling.
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Affiliation(s)
- Yuting Wu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Seyed-Fakhreddin Torabi
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ryan J. Lake
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shanni Hong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhengxin Yu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Peiwen Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhenglin Yang
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kevin Nelson
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weijie Guo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Molecular Bioscience, University of Texas at Austin, Austin, TX 78712, USA
| | - Gregory T. Pawel
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Xiangli Shao
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Liviu M. Mirica
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Molecular Bioscience, University of Texas at Austin, Austin, TX 78712, USA
- Corresponding author.
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3
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Zhang Q, Liang Y, Xing H. Caging-Decaging Strategies to Realize Spatiotemporal Control of DNAzyme Activity for Biosensing and Bioimaging. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-2137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Sun L, Liu J, Li L, Zhen D, Dai Z, Tang S, Zhu B, Chen L, Chen H, Gong M, Tang Z, Hu Y. Advances of biosensors for UO22+ detecting based on specific DNAzyme. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Feng T, Yuan Y, Zhao S, Feng L, Yan B, Cao M, Zhang J, Sun W, Lin K, Wang N. Ultrasensitive Detection of Aqueous Uranyl Based on Uranyl-Triggered Protein Photocleavage. Angew Chem Int Ed Engl 2022; 61:e202115886. [PMID: 34981631 DOI: 10.1002/anie.202115886] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Indexed: 12/26/2022]
Abstract
The detection of environmental uranyl is attracting increasing attention. However, the available detection strategies mainly depend on the selective recognition of uranyl, which is subject to severe interference by coexisting metal ions. Herein, based on the unique uranyl-triggered photocleavage property, the protein BSA is labelled with fluorescent molecules that exhibit an aggregation-induced emission effect for uranyl detection. Uranyl-triggered photocleavage causes the separation of the fluorescent-molecule-labelled protein fragments, leading to attenuation of the emission fluorescence, which is used as a signal for uranyl detection. This detection strategy shows high selectivity for uranyl and an ultralow detection limit of 24 pM with a broad detection range covering five orders of magnitude. The detection method also shows high reliability and stability, making it a promising technique for practical applications in diverse environments.
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Affiliation(s)
- Tiantian Feng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
| | - Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
| | - Shilei Zhao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
| | - Lijuan Feng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
| | - Bingjie Yan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
| | - Meng Cao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
| | - Jiacheng Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
| | - Wenyan Sun
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
| | - Ke Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
| | - Ning Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
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6
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Feng T, Yuan Y, Zhao S, Feng L, Yan B, Cao M, Zhang J, Sun W, Lin K, Wang N. Ultrasensitive Detection of Aqueous Uranyl Based on Uranyl‐Triggered Protein Photocleavage. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tiantian Feng
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University Haikou 570228 P. R. China
| | - Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University Haikou 570228 P. R. China
| | - Shilei Zhao
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University Haikou 570228 P. R. China
| | - Lijuan Feng
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University Haikou 570228 P. R. China
| | - Bingjie Yan
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University Haikou 570228 P. R. China
| | - Meng Cao
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University Haikou 570228 P. R. China
| | - Jiacheng Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University Haikou 570228 P. R. China
| | - Wenyan Sun
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University Haikou 570228 P. R. China
| | - Ke Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University Haikou 570228 P. R. China
| | - Ning Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University Haikou 570228 P. R. China
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7
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Behera N, Sethi S. Unprecedented Catalytic Behavior of Uranyl(VI) Compounds in Chemical Reactions. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Nabakrushna Behera
- School of Chemistry Sambalpur University Jyoti Vihar – 768019 Sambalpur Odisha India
| | - Sipun Sethi
- School of Chemistry Sambalpur University Jyoti Vihar – 768019 Sambalpur Odisha India
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8
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Yuan Y, Liu T, Xiao J, Yu Q, Feng L, Niu B, Feng S, Zhang J, Wang N. DNA nano-pocket for ultra-selective uranyl extraction from seawater. Nat Commun 2020; 11:5708. [PMID: 33177515 PMCID: PMC7659010 DOI: 10.1038/s41467-020-19419-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/07/2020] [Indexed: 12/18/2022] Open
Abstract
Extraction of uranium from seawater is critical for the sustainable development of nuclear energy. However, the currently available uranium adsorbents are hampered by co-existing metal ion interference. DNAzymes exhibit high selectivity to specific metal ions, yet there is no DNA-based adsorbent for extraction of soluble minerals from seawater. Herein, the uranyl-binding DNA strand from the DNAzyme is polymerized into DNA-based uranium extraction hydrogel (DNA-UEH) that exhibits a high uranium adsorption capacity of 6.06 mg g−1 with 18.95 times high selectivity for uranium against vanadium in natural seawater. The uranium is found to be bound by oxygen atoms from the phosphate groups and the carbonyl groups, which formed the specific nano-pocket that empowers DNA-UEH with high selectivity and high binding affinity. This study both provides an adsorbent for uranium extraction from seawater and broadens the application of DNA for being used in recovery of high-value soluble minerals from seawater. The extraction of metals from seawater is an area of great potential; especially for the extraction of uranium. Here, the authors report on the synthesis of a DNA based uranium adsorbent with high selectivity and demonstrate the potential for the DNA based extraction of high-value soluble minerals from seawater.
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Affiliation(s)
- Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Tingting Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Juanxiu Xiao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Qiuhan Yu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Lijuan Feng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Biye Niu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Shiwei Feng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Jiacheng Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Ning Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China.
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9
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Cowie BE, Purkis JM, Austin J, Love JB, Arnold PL. Thermal and Photochemical Reduction and Functionalization Chemistry of the Uranyl Dication, [UVIO2]2+. Chem Rev 2019; 119:10595-10637. [DOI: 10.1021/acs.chemrev.9b00048] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Bradley E. Cowie
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, The King’s Buildings, Edinburgh EH9 3FJ, U.K
| | - Jamie M. Purkis
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, The King’s Buildings, Edinburgh EH9 3FJ, U.K
| | - Jonathan Austin
- National Nuclear Laboratory, Chadwick House,
Warrington Road, Birchwood Park, Warrington WA3 6AE, U.K
| | - Jason B. Love
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, The King’s Buildings, Edinburgh EH9 3FJ, U.K
| | - Polly L. Arnold
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, The King’s Buildings, Edinburgh EH9 3FJ, U.K
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10
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Li C, Xue C, Wang J, Luo M, Shen Z, Wu ZS. Oriented Tetrahedron-Mediated Protection of Catalytic DNA Molecular-Scale Detector against in Vivo Degradation for Intracellular miRNA Detection. Anal Chem 2019; 91:11529-11536. [DOI: 10.1021/acs.analchem.9b00860] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Congcong Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Fujian Engineering Research Center for Drug and Diagnoses-Treat of Photodynamic Therapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Chang Xue
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Fujian Engineering Research Center for Drug and Diagnoses-Treat of Photodynamic Therapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Jue Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, People’s Republic of China
| | - Mengxue Luo
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Fujian Engineering Research Center for Drug and Diagnoses-Treat of Photodynamic Therapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, People’s Republic of China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Fujian Engineering Research Center for Drug and Diagnoses-Treat of Photodynamic Therapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, People’s Republic of China
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11
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Feng M, Gu C, Sun Y, Zhang S, Tong A, Xiang Y. Enhancing Catalytic Activity of Uranyl-Dependent DNAzyme by Flexible Linker Insertion for More Sensitive Detection of Uranyl Ion. Anal Chem 2019; 91:6608-6615. [PMID: 31016961 DOI: 10.1021/acs.analchem.9b00490] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The uranyl-dependent DNAzyme 39E cleaves its nucleic acid substrate in the presence of uranyl ion (UO22+). It has been widely utilized in many sensor designs for selective and sensitive detection of UO22+ in the environment and inside live cells. In this work, by inserting a flexible linker (C3 Spacer) into one critical site (A20) of the 39E catalytic core, we successfully enhanced the original catalytic activity of 39E up to 8.1-fold at low UO22+ concentrations. Applying such a modified DNAzyme (39E-A20-C3) in a label-free fluorescent sensor for UO22+ detection achieved more than 1 order of magnitude sensitivity enhancement over using native 39E, with the UO22+ detection limit improved from 2.6 nM (0.63 ppb) to 0.19 nM (0.047 ppb), while the high selectivity to UO22+ over other metal ions was fully preserved. The method was also successfully applied for the detection of UO22+-spiked environmental water samples to demonstrate its practical usefulness.
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Affiliation(s)
- Mengli Feng
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
| | - Chunmei Gu
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
| | - Yanping Sun
- School of Chemistry and Biological Engineering , University of Science and Technology Beijing , Beijing 100083 , People's Republic of China
| | - Shuyuan Zhang
- School of Chemistry and Biological Engineering , University of Science and Technology Beijing , Beijing 100083 , People's Republic of China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
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12
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Rossberg A, Abe T, Okuwaki K, Barkleit A, Fukuzawa K, Nakano T, Mochizuki Y, Tsushima S. Destabilization of DNA through interstrand crosslinking by UO 22. Chem Commun (Camb) 2019; 55:2015-2018. [PMID: 30643910 DOI: 10.1039/c8cc09329f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
UO22+ was shown to form an interstrand crosslink between two different strands of a single DNA molecule. This crosslink hardly affected the hydrogen bonds between nucleobase pairs but destabilized the π-π stacking between the two nucleobases in the vicinity of UO22+-bound phosphate. Thereby, the fragility of the DNA backbone increased upon UO22+ binding.
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Affiliation(s)
- André Rossberg
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, 01328, Germany.
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13
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Manochehry S, McConnell EM, Tram KQ, Macri J, Li Y. Colorimetric Detection of Uranyl Using a Litmus Test. Front Chem 2018; 6:332. [PMID: 30140672 PMCID: PMC6095041 DOI: 10.3389/fchem.2018.00332] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/16/2018] [Indexed: 01/10/2023] Open
Abstract
Ingestion of water containing toxic contaminants above levels deemed safe for human consumption can occur unknowingly since numerous common contaminants in drinking water are colorless and odorless. Uranyl is particularly problematic as it has been found at dangerous levels in sources of drinking water. Detection of this heavy metal-ion species in drinking water currently requires sending a sample to a laboratory where trained personnel use equipment to perform the analysis and turn-around times can be long. A pH-responsive colorimetric biosensor was developed to enable detection of uranyl in water which coupled the uranyl-specific 39E DNAzyme as a recognition element, and an enzyme capable of producing a pH change as the reporter element. The rapid colorimetric assay presented herein can detect uranyl in lake and well water at concentrations relevant for environmental monitoring, as demonstrated by the detection of uranyl at levels below the limits set for drinking water by major regulatory agencies including the World Health Organization (30 μg/L). This simple and inexpensive DNAzyme-based assay enabled equipment-free visual detection of 15 μg/L uranyl, using both solution-based and paper-based pH-dependent visualization strategies.
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Affiliation(s)
- Sepehr Manochehry
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
| | - Erin M. McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
| | - Kha Q. Tram
- Department of Chemistry and Chemical Biology, McMaster UniversityHamilton, ON, Canada
| | - Joseph Macri
- Department of Pathology and Molecular Medicine, McMaster UniversityHamilton, ON, Canada
- Hamilton Regional Laboratory Medicine ProgramHamilton, ON, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster UniversityHamilton, ON, Canada
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14
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Yuan Y, Zhao Y, Chen L, Wu J, Chen G, Li S, Zou J, Chen R, Wang J, Jiang F, Tang Z. Selective tumor cell death induced by irradiated riboflavin through recognizing DNA G-T mismatch. Nucleic Acids Res 2017; 45:8676-8683. [PMID: 28911109 PMCID: PMC5587794 DOI: 10.1093/nar/gkx602] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 07/04/2017] [Indexed: 12/04/2022] Open
Abstract
Riboflavin (vitamin B2) has been thought to be a promising antitumoral agent in photodynamic therapy, though the further application of the method was limited by the unclear molecular mechanism. Our work reveals that riboflavin was able to recognize G–T mismatch specifically and induce single-strand breaks in duplex DNA targets efficiently under irradiation. In the presence of riboflavin, the photo-irradiation could induce the death of tumor cells that are defective in mismatch repair system selectively, highlighting the G–T mismatch as potential drug target for tumor cells. Moreover, riboflavin is a promising leading compound for further drug design due to its inherent specific recognition of the G–T mismatch.
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Affiliation(s)
- Yi Yuan
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China.,College of pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, PR China
| | - Yongyun Zhao
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Lianqi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Jiasi Wu
- College of pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, PR China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Sheng Li
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Jiawei Zou
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Rong Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Jian Wang
- College of pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, PR China
| | - Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
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15
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Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence. Biochimie 2017; 145:145-150. [PMID: 28711684 DOI: 10.1016/j.biochi.2017.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 07/04/2017] [Indexed: 12/28/2022]
Abstract
The RNA-cleaving Ag10c DNAzyme was recently isolated via in vitro selection and it can bind two Ag+ ions for activity. The Ag10c contains a well-defined Ag+ binding aptamer as indicated by DMS footprinting. Since aptamer binding is often accompanied with conformational changes, we herein used 2-aminopurine (2AP) to probe its folding in the presence of Ag+. The Ag10c was respectively labeled with 2AP at three different positions, both in the substrate strand and in the enzyme strand, one at a time. Ag+-induced folding was observed at the substrate cleavage junction and the A9 position of the enzyme strand, consistent with aptamer binding. The measured Kd at the A9 position was 18 μM Ag+ with a Hill coefficient of 2.17, similar to those obtained from the previous cleavage activity based assays. However, labeling a 2AP at the A2 position inhibited the activity and folding. Compared to other metal ions, Ag+ has a unique sigmoidal folding profile indicative of multiple silver binding cooperatively. This suggests that Ag+ can induce a local folding in the enzyme loop and this folding is important for activity. This study provides important biophysical insights into this new DNAzyme, suggesting the possibility of designing folding-based biosensors for Ag+.
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16
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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17
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A microRNA-initiated DNAzyme motor operating in living cells. Nat Commun 2017; 8:14378. [PMID: 28262725 PMCID: PMC5343503 DOI: 10.1038/ncomms14378] [Citation(s) in RCA: 382] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 12/16/2016] [Indexed: 12/21/2022] Open
Abstract
Synthetic DNA motors have great potential to mimic natural protein motors in cells but the operation of synthetic DNA motors in living cells remains challenging and has not been demonstrated. Here we report a DNAzyme motor that operates in living cells in response to a specific intracellular target. The whole motor system is constructed on a 20 nm gold nanoparticle (AuNP) decorated with hundreds of substrate strands serving as DNA tracks and dozens of DNAzyme molecules each silenced by a locking strand. Intracellular interaction of a target molecule with the motor system initiates the autonomous walking of the motor on the AuNP. An example DNAzyme motor responsive to a specific microRNA enables amplified detection of the specific microRNA in individual cancer cells. Activated by specific intracellular targets, these self-powered DNAzyme motors will have diverse applications in the control and modulation of biological functions. Synthetic DNA nanomachines have been designed to perform a variety of tasks in vitro. Here, the authors build a nanomotor system that integrates a DNAzyme and DNA track on a gold nanoparticle, to facilitate cellular uptake, and apply it as a real-time miRNA imaging tool in living cells.
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18
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Dual-color encoded DNAzyme nanostructures for multiplexed detection of intracellular metal ions in living cells. Biosens Bioelectron 2016; 85:573-579. [DOI: 10.1016/j.bios.2016.05.058] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/15/2016] [Accepted: 05/19/2016] [Indexed: 11/19/2022]
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19
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Zhou W, Ding J, Liu J. A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing. Nucleic Acids Res 2016; 44:10377-10385. [PMID: 27655630 PMCID: PMC5137442 DOI: 10.1093/nar/gkw845] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/10/2016] [Accepted: 09/13/2016] [Indexed: 12/12/2022] Open
Abstract
Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na+ is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na+ aptamer using 2-aminopurine (2AP), a fluorescent adenine analog. This aptamer has two DNA strands derived from the Ce13d DNAzyme. By introducing a 2AP at the cleavage site of the substrate strand, Na+ induces ∼40% fluorescence increase. The signaling is improved by a series of rational mutations, reaching >600% with the C10A20 double mutant. This fluorescence enhancement suggests relaxed base stacking near the 2AP label upon Na+ binding. By replacing a non-conserved adenine in the enzyme strand by 2AP, Na+-dependent fluorescence quenching is observed, suggesting that the enzyme loop folds into a more compact structure upon Na+ binding. The fluorescence changes allow for Na+ detection. With an optimized sequence, a detection limit of 0.4 mM Na+ is achieved, reaching saturated signal in less than 10 s. The sensor response is insensitive to ionic strength, which is critical for Na+ detection.
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Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Juewen Liu
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China .,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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20
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Zhang J, Cheng F, Li J, Zhu JJ, Lu Y. Fluorescent nanoprobes for sensing and imaging of metal ions: recent advances and future perspectives. NANO TODAY 2016; 11:309-329. [PMID: 27818705 PMCID: PMC5089816 DOI: 10.1016/j.nantod.2016.05.010] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Recent advances in nanoscale science and technology have generated nanomaterials with unique optical properties. Over the past decade, numerous fluorescent nanoprobes have been developed for highly sensitive and selective sensing and imaging of metal ions, both in vitro and in vivo. In this review, we provide an overview of the recent development of the design and optical properties of the different classes of fluorescent nanoprobes based on noble metal nanomaterials, upconversion nanoparticles, semiconductor quantum dots, and carbon-based nanomaterials. We further detail their application in the detection and quantification of metal ions for environmental monitoring, food safety, medical diagnostics, as well as their use in biomedical imaging in living cells and animals.
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Affiliation(s)
- JingJing Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - FangFang Cheng
- College of Chemistry, Nanjing University, Nanjing, P. R. China
| | - JingJing Li
- College of Chemistry, Nanjing University, Nanjing, P. R. China
| | - Jun-Jie Zhu
- College of Chemistry, Nanjing University, Nanjing, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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21
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Hwang K, Hosseinzadeh P, Lu Y. Biochemical and Biophysical Understanding of Metal Ion Selectivity of DNAzymes. Inorganica Chim Acta 2016; 452:12-24. [PMID: 27695134 DOI: 10.1016/j.ica.2016.04.017] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This review summarizes research into the metal-binding properties of catalytic DNAzymes, towards the goal of understanding the structural properties leading to metal ion specificity. Progress made and insight gained from a range of biochemical and biophysical techniques are covered, and promising directions for future investigations are discussed.
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Affiliation(s)
- Kevin Hwang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Parisa Hosseinzadeh
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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22
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Räz MH, Hollenstein M. Probing the effect of minor groove interactions on the catalytic efficiency of DNAzymes 8-17 and 10-23. MOLECULAR BIOSYSTEMS 2016; 11:1454-61. [PMID: 25854917 DOI: 10.1039/c5mb00102a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNAzymes (Dz) 8-17 and 10-23 are two widely studied and well-characterized RNA-cleaving DNA catalysts. In an effort to further improve the understanding of the fragile interactions and dynamics of the enzymatic mechanism, this study examines the catalytic efficiency of minimally modified DNAzymes. Five single mutants of Dz8-17 and Dz10-23 were prepared by replacing the adenine residues in the corresponding catalytic cores with 3-deazaadenine units. Kinetic assays were used to assess the effect on the catalytic activity and thereby identify the importance of hydrogen bonding that arises from the N3 atoms. The results suggest that modifications at A15 and A15.0 of Dz8-17 have a significant influence and show a reduction in catalytic activity. Modification at each location in Dz10-23 results in a decrease of the observed rate constants, with A12 appearing to be the most affected with a reduction of ∼80% of kobs and ∼25% of the maximal cleavage rate compared to the wild-type DNAzyme. On the other hand, modification of A12 in Dz8-17 showed an ∼130% increase in kobs, thus unraveling a new potential site for the introduction of chemical modifications. A pH-profile analysis showed that the chemical cleavage step is rate-determining, regardless of the presence and/or location of the mutation. These findings point towards the importance of the N3-nitrogens of certain adenine nucleotides located within the catalytic cores of the DNAzymes for efficient catalytic activity and further suggest that they might directly partake in maintaining the appropriate tertiary structure. Therefore, it appears that minor groove interactions constitute an important feature of DNAzymes as well as ribozymes.
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Affiliation(s)
- Michael H Räz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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Huang PJJ, Liu J. Rational evolution of Cd2+-specific DNAzymes with phosphorothioate modified cleavage junction and Cd2+ sensing. Nucleic Acids Res 2015; 43:6125-33. [PMID: 25990730 PMCID: PMC4499143 DOI: 10.1093/nar/gkv519] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/07/2015] [Indexed: 11/30/2022] Open
Abstract
In vitro selection of RNA-cleaving DNAzymes is a powerful method for isolating metal-specific DNA. A few successful examples are known, but it is still difficult to target some thiophilic metals such as Cd2+ due to limited functional groups in DNA. While using modified bases expands the chemical functionality of DNA, a single phosphorothioate modification might boost its affinity for thiophilic metals without complicating the selection process or using bases that are not commercially available. In this work, the first such in vitro selection for Cd2+ is reported. After using a blocking DNA and negative selections to rationally direct the library outcome, a highly specific DNAzyme with only 12 nucleotides in the catalytic loop is isolated. This DNAzyme has a cleavage rate of 0.12 min−1 with 10 μM Cd2+ at pH 6.0. The Rp form of the substrate is cleaved ∼100-fold faster than the Sp form. The DNAzyme is most active with Cd2+ and its selectivity against Zn2+ is over 100 000-fold. Its application in detecting Cd2+ is also demonstrated. The idea of introducing single modifications in the fixed region expands the scope of DNA/metal interactions with minimal perturbation of DNA structure and property.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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24
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Huang PJJ, Liu J. Sensing parts-per-trillion Cd(2+), Hg(2+), and Pb(2+) collectively and individually using phosphorothioate DNAzymes. Anal Chem 2014; 86:5999-6005. [PMID: 24851672 DOI: 10.1021/ac501070a] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cadmium, mercury, and lead are collectively banned by many countries and regions in electronic devices due to their extremely high toxicity. To date, no sensing method can detect them as a group and also individually with sufficient sensitivity and selectivity. An RNA-cleaving DNAzyme (Ce13d) was recently reported to be active with trivalent lanthanides, which are hard Lewis acids. In this work, phosphorothioate (PS) modifications were systematically made on Ce13d. A single PS modification at the substrate cleavage site shifts the activity from being dependent on lanthanides to soft thiophilic metals. By incorporating the PS modification to another DNAzyme, a sensor array was prepared to detect each metal. Individual sensors have excellent sensitivity (limit of detection = 4.8 nM Cd(2+), 2.0 nM Hg(2+), and 0.1 nM Pb(2+)). This study provides a new route to obtain metal-specific DNAzymes by atomic replacement and also offers important mechanistic insights into metal binding and DNAzyme catalysis.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario Canada , N2L 3G1
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Huang PJJ, Liu J. Two Pb2+-specific DNAzymes with opposite trends in split-site-dependent activity. Chem Commun (Camb) 2014; 50:4442-4. [PMID: 24643441 DOI: 10.1039/c4cc00864b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By splitting the catalytic core of DNAzymes into two halves, two Pb(2+)-specific DNAzymes retain partial activity, while they show opposite trends of activity as a function of the split site, revealing important nucleotides for catalysis and metal binding.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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