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Jiang L, Teng J, Liu X, Xu L, Yang T, Hu X, Ding S, Li J, Jiang Y, Cheng W. Interaction analysis of RNA G-quadruplex with ligands and in situ imaging application. Anal Biochem 2024; 694:115613. [PMID: 39002744 DOI: 10.1016/j.ab.2024.115613] [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: 03/09/2024] [Revised: 06/09/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
RNA G4, as an integral branch of G4 structure, possesses distinct interactions with ligands compared to the common DNA G4, thus the investigation of RNA G4/ligand interactions might be considered as a fresh breakthrough to improve the biosensing performance of G4/ligand system. In this study, we comparatively explored the structural and functional mechanisms of RNA G4 and DNA G4 in the interaction with ligands, hemin and thioflavin T (ThT), utilizing the classical PS2.M sequence as a model. We found that although the catalytic performance of RNA G4/hemin system was lower than DNA G4/hemin, RNA G4/ThT fluorescence system exhibited a significant improvement (2∼3-fold) compared to DNA G4/ThT, and adenine modification could further enhance the signaling. Further, by exploring the interaction between RNA G4 and ThT, we deemed that RNA G4 and ThT were stacked in a bimolecular mode compared to single-molecule binding of DNA G4/ThT, thus more strongly limiting the structural spin in ThT excited state. Further, RNA G4/ThT displayed higher environmental tolerance and lower ion dependence than DNA G4/ThT. Finally, we employed RNA G4/ThT as a highly sensitive label-free fluorescent signal output system for in situ imaging of isoforms BCR-ABL e13a2 and e14a2. Overall, this study successfully screened a high-performance RNA G4 biosensing system through systematic RNA G4/ligands interaction studies, which was expected to provide a promising reference for subsequent G4/ligand research.
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Affiliation(s)
- Lanxin Jiang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Jie Teng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China; Department of Laboratory Medicine, West China Second Hospital of Sichuan University, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, 610066, PR China
| | - Xiaojuan Liu
- Department of Laboratory Medicine, West China Second Hospital of Sichuan University, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, 610066, PR China
| | - Lulu Xu
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, PR China
| | - Tiantian Yang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Xingping Hu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Jia Li
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
| | - Yongmei Jiang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China; Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
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2
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Park KS, Cha H, Niu J, Soh HT, Lee JH, Pack SP. DNA-controlled protein fluorescence: Design of aptamer-split peptide hetero-modulator for GFP to respond to intracellular ATP levels. Nucleic Acids Res 2024; 52:8063-8071. [PMID: 38917331 DOI: 10.1093/nar/gkae532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 05/15/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Enabling the precise control of protein functions with artificially programmed reaction patterns is beneficial for investigating biological processes. Although several strategies have been established that employ the programmability of nucleic acid, they have been limited to DNA hybridization without external stimuli or target binding. Here, we report an approach for the DNA-mediated control of the tripartite split-GFP assembly via aptamers with responsiveness to intracellular small molecules as stimuli. We designed a novel structure-switching aptamer-peptide conjugate as a hetero modulator for split GFP in response to ATP. By conjugating two peptides (S10/11) derived from the tripartite split-GFP to ATP aptamer, we achieved GFP reassembly using only ATP as a trigger molecule. The response to ATP at ≥4 mM concentrations indicated that it can be applied to respond to intracellular ATP in live cells. Furthermore, our hetero-modulator exhibited high and long-term stability, with a half-life of approximately four days in a serum stability assay, demonstrating resistance to nuclease degradation. We validated that our aptamer-modulator split GFP was successfully reconstituted in the cell in response to intracellular ATP levels. Our aptamer-modulated split GFP platform can be utilized to monitor a wide range of intracellular metabolites by replacing the aptamer sequence.
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Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
- Biological Clock-based Anti-Aging Convergence RLRC, Korea University, Sejong 30019, Republic of Korea
| | - Hanvit Cha
- Biological Clock-based Anti-Aging Convergence RLRC, Korea University, Sejong 30019, Republic of Korea
- Department of Food and Biotechnology, Korea University, Sejong 30019, Republic of Korea
| | - Jia Niu
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Hyongsok Tom Soh
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Jin Hyup Lee
- Biological Clock-based Anti-Aging Convergence RLRC, Korea University, Sejong 30019, Republic of Korea
- Department of Food and Biotechnology, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
- Biological Clock-based Anti-Aging Convergence RLRC, Korea University, Sejong 30019, Republic of Korea
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3
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Wang M, Liu Z, Liu C, He W, Qin D, You M. DNAzyme-based ultrasensitive immunoassay: Recent advances and emerging trends. Biosens Bioelectron 2024; 251:116122. [PMID: 38382271 DOI: 10.1016/j.bios.2024.116122] [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: 10/18/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
Immunoassay, as the most commonly used method for protein detection, is simple to operate and highly specific. Sensitivity improvement is always the thrust of immunoassays, especially for the detection of trace quantities. The emergence of artificial enzyme, i.e., DNAzyme, provides a novel approach to improve the detection sensitivity of immunoassay. Simultaneously, its advantages of simple synthesis and high stability enable low cost, broad applicability and long shelf life for immunoassay. In this review, we summarized the recent advances in DNAzyme-based immunoassay. First, we summarized the existing different DNAzymes based on their catalytic activities. Next, the common signal amplification strategies used for DNAzyme-based immunoassays were reviewed to cater to diverse detection requirements. Following, the wide applications in disease diagnosis, environmental monitoring and food safety were discussed. Finally, the current challenges and perspectives on the future development of DNAzyme-based immunoassays were also provided.
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Affiliation(s)
- Meng Wang
- Department of Biomedical Engineering, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Zhe Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China; Department of Rehabilitation Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, PR China
| | - Chang Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Wanghong He
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China; Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, 100050, PR China
| | - Dui Qin
- Department of Biomedical Engineering, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China.
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China.
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Liu J, Cui L, Shi X, Yan J, Wang Y, Ni Y, He J, Wang X. Generation of DNAzyme in Bacterial Cells by a Bacterial Retron System. ACS Synth Biol 2024; 13:300-309. [PMID: 38171507 DOI: 10.1021/acssynbio.3c00509] [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: 01/05/2024]
Abstract
DNAzymes are catalytically active single-stranded DNAs in which DNAzyme 10-23 (Dz 10-23) consists of a catalytic core and a substrate-binding arm that reduces gene expression through sequence-specific mRNA cleavage. However, the in vivo application of Dz 10-23 depends on exogenous delivery, which leads to its inability to be synthesized and stabilized in vivo, thus limiting its application. As a unique reverse transcription system, the bacterial retron system can synthesize single-stranded DNA in vivo using ncRNA msr/msd as a template. The objective of this work is to reduce target gene expression using Dz 10-23 generated in vivo by the retron system. In this regard, we successfully generated Dz 10-23 by cloning the Dz 10-23 coding sequence into the retron msd gene and tested its ability to reduce specific gene expression by examining the mRNA levels of cfp encoding cyan fluorescence protein and other functional genes such as mreB and ftsZ. We found that Dz had different repressive effects when targeting different mRNA regions, and in general, the repressive effect was stronger when targeting downstream of mRNAs. Our results also suggested that the reduction effect was due to cleavage of the substrate mRNA by Dz 10-23 rather than the antisense effect of the substrate-binding arm. Therefore, this study not only provided a retron-based method for the intracellular generation of Dz 10-23 but also demonstrated that Dz 10-23 could reduce gene expression by cleaving target mRNAs in cells. We believe that this new strategy would have great potential in the regulation of gene expression.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lina Cui
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xinyu Shi
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jiahao Yan
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yifei Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuyang Ni
- College of Life Sciences, Shangrao Normal University, Shangrao 334001, PR China
| | - Jin He
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xun Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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5
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Andregic N, Weaver C, Basu S. The binding of a c-MYC promoter G-quadruplex to neurotransmitters: An analysis of G-quadruplex stabilization using DNA melting, fluorescence spectroscopy, surface-enhanced Raman scattering and molecular docking. Biochim Biophys Acta Gen Subj 2023; 1867:130473. [PMID: 37778448 DOI: 10.1016/j.bbagen.2023.130473] [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: 07/14/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
The interactions of several neurotransmitter and neural hormone molecules with the c-MYC G-quadruplex DNA sequence were analyzed using a combination of spectroscopic and computational techniques. The interactions between indole, catecholamine, and amino acid neurotransmitters and DNA sequences could potentially add to the understanding of the role of G-quadruplex structures play in various diseases. Also, the interaction of the DNA sequence derived from the nuclear hypersensitivity element (NHE) III1 region of c-MYC oncogene (Pu22), 5'-TGAGGGTGGGTAGGGTGGGTAA-3', has added significance in that these molecules may promote or inhibit the formation of G-quadruplex DNA which could lead to the development of promising drugs for anticancer therapy. The results showed that these molecules did not disrupt G-quadruplex formation even in the absence of quadruplex-stabilizing cations. There was also evidence of concentration-dependent binding and high binding affinities based on the Stern-Volmer model, and thermodynamically favorable interactions in the form of hydrogen-bonding and interactions involving the π system of the aromatic neurotransmitters.
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Affiliation(s)
- Nicole Andregic
- Department of Biology, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Caitlin Weaver
- Department of Biology, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Swarna Basu
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA.
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6
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Bhuyan SK, Wang L, Jinata C, Kinghorn AB, Liu M, He W, Sharma R, Tanner JA. Directed Evolution of a G-Quadruplex Peroxidase DNAzyme and Application in Proteomic DNAzyme-Aptamer Proximity Labeling. J Am Chem Soc 2023. [PMID: 37276197 DOI: 10.1021/jacs.3c02625] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNAzymes have been limited in application by their low catalytic rates. Here, we evolved a new peroxidase DNAzyme mSBDZ-X-3 through a directed evolution method based on the capture of self-biotinylated DNA catalyzed by its intrinsic peroxidase activity. The mSBDX-X-3 DNAzyme has a parallel G-quadruplex structure and has more favorable catalytic properties than all previously reported peroxidase DNAzyme variants. We applied mSBDZ-X-3 in an aptamer-coupled proximity-based labeling proteomic assay to determine the proteins that bind to cell surface cancer biomarkers EpCAM and nucleolin. Confocal microscopy, western blot analysis, and LC-MS/MS showed that the hybrid DNAzyme aptamer-coupled proximity assay-labeled proteins associated with EpCAM and nucleolin within 6-12 min in fixed cancer cells. The labeled proteins were identified by mass spectrometry. This study provides a highly efficient peroxidase DNAzyme, a methodology for selection of such variants, and a method for its application in spatial proteomics using entirely nucleic acid-based tooling.
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Affiliation(s)
- Soubhagya K Bhuyan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
| | - Lin Wang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
| | - Chandra Jinata
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mengping Liu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Weisi He
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Rakesh Sharma
- Proteomics and Metabolomics Core Facility, Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Julian A Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
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7
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Pandey R, Lu Y, McConnell EM, Osman E, Scott A, Gu J, Hoare T, Soleymani L, Li Y. Electrochemical DNAzyme-based biosensors for disease diagnosis. Biosens Bioelectron 2023; 224:114983. [PMID: 36640547 DOI: 10.1016/j.bios.2022.114983] [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: 09/10/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 01/01/2023]
Abstract
DNAzyme-based electrochemical biosensors provide exceptional analytical sensitivity and high target recognition specificity for disease diagnosis. This review provides a critical perspective on the fundamental and applied impact of incorporating DNAzymes in the field of electrochemical biosensing. Specifically, we highlight recent advances in creating DNAzyme-based electrochemical biosensors for diagnosing infectious diseases, cancer and regulatory diseases. We also develop an understanding of challenges around translating the research in the field of DNAzyme-based electrochemical biosensors from labs to clinics, followed by a discussion on different strategies that can be applied to enhance the performance of the currently existing technologies to create truly point-of-care electrochemical DNAzyme biosensors.
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Affiliation(s)
- Richa Pandey
- Department of Engineering Physics, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
| | - Yang Lu
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Enas Osman
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Alexander Scott
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Todd Hoare
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Chemical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Michael G. DeGroot Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
| | - Yingfu Li
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Michael G. DeGroot Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
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8
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Wang B, Wang M, Peng F, Fu X, Wen M, Shi Y, Chen M, Ke G, Zhang XB. Construction and Application of DNAzyme-based Nanodevices. Chem Res Chin Univ 2023; 39:42-60. [PMID: 36687211 PMCID: PMC9841151 DOI: 10.1007/s40242-023-2334-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023]
Abstract
The development of stimuli-responsive nanodevices with high efficiency and specificity is very important in biosensing, drug delivery, and so on. DNAzymes are a class of DNA molecules with the specific catalytic activity. Owing to their unique catalytic activity and easy design and synthesis, the construction and application of DNAzymes-based nanodevices have attracted much attention in recent years. In this review, the classification and properties of DNAzyme are first introduced. The construction of several common kinds of DNAzyme-based nanodevices, such as DNA motors, signal amplifiers, and logic gates, is then systematically summarized. We also introduce the application of DNAzyme-based nanodevices in sensing and therapeutic fields. In addition, current limitations and future directions are discussed.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Menghui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiaoyi Fu
- Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, 310022 P. R. China
| | - Mei Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Yuyan Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Mei Chen
- College of Materials Science and Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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Xiao Y, Zhang X, Ma L, Fang H, Yang H, Zhou Y. Fluorescence and absorbance dual-mode immunoassay for detecting Ochratoxin A. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 279:121440. [PMID: 35660151 DOI: 10.1016/j.saa.2022.121440] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/11/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
In this work, a simple dual-mode immunoassay for detecting Ochratoxin A (OTA) was developed by mixing G-quadruplex/N-methylmesoporphyrin IX (G4/NMM) and 3,3',5,5'-tetramethylbenzidine (TMB). The fluorescence of G4/NMM can be quenched by oxidized TMB (oxTMB) because the absorbance of oxTMB overlapped with the fluorescence emission of G4/NMM. In the absence of OTA, large amounts of oxTMB were formed with blue color and the fluorescence of G4/NMM was quenched. In the presence of OTA, the concentration of oxTMB was decreased, therefore the fluorescence of G4/NMM increased. The linear range of fluorescence immunoassay was 0.195-25 ng/mL, and the linear range of the absorbance immunoassay was 0.049-1.563 ng/mL. Thus, the linear range of this dual-mode immunoassay can be expanded to 0.049-25 ng/mL. Meanwhile, the new method showed good selectivity for OTA. Besides, the satisfactory recovery rates implied the new method had a potential value for practical sample detection.
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Affiliation(s)
- Yao Xiao
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei 434025, China
| | - Xingping Zhang
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei 434025, China; State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Liyuan Ma
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei 434025, China
| | - Huajuan Fang
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei 434025, China
| | - Hualin Yang
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei 434025, China.
| | - Yu Zhou
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei 434025, China; College of Animal Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei 434025, China.
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10
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Sun H, Wu H, Teng Q, Liu Y, Wang H, Wang ZG. Enzyme-Mimicking Materials from Designed Self-Assembly of Lysine-Rich Peptides and G-Quadruplex DNA/Hemin DNAzyme: Charge Effect of the Key Residues on the Catalytic Functions. Biomacromolecules 2022; 23:3469-3476. [PMID: 35901109 DOI: 10.1021/acs.biomac.2c00620] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In enzymatic active sites, the essential functional groups are spatially arranged as a result of the enzyme three-dimensional folding, which leads to remarkable catalytic properties. We are inspired to self-assemble the polylysine peptides with guanine-rich DNA and hemin as cofactor to fabricate the peroxidase-mimicking catalytic nanomaterials. The DNA can fold into G-quadruplex to provide a supramolecular scaffold and a nucleobase for supporting and coordinating hemin, and the polylysine provides amine as distal groups to promote the H2O2 adsorption to the iron of hemin. The polylysine and DNA components synergistically accelerated the hemin-catalyzed reactions, and the complex containing ε-polylysine exhibited higher activity than α-polylysine. This activity difference is attributed to the higher pKa value and more susceptible protonation of amine of ε-polylysine than α-polylysine. The ε-polylysine/DNA/hemin had similar coordination states of hemin and conformations of the components to α-polylysine/DNA/hemin but accelerated the formation of the intermediate compound I faster than α-polylysine. Theoretical simulation reveals that the unprotonated NH2 behaved like a base catalyst, similar to His-42 residue in the natural heme pocket, while the protonated NH3+ acted as an acid, which indicated that the base catalyst on the distal side of the hemin pocket is more active than the acid. This work provides an avenue to control the distribution of the catalytic residues in an enzyme-like active site and to understand the roles of the key residues of native enzymes.
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Affiliation(s)
- Hao Sun
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules, Beijing University of Chemical Technology, Ministry of Education, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules, Beijing University of Chemical Technology, Ministry of Education, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qiao Teng
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules, Beijing University of Chemical Technology, Ministry of Education, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules, Beijing University of Chemical Technology, Ministry of Education, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hui Wang
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules, Beijing University of Chemical Technology, Ministry of Education, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
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11
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Zhang X, Wang J, Juan Y, Yang H, Wei W, Zhao J. A novel fluorescence method for detection of phosphate anions based on porphyrin metalation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 274:121136. [PMID: 35299095 DOI: 10.1016/j.saa.2022.121136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/24/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
In this work, a novel fluorescence method for the detection of phosphate anions (PO43-) was developed based on porphyrin metalation. Through catalysis by G-quadruplex (G4), Cu2+ could insert into the porphyrins to quench their fluorescence. G4 simultaneously improved the fluorescence of the porphyrins but not that of Cu2+-porphyrin. In the absence of PO43-, the porphyrins were metallized by Cu2+, and no fluorescence was observed. In the presence of PO43-, PO43- could coordinate with Cu2+ to prevent porphyrin metalation. Free porphyrin could bind with G4 to emit strong fluorescence. By comparing four common porphyrins, we found that G4 had the greatest effect on increasing the fluorescence intensity of N-methylmesoporphyrin IX (NMM). Thus, NMM/G4 was chosen for the design of a biosensor. Under optimal experimental conditions, this method showed high sensitivity and satisfactory selectivity for PO43- with a detection limit of 44 nM in a linear range of 0.01-1.0 μM. The recovery experiments showed recovery rates of 93.75-106.00%, suggesting a great potential for measuring PO43- in real samples.
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Affiliation(s)
- Xingping Zhang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China; School of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Jiujun Wang
- School of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Yewen Juan
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China; School of Life Sciences, Nanjing University, Nanjing, China
| | - Hualin Yang
- School of Life Science, Yangtze University, Jingzhou, Hubei, China.
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China; School of Life Sciences, Nanjing University, Nanjing, China; Shenzhen Research Institute, Nanjing University, Shenzhen, China.
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China; Shenzhen Research Institute, Nanjing University, Shenzhen, China.
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12
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Wang J, Zhu L, Li T, Li X, Huang K, Xu W. Multiple functionalities of functional nucleic acids for developing high-performance lateral flow assays. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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13
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Gertzen CGW, Gohlke H. Molecular Modeling and Simulations of DNA and RNA: DNAzyme as a Model System. Methods Mol Biol 2022; 2439:153-170. [PMID: 35226321 DOI: 10.1007/978-1-0716-2047-2_11] [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: 06/14/2023]
Abstract
Nowadays, the structural dynamics of DNA and RNA is accessible on an atomistic level on a micro- to millisecond time scale via molecular dynamics simulations. However, as DNA or RNA are highly charged molecules, performing such simulations is challenging as to the representation of intramolecular electrostatic interactions and those to solvent molecules and ions. This is particularly true for DNAzymes, where DNA and RNA backbones can come as close as 2.4 Å with their charged phosphate groups during the catalytic cycle. Here, we present tools to simulate the structural dynamics of a DNAzyme, with a focus on detailed instructions for the Amber suite of programs. Furthermore, we will show how to analyze metal ion binding within the DNAzyme.
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Affiliation(s)
- Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Institute of Bio- and Geoscences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany.
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14
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Xia LY, Tang YN, Zhang J, Dong TY, Zhou RX. Advances in the DNA Nanotechnology for the Cancer Biomarkers Analysis: Attributes and Applications. Semin Cancer Biol 2022; 86:1105-1119. [PMID: 34979273 DOI: 10.1016/j.semcancer.2021.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023]
Abstract
The most commonly used clinical methods are enzyme-linked immunosorbent assay (ELISA) and quantitative PCR (qPCR) in which ELISA was applied for the detection of protein biomarkers and qPCR was especially applied for nucleic acid biomarker analysis. Although these constructed methods have been applied in wide range, they also showed some inherent shortcomings such as low sensitivity, large sample volume and complex operations. At present, many methods have been successfully constructed on the basis of DNA nanotechnology with the merits of high accuracy, rapid and simple operation for cancer biomarkers assay. In this review, we summarized the bioassay strategies based on DNA nanotechnology from the perspective of the analytical attributes for the first time and discussed and the feasibility of the reported strategies for clinical application in the future.
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Affiliation(s)
- Ling-Ying Xia
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China; Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Ya-Nan Tang
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Jie Zhang
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Tian-Yu Dong
- College of Chemistry, Sichuan University Chengdu, Sichuan 610064, PR China
| | - Rong-Xing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China.
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15
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Wang X, Zhang W, Wang S, Liu W, Liu N, Zhang D. A visual cardiovascular biomarker detection strategy based on distance as readout by the coffee-ring effect on microfluidic paper. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Insight into the function of active site residues in the catalytic mechanism of human ferrochelatase. Biochem J 2021; 478:3239-3252. [PMID: 34402499 DOI: 10.1042/bcj20210460] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Ferrochelatase catalyzes the insertion of ferrous iron into a porphyrin macrocycle to produce the essential cofactor, heme. In humans this enzyme not only catalyzes the terminal step, but also serves a regulatory step in the heme synthesis pathway. Over a dozen crystal structures of human ferrochelatase have been solved and many variants have been characterized kinetically. In addition, hydrogen deuterium exchange, resonance Raman, molecular dynamics, and high level quantum mechanic studies have added to our understanding of the catalytic cycle of the enzyme. However, an understanding of how the metal ion is delivered and the specific role that active site residues play in catalysis remain open questions. Data are consistent with metal binding and insertion occurring from the side opposite from where pyrrole proton abstraction takes place. To better understand iron delivery and binding as well as the role of conserved residues in the active site, we have constructed and characterized a series of enzyme variants. Crystallographic studies as well as rescue and kinetic analysis of variants were performed. Data from these studies are consistent with the M76 residue playing a role in active site metal binding and formation of a weak iron protein ligand being necessary for product release. Additionally, structural data support a role for E343 in proton abstraction and product release in coordination with a peptide loop composed of Q302, S303 and K304 that act a metal sensor.
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17
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Chang T, He S, Amini R, Li Y. Functional Nucleic Acids Under Unusual Conditions. Chembiochem 2021; 22:2368-2383. [PMID: 33930229 DOI: 10.1002/cbic.202100087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/24/2021] [Indexed: 02/06/2023]
Abstract
Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.
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Affiliation(s)
- Tianjun Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
- Department of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, Henan, P. R. China
| | - Sisi He
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
- School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen, 518055, Guangdong, P. R. China
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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18
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Yang H, Peng Y, Xu M, Xu S, Zhou Y. Development of DNA Biosensors Based on DNAzymes and Nucleases. Crit Rev Anal Chem 2021; 53:161-176. [PMID: 34225516 DOI: 10.1080/10408347.2021.1944046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.
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Affiliation(s)
- Hualin Yang
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Peng
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Mingming Xu
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Shuxia Xu
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China.,College of Ecology and Environment, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Zhou
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,College of Animal Science, Yangtze University, Jingzhou, Hubei, China
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19
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Pandey R, Chang D, Smieja M, Hoare T, Li Y, Soleymani L. Integrating programmable DNAzymes with electrical readout for rapid and culture-free bacterial detection using a handheld platform. Nat Chem 2021; 13:895-901. [PMID: 34168325 DOI: 10.1038/s41557-021-00718-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/29/2021] [Indexed: 11/09/2022]
Abstract
The detection and identification of bacteria currently rely on enrichment steps such as bacterial culture and nucleic acid amplification to increase the concentration of target analytes. These steps increase assay time, cost and complexity, making it difficult to realize a truly rapid point-of-care test. Here we report the development of an electrical assay that uses electroactive RNA-cleaving DNAzymes (e-RCDs) to identify specific bacterial targets and subsequently release a DNA barcode for transducing a signal onto an electrical chip. Integrating e-RCDs into a two-channel electrical chip with nanostructured electrodes provides the analytical sensitivity and specificity needed for clinical analysis. The e-RCD assay is capable of detecting 10 CFU (equivalent to 1,000 CFU ml-1) of Escherichia coli selectively from a panel containing multiple non-specific bacterial species. Clinical evaluation of this assay using 41 patient urine samples demonstrated a diagnostic sensitivity of 100% and specificity of 78% at an analysis time of less than one hour compared with the several hours needed for currently used culture-based methods.
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Affiliation(s)
- Richa Pandey
- Department of Engineering Physics, McMaster University, Hamilton, Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Marek Smieja
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research (IIDR), McMaster University, Hamilton, Canada
| | - Todd Hoare
- Department of Chemical Engineering, McMaster University, Hamilton, Canada.,School of Biomedical Engineering, McMaster University, Hamilton, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada. .,Michael G. DeGroote Institute for Infectious Disease Research (IIDR), McMaster University, Hamilton, Canada. .,School of Biomedical Engineering, McMaster University, Hamilton, Canada.
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, Hamilton, Canada. .,School of Biomedical Engineering, McMaster University, Hamilton, Canada.
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20
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Ning Z, Chen M, Wu G, Zhang Y, Shen Y. Recent advances of functional nucleic acids-based electrochemiluminescent sensing. Biosens Bioelectron 2021; 191:113462. [PMID: 34198172 DOI: 10.1016/j.bios.2021.113462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/12/2021] [Accepted: 06/21/2021] [Indexed: 12/19/2022]
Abstract
Electroluminescence (ECL) has been used in extensive applications ranging from bioanalysis to clinical diagnosis owing to its simple device requirement, low background, high sensitivity, and wide dynamic range. Nucleic acid is a significant theme in ECL bioanalysis. The inherent versatile selective molecular recognition of nucleic acids and their programmable self-assembly make it desirable for the robust construction of nanostructures. Benefiting from their unique structures and physiochemical properties, ECL biosensing based on nucleic acids has experienced rapid growth. This review focuses on recent applications of nucleic acids in ECL sensing systems, particularly concerning the employment of nucleic acids as molecular recognition elements, signal amplification units, and sensing interface schemes. In the end, an outlook of nucleic acid-based ECL biosensing will be provided for future developments and directions. We envision that nucleic acids, which act as an essential component for both bioanalysis and clinical diagnosis, will provide a new thinking model and driving force for developing next-generation sensing systems.
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Affiliation(s)
- Zhenqiang Ning
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, China
| | - Mengyuan Chen
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, China
| | - Guoqiu Wu
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, China; Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China; Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, 210009, China
| | - Yuanjian Zhang
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, China
| | - Yanfei Shen
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, China; Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China; Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, 210009, China.
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21
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Zhao H, Zhang Z, Zuo D, Li L, Li F, Yang D. A Synergistic DNA-polydopamine-MnO 2 Nanocomplex for Near-Infrared-Light-Powered DNAzyme-Mediated Gene Therapy. NANO LETTERS 2021; 21:5377-5385. [PMID: 34100622 DOI: 10.1021/acs.nanolett.1c01727] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNAzyme is emerging for gene therapy. The administration of the in vivo catalytic activity of DNAzyme has proven important but challenging for clinical applications. Herein, we report a synergistic DNA-polydopamine-MnO2 nanocomplex, which enables near-infrared (NIR)-light-powered catalytic activity of DNAzyme in vivo. The nanocomplex has a hierarchical structure: a DNA nanoframework as the scaffold and polydopamine-MnO2 (PM) as the coating layer. The DNA nanoframework contains repeated DNAzyme sequences. PM assembles on the surface of the DNA nanoframework. When the nanocomplex accumulates at tumor sites, upon NIR-light radiation, polydopamine induces a temperature elevation at tumor sites via photothermal conversion; meanwhile, glutathione triggers decomposition of PM to release Mn2+ to activate DNAzyme in the cytoplasm for gene regulation. In vitro and in vivo experiments show that the PM-induced temperature elevation enhances the Egr-1 mRNA cleavage activity of DNAzyme, promoting downregulation of the Egr-1 protein in tumor cells. In addition, the temperature elevation induces heat stress, achieving a synergistic tumor ablation effect.
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Affiliation(s)
- Huaixin Zhao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Zhili Zhang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Duo Zuo
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, People's Republic of China
| | - Linghui Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
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22
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Abstract
In this review, DNA and nanomaterial based catalysts for porphyrin metalation reactions are summarized, including the selection of DNAzymes, choice of nanomaterials, their catalytic mechanisms, and applications of the reactions.
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Affiliation(s)
- Hualin Yang
- College of Life Science
- Yangtze University
- Jingzhou
- China
- Department of Chemistry
| | - Yu Zhou
- College of Life Science
- Yangtze University
- Jingzhou
- China
- College of Animal Science
| | - Juewen Liu
- Department of Chemistry
- Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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23
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Huo B, Hu Y, Gao Z, Li G. Recent advances on functional nucleic acid-based biosensors for detection of food contaminants. Talanta 2020; 222:121565. [PMID: 33167261 DOI: 10.1016/j.talanta.2020.121565] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023]
Abstract
It has seen increasing development of reliable, robust, and flexible biosensors for rapid food-safety analysis in the past few decades. Recently, functional nucleic acid-based biosensors have attracted attention because of their programmability, bottom-up characteristics, and structural switches. However, few systematic reviews devoted to categorizing the potential of DNA nanostructures and devices were found for detecting food contaminants. Hence, the applications of functional nucleic acid-based biosensors were reviewed for analyzing food contaminants, including foodborne pathogen bacteria, biotoxins, heavy metals, and et al. In addition to categorizing the various biosensors, multiple signal readout strategies, such as optical, electrochemical, and mass-based signals were also examined. Finally, the future changes and potential opportunities, as well as practical applications of functional nucleic acid-based biosensors were discussed.
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Affiliation(s)
- Bingyang Huo
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuling Hu
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Gongke Li
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China.
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24
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Colorimetric detection of miRNA-21 by DNAzyme-coupled branched DNA constructs. Talanta 2020; 216:120913. [DOI: 10.1016/j.talanta.2020.120913] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/18/2020] [Accepted: 03/08/2020] [Indexed: 11/20/2022]
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25
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Sitte E, Senge MO. The Red Color of Life Transformed - Synthetic Advances and Emerging Applications of Protoporphyrin IX in Chemical Biology. European J Org Chem 2020; 2020:3171-3191. [PMID: 32612451 PMCID: PMC7319466 DOI: 10.1002/ejoc.202000074] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Indexed: 01/10/2023]
Abstract
Protoporphyrin IX (PPIX) is the porphyrin scaffold of heme b, a ubiquitous prosthetic group of proteins responsible for oxygen binding (hemoglobin, myoglobin), electron transfer (cytochrome c) and catalysis (cytochrome P450, catalases, peroxidases). PPIX and its metallated derivatives frequently find application as therapeutic agents, imaging tools, catalysts, sensors and in light harvesting. The vast toolkit of accessible porphyrin functionalization reactions enables easy synthetic modification of PPIX to meet the requirements for its multiple uses. In the past few years, particular interest has arisen in exploiting the interaction of PPIX and its synthetic derivatives with biomolecules such as DNA and heme-binding proteins to evolve molecular devices with new functions as well as to uncover potential therapeutic toeholds. This review strives to shine a light on the most recent developments in the synthetic chemistry of PPIX and its uses in selected fields of chemical biology.
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Affiliation(s)
- Elisabeth Sitte
- School of ChemistryTrinity College DublinThe University of DublinTrinity Biomedical Sciences Institute152‐160 Pearse Street2DublinIreland
| | - Mathias O. Senge
- School of ChemistryTrinity College DublinThe University of DublinTrinity Biomedical Sciences Institute152‐160 Pearse Street2DublinIreland
- Institute for Advanced Study (TUM‐IAS)Technische Universität MünchenLichtenberg‐Str. 2a85748GarchingGermany
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26
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McConnell EM, Nguyen J, Li Y. Aptamer-Based Biosensors for Environmental Monitoring. Front Chem 2020; 8:434. [PMID: 32548090 PMCID: PMC7272472 DOI: 10.3389/fchem.2020.00434] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/27/2020] [Indexed: 12/20/2022] Open
Abstract
Due to their relative synthetic and chemical simplicity compared to antibodies, aptamers afford enhanced stability and functionality for the detection of environmental contaminants and for use in environmental monitoring. Furthermore, nucleic acid aptamers can be selected for toxic targets which may prove difficult for antibody development. Of particular relevance, aptamers have been selected and used to develop biosensors for environmental contaminants such as heavy metals, small-molecule agricultural toxins, and water-borne bacterial pathogens. This review will focus on recent aptamer-based developments for the detection of diverse environmental contaminants. Within this domain, aptamers have been combined with other technologies to develop biosensors with various signal outputs. The goal of much of this work is to develop cost-effective, user-friendly detection methods that can complement or replace traditional environmental monitoring strategies. This review will highlight recent examples in this area. Additionally, with innovative developments such as wearable devices, sentinel materials, and lab-on-a-chip designs, there exists significant potential for the development of multifunctional aptamer-based biosensors for environmental monitoring. Examples of these technologies will also be highlighted. Finally, a critical perspective on the field, and thoughts on future research directions will be offered.
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Affiliation(s)
| | | | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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27
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Yang H, Peng D, Zhou Y, Liu J. Pb 2+ as a Substrate and a Cofactor of a Porphyrin Metalation DNAzyme. Chembiochem 2020; 21:2259-2263. [PMID: 32202058 DOI: 10.1002/cbic.202000073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/21/2020] [Indexed: 11/11/2022]
Abstract
We herein report a DNAzyme named T30695 (sequence: (G3 T)4 ) that can catalyze Zn2+ insertion into three different porphyrins in the presence of Pb2+ as a cofactor. Meanwhile, T30695 with Pb2+ alone was found to cause a shift in both the fluorescence and UV-vis spectra of protoporphyrin IX (PPIX), thus suggesting that metalation of Pb2+ was also achieved at room temperature. From kinetic measurements, the reaction required two Pb2+ ions; this is consistent with one being a cofactor and the other being a substrate. No previous reports inserted Pb2+ into porphyrins by using DNAzymes or protein-based enzymes. This reaction was most significantly inhibited in the presence of K+ followed by Na+ and Li+ , suggesting the importance of the Pb2+ -stabilized G-quadruplex. When Pb2+ is inserted into PPIX, its emission blue shifts from 635 to 590 nm, thus allowing simple ratiometric fluorescent sensing with a detection limit of 1.2 nM Pb2+ .
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Affiliation(s)
- Hualin Yang
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei, 434025, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Dong Peng
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada.,College of Chemistry20, Nanchang University, 999 Xuefu Avenue, Nanchang, 330031, Jiangxi, China
| | - Yu Zhou
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei, 434025, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
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28
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Abstract
Catalytic DNAs (DNAzymes) with peroxidase-like activity have great potential in bioanalytical chemistry [1], owing to numerous advantages that DNA enzymes offer over conventional protein enzymes, including structural simplicity, low cost, thermal stability, and straightforward handling and preparation. Maximizing the efficiency of the peroxidase activity of such DNAzymes is a subject in need of review. In this chapter, we discuss the optimal experimental conditions for the peroxidase activity of these DNAzymes and describe general procedures for their utilization.
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29
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Nucleic acid-cleaving catalytic DNA for sensing and therapeutics. Talanta 2020; 211:120709. [PMID: 32070594 DOI: 10.1016/j.talanta.2019.120709] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 12/21/2022]
Abstract
DNAzymes with nucleic acid-cleaving catalytic activity are increasing in versatility through concerted efforts to discover new sequences with unique functions, and they are generating excitement in the sensing community as cheap, stable, amplifiable detection elements. This review provides a comprehensive list and detailed descriptions of the DNAzymes identified to date, classified by their associated small molecule or ion needed for catalysis; of note, this classification clarifies conserved regions of various DNAzymes that are not obvious in the literature. Furthermore, we detail the breadth of functionality of these DNA sequences as well as the range of reaction conditions under which they are useful. In addition, the utility of the DNAzymes in a variety of sensing and therapeutic applications is presented, detailing both their advantages and disadvantages.
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30
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Liu R, McConnell EM, Li J, Li Y. Advances in functional nucleic acid based paper sensors. J Mater Chem B 2020; 8:3213-3230. [DOI: 10.1039/c9tb02584g] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This article provides an extensive review of paper-based sensors that utilize functional nucleic acids, particularly DNA aptamers and DNAzymes, as recognition elements.
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Affiliation(s)
- Rudi Liu
- Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
| | - Erin M. McConnell
- Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
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31
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Hu L, Fu X, Kong G, Yin Y, Meng HM, Ke G, Zhang XB. DNAzyme–gold nanoparticle-based probes for biosensing and bioimaging. J Mater Chem B 2020; 8:9449-9465. [DOI: 10.1039/d0tb01750g] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The design and applications of DNAzyme–gold nanoparticle-based probes in biosensing and bioimaging are summarized here.
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Affiliation(s)
- Ling Hu
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Xiaoyi Fu
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Gezhi Kong
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Yao Yin
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Hong-Min Meng
- College of Chemistry
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Guoliang Ke
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Xiao-Bing Zhang
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
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32
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Lin Y, Yang Z, Lake RJ, Zheng C, Lu Y. Enzyme‐Mediated Endogenous and Bioorthogonal Control of a DNAzyme Fluorescent Sensor for Imaging Metal Ions in Living Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yao Lin
- Department of ChemistryDepartment of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
- Key Laboratory of Green Chemistry & TechnologyMinistry of EducationCollege of ChemistrySichuan University Chengdu Sichuan 610064 China
| | - Zhenglin Yang
- Department of ChemistryDepartment of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Ryan J. Lake
- Department of ChemistryDepartment of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Chengbin Zheng
- Key Laboratory of Green Chemistry & TechnologyMinistry of EducationCollege of ChemistrySichuan University Chengdu Sichuan 610064 China
| | - Yi Lu
- Department of ChemistryDepartment of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
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33
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Lin Y, Yang Z, Lake RJ, Zheng C, Lu Y. Enzyme-Mediated Endogenous and Bioorthogonal Control of a DNAzyme Fluorescent Sensor for Imaging Metal Ions in Living Cells. Angew Chem Int Ed Engl 2019; 58:17061-17067. [PMID: 31529664 PMCID: PMC7174831 DOI: 10.1002/anie.201910343] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Indexed: 11/09/2022]
Abstract
Bioorthogonal control of metal-ion sensors for imaging metal ions in living cells is important for understanding the distribution and fluctuation of metal ions. Reported here is the endogenous and bioorthogonal activation of a DNAzyme fluorescent sensor containing an 18-base pair recognition site of a homing endonuclease (I-SceI), which is found by chance only once in 7×1010 bp of genomic sequences, and can thus form a near bioorthogonal pair with I-SceI for DNAzyme activation with minimal effect on living cells. Once I-SceI is expressed inside cells, it cleaves at the recognition site, allowing the DNAzyme to adopt its active conformation. The activated DNAzyme sensor is then able to specifically catalyze cleavage of a substrate strand in the presence of Mg2+ to release the fluorophore-labeled DNA fragment and produce a fluorescent turn-on signal for Mg2+ . Thus I-SceI bioorthogonally activates the 10-23 DNAzyme for imaging of Mg2+ in HeLa cells.
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Affiliation(s)
- Yao Lin
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zhenglin Yang
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ryan J. Lake
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chengbin Zheng
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
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34
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Stefan L, Monchaud D. Applications of guanine quartets in nanotechnology and chemical biology. Nat Rev Chem 2019. [DOI: 10.1038/s41570-019-0132-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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35
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Peng D, Li Y, Huang Z, Liang RP, Qiu JD, Liu J. Efficient DNA-Catalyzed Porphyrin Metalation for Fluorescent Ratiometric Pb 2+ Detection. Anal Chem 2019; 91:11403-11408. [PMID: 31414597 DOI: 10.1021/acs.analchem.9b02759] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Developing biosensors for Pb2+ is an important analytical topic. DNA-based Pb2+ sensors have been designed mainly based on RNA-cleaving DNAzymes and Pb2+-induced folding of G-quadruplex (G4) DNA. Porphyrin metalation is a key reaction in biology and catalysis. Many enzyme mimics have been developed to catalyze this reaction, and some metalation DNAzymes were reported with a G4 structure. Inspired by the excellent G4 binding properties of certain divalent metal ions, we herein screened a few metals and G-rich DNA sequences. The metalation activity of a DNA named T30695 (sequence: (G3T)4) was significantly accelerated by Pb2+. The reaction of Cu2+ insertion into the mesoporphyrin IX had a kcat of 0.89 min-1 and a Km of 9.8 μM, representing a catalytic efficiency similar to that of human ferrochelatase. The reason for the acceleration was attributed to Pb2+ binding of the G4 DNA and the catalytic activity of the large Pb2+ ion for this reaction. A ratiometric sensor for Pb2+ was developed by inserting Zn2+ with a detection limit of 23.5 nM Pb2+. This work has established a new DNA-based reaction that can be used for Pb2+ detection, and it also provides a highly efficient new DNAzyme for porphyrin metalation, which might be used for signal production for other biosensors.
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Affiliation(s)
- Dong Peng
- College of Chemistry , Nanchang University , 999 Xuefu Avenue , Nanchang , 330031 Jiangxi , China.,Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Ru-Ping Liang
- College of Chemistry , Nanchang University , 999 Xuefu Avenue , Nanchang , 330031 Jiangxi , China
| | - Jian-Ding Qiu
- College of Chemistry , Nanchang University , 999 Xuefu Avenue , Nanchang , 330031 Jiangxi , China.,Environmental Protection Materials and Equipment Engineering Technology Center of Jiangxi, Department of Materials and Chemical Engineering , Pingxiang University , 211 Pingan North Road , Pingxiang , 337055 Jiangxi , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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36
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Xu J, Lee ES, Gye MC, Kim YP. Rapid and sensitive determination of bisphenol A using aptamer and split DNAzyme. CHEMOSPHERE 2019; 228:110-116. [PMID: 31026631 DOI: 10.1016/j.chemosphere.2019.04.110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 06/09/2023]
Abstract
Despite the increasing concern regarding bisphenol A (BPA) as an endocrine disrupting chemical (EDC) upon environmental or human exposure, development of simple method for BPA detection has been hampered, due to the lack of a stable bioreceptor and signal generator. Here, we report a nucleic acid-based rapid and sensitive method for BPA detection, which constitutes a ssDNA aptamer and ssDNAzyme. When the peroxidase-like DNAzyme sequence was split into two parts (one incorporated into the anti-BPA aptamer as a target recognition element and the other into the complementary sequence as a bait), the presence of BPA hindered the association of the split DNA sequence, leading to a reduced signal in the DNAzyme-triggered chemiluminescence (CL). Thus, this NA-based CL measurement permitted the detection of BPA at as low as 5 nM with a broad dynamic range of five orders and with high selectivity towards BPA over other EDCs with structural similarity. With the development of aptamers, our detection method is expected to facilitate studies to monitor EDCs with high simplicity and sensitivity in the field of environmental science.
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Affiliation(s)
- Jing Xu
- Department of Environmental Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Eun-Song Lee
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
| | - Myung Chan Gye
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Young-Pil Kim
- Department of Environmental Sciences, Hanyang University, Seoul, 04763, Republic of Korea; Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea; Institute of Nano Science and Technology, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
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37
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Luo Y, Yu H, Alkhamis O, Liu Y, Lou X, Yu B, Xiao Y. Label-Free, Visual Detection of Small Molecules Using Highly Target-Responsive Multimodule Split Aptamer Constructs. Anal Chem 2019; 91:7199-7207. [PMID: 31050407 PMCID: PMC6615563 DOI: 10.1021/acs.analchem.9b00507] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Colorimetric aptamer-based sensors offer a simple means of on-site or point-of-care analyte detection. However, these sensors are largely incapable of achieving naked-eye detection, because of the poor performance of the target-recognition and signal-reporting elements employed. To address this problem, we report a generalizable strategy for engineering novel multimodule split DNA constructs termed "CBSAzymes" that utilize a cooperative binding split aptamer (CBSA) as a highly target-responsive bioreceptor and a new, highly active split DNAzyme as an efficient signal reporter. CBSAzymes consist of two fragments that remain separate in the absence of target, but effectively assemble in the presence of the target to form a complex that catalyzes the oxidation of 2,2'-azino-bis(3-ethylbenzthiazoline)-6-sulfonic acid, developing a dark green color within 5 min. Such assay enables rapid, sensitive, and visual detection of small molecules, which has not been achieved with any previously reported split-aptamer-DNAzyme conjugates. In an initial demonstration, we generate a cocaine-binding CBSAzyme that enables naked-eye detection of cocaine at concentrations as low as 10 μM. Notably, CBSAzyme engineering is straightforward and generalizable. We demonstrate this by developing a methylenedioxypyrovalerone (MDPV)-binding CBSAzyme for visual detection of MDPV and 10 other synthetic cathinones at low micromolar concentrations, even in biological samples. Given that CBSAzyme-based assays are simple, label-free, rapid, robust, and instrument-free, we believe that such assays should be readily applicable for on-site visual detection of various important small molecules such as illicit drugs, medical biomarkers, and toxins in various sample matrices.
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Affiliation(s)
- Yingping Luo
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Department of Complex Prescription of TCM, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Rd. 105, Beijing, China, 100048
| | - Boyang Yu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Department of Complex Prescription of TCM, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
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38
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Yang L, Ding P, Luo Y, Wang J, Lv H, Li W, Cao Y, Pei R. Exploration of Catalytic Nucleic Acids on Porphyrin Metalation and Peroxidase Activity by in Vitro Selection of Aptamers for N-Methyl Mesoporphyrin IX. ACS COMBINATORIAL SCIENCE 2019; 21:83-89. [PMID: 30602113 DOI: 10.1021/acscombsci.8b00129] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To develop a novel light-up probe and DNAzyme, we selected aptamers for N-methyl mesoporphyrin IX (NMM), a common fluorogenic analogue of coenzyme hemin, by a modified affinity chromatography-based systematic evolution of ligands by exponential enrichment (SELEX). Two truncated aptamers Nm1 and Nm2 with low micromolar dissociation constants (0.75 and 13.27 μM) were obtained after 11 rounds of selection and the final minimized 39-mer aptamer Nm2.1 showed 24-fold fluorescence enhancement for NMM at saturated concentration. Study of the interactions between aptamers and other porphyrin compounds by circular dichroism (CD) and absorption spectroscopy showed that Nm1 mainly assembled as a stem-loop structure, which exhibited a catalytic activity for the metal insertion reaction of mesoporphyrin IX with 3.3-fold rate enhancement. In contrast, the G-rich Nm2 and Nm2.1 were likely to form G-quadruplexes in the presence of alkali metal cations (K+ and Na+), which displayed excellent peroxidase activity exhibiting 19-fold higher catalytic efficiency than hemin alone. The selected aptamers could therefore be used as novel light-up fluorescent probes and DNAzymes by pairing with porphyrin compounds that have potential to construct sensors for various applications.
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Affiliation(s)
- Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123, China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Yu Luo
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123, China
| | - Jine Wang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Haiyin Lv
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123, China
| | - Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- School of Nano Technology and Nano Bionics, University of Science and Technology of China, Hefei 230026, China
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39
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Gao Y, Liu X, Sun L, Xu Y, Yang S, Fan C, Li D. Alleviated Inhibition of Single Enzyme in Confined and Crowded Environment. J Phys Chem Lett 2019; 10:82-89. [PMID: 30565943 DOI: 10.1021/acs.jpclett.8b03736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Most proteins perform functions in intracellular milieu. The crowding, compartmentalized cytosol environment affects the protein structure, folding, conformational stability, substrate diffusion, and substrate-enzyme binding. Moreover, enzymes are available at single or very low copy numbers in a cell, and thus the conformation fluctuations of a single enzyme in a crowding environment could also greatly influence its kinetics. However, the crowding effect is poorly understood in the kinetical aspect of enzymatic reactions. In the present study, individual horseradish peroxidase (HRP) is encapsulated in a liposome containing crowding reagents as mimics of viscous cytosol. The confined crowding environment possesses a profound influence on both the catalytic activity and the product inhibition of enzymes. By analyzing the correlation between product generation and product inhibition, we find that the allosteric noncompetitive inhibition of HRP is alleviated in the crowded and confined milieu. Small-angle X-ray scattering experiments provide straightforward proofs of structural changes of enzymes in crowding environments, which are responsible for the reduced enzyme activity and increased enzyme-substrate affinity. We expect that this work may deepen the understanding of correlations between enzymatic conformations and activity performance in real cellular environments.
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Affiliation(s)
- Yanjing Gao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Lele Sun
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yan Xu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- National Engineering Research Center for Nanotechnology , Shanghai 200241 , China
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Di Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
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40
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Cheng Y, Cheng M, Hao J, Jia G, Li C. Fluorescence Spectroscopic Insight into the Supramolecular Interactions in DNA-Based Enantioselective Sulfoxidation. Chembiochem 2018; 19:2233-2240. [PMID: 30070000 DOI: 10.1002/cbic.201800393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 12/31/2022]
Abstract
Interactions of copper(II)-bipyridine cofactors and thioanisole substrate with human telomeric G-quadruplex DNA were studied by UV/Vis absorption, circular dichroism, and fluorescence quenching titration. Three copper(II)-bipyridine complexes are equivalently anchored to the G-quadruplex scaffold at all five fluorescently labeled sites. Thioanisole interacts with the DNA architecture at both the second loop and 3' terminus in the absence or presence of copper(II)-bipyridine complexes. These nonspecificities in the weak interactions of CuII complexes and thioanisole with G-quadruplex might explain why DNA only affords a modest enantioselectivity in the oxidation of thioanisole. These findings provide insights toward the construction of highly enantioselective DNA-based catalysts.
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Affiliation(s)
- Yu Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P.R. China.,Department of Chemical Physics, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, P.R. China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P.R. China.,Department of Chemical Physics, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, P.R. China
| | - Jingya Hao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P.R. China.,Department of Chemical Physics, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, P.R. China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P.R. China
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P.R. China
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41
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Xing Y, Liu X, Pu Q, Wu M, Zhao JX. Biocompatible G-Quadruplex/Hemin for Enhancing Antibacterial Activity of H2O2. ACS APPLIED BIO MATERIALS 2018; 1:1019-1027. [DOI: 10.1021/acsabm.8b00211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yuqian Xing
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Xiao Liu
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Qinqin Pu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Julia Xiaojun Zhao
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
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42
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Peng H, Newbigging AM, Wang Z, Tao J, Deng W, Le XC, Zhang H. DNAzyme-Mediated Assays for Amplified Detection of Nucleic Acids and Proteins. Anal Chem 2017; 90:190-207. [DOI: 10.1021/acs.analchem.7b04926] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hanyong Peng
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Ashley M. Newbigging
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Zhixin Wang
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Wenchan Deng
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - X. Chris Le
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
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43
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Wu Z, Fan H, Satyavolu NSR, Wang W, Lake R, Jiang JH, Lu Y. Imaging Endogenous Metal Ions in Living Cells Using a DNAzyme-Catalytic Hairpin Assembly Probe. Angew Chem Int Ed Engl 2017; 56:8721-8725. [PMID: 28557357 PMCID: PMC5814595 DOI: 10.1002/anie.201703540] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/03/2017] [Indexed: 12/16/2022]
Abstract
DNAzymes are a promising platform for metal ion detection, and a few DNAzyme-based sensors have been reported to detect metal ions inside cells. However, these methods required an influx of metal ions to increase their concentrations for detection. To address this major issue, the design of a catalytic hairpin assembly (CHA) reaction to amplify the signal from photocaged Na+ -specific DNAzyme to detect endogenous Na+ inside cells is reported. Upon light activation and in the presence of Na+ , the NaA43 DNAzyme cleaves its substrate strand and releases a product strand, which becomes an initiator that trigger the subsequent CHA amplification reaction. This strategy allows detection of endogenous Na+ inside cells, which has been demonstrated by both fluorescent imaging of individual cells and flow cytometry of the whole cell population. This method can be generally applied to detect other endogenous metal ions and thus contribute to deeper understanding of the role of metal ions in biological systems.
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Affiliation(s)
- Zhenkun Wu
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Huanhuan Fan
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | | | - WenJing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- State Key Laboratory of Analytical Chemistry for Life Science and School of Chemistry & Chemical Engineering, Nanjing University, N, anjing, 210093, P. R. China
| | - Ryan Lake
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Jian-Hui Jiang
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
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44
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Jafari M, Rezaei M, Kalantari H, Tabarzad M, Daraei B. DNAzyme-aptamer or aptamer-DNAzyme paradigm: Biochemical approach for aflatoxin analysis. Biotechnol Appl Biochem 2017; 65:274-280. [PMID: 28326608 DOI: 10.1002/bab.1563] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/15/2017] [Indexed: 12/22/2022]
Abstract
DNAzyme and aptamer conjugations have already been used for sensitive and accurate detection of several molecules. In this study, we tested the relationship between conjugation orientation of DNAzyme and aflatoxin B1 aptamer and their subsequent peroxidase activity. Circular dichroism (CD) spectroscopy and biochemical analysis were used here to differentiate between these two conjugation patterns. Results showed that DNAzyme-aptamer has more catalytic activity and efficiency than aptamer-DNAzyme. Thereby, DNAzyme-aptamer with its superior efficiency can be used for design and development of more sensitive aflatoxin B1 DNA based biosensors.
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Affiliation(s)
- Marzieh Jafari
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohsen Rezaei
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Toxicology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Heibatullah Kalantari
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Daraei
- Department of Toxicology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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45
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Wu Z, Fan H, Satyavolu NSR, Wang W, Lake R, Jiang JH, Lu Y. Imaging Endogenous Metal Ions in Living Cells Using a DNAzyme-Catalytic Hairpin Assembly Probe. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703540] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zhenkun Wu
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
| | - Huanhuan Fan
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
| | | | - WenJing Wang
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
- State Key Laboratory of Analytical Chemistry for Life Science and School of Chemistry & Chemical Engineering; Nanjing University, N; anjing 210093 P. R. China
| | - Ryan Lake
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
| | - Jian-Hui Jiang
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Yi Lu
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
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46
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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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47
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Cheng N, Shang Y, Xu Y, Zhang L, Luo Y, Huang K, Xu W. On-site detection of stacked genetically modified soybean based on event-specific TM-LAMP and a DNAzyme-lateral flow biosensor. Biosens Bioelectron 2017; 91:408-416. [PMID: 28064126 DOI: 10.1016/j.bios.2016.12.066] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/25/2016] [Accepted: 12/29/2016] [Indexed: 11/26/2022]
Abstract
Stacked genetically modified organisms (GMO) are becoming popular for their enhanced production efficiency and improved functional properties, and on-site detection of stacked GMO is an urgent challenge to be solved. In this study, we developed a cascade system combining event-specific tag-labeled multiplex LAMP with a DNAzyme-lateral flow biosensor for reliable detection of stacked events (DP305423× GTS 40-3-2). Three primer sets, both event-specific and soybean species-specific, were newly designed for the tag-labeled multiplex LAMP system. A trident-like lateral flow biosensor displayed amplified products simultaneously without cross contamination, and DNAzyme enhancement improved the sensitivity effectively. After optimization, the limit of detection was approximately 0.1% (w/w) for stacked GM soybean, which is sensitive enough to detect genetically modified content up to a threshold value established by several countries for regulatory compliance. The entire detection process could be shortened to 120min without any large-scale instrumentation. This method may be useful for the in-field detection of DP305423× GTS 40-3-2 soybean on a single kernel basis and on-site screening tests of stacked GM soybean lines and individual parent GM soybean lines in highly processed foods.
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Affiliation(s)
- Nan Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ying Shang
- Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yuancong Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Li Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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48
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Han H, Huang Q, Liu H, Zhang J. Highly Efficient Cofactors of Cu 2+
-Dependent Deoxyribozymes. ChemistrySelect 2017. [DOI: 10.1002/slct.201700424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Haiyan Han
- School of Pharmacy; East China University of Science and Technology; No. 130 Meilong Road, Xuhui District Shanghai 200237 P. R. China
| | - Qiping Huang
- School of Pharmacy; East China University of Science and Technology; No. 130 Meilong Road, Xuhui District Shanghai 200237 P. R. China
| | - Hui Liu
- School of Pharmacy; East China University of Science and Technology; No. 130 Meilong Road, Xuhui District Shanghai 200237 P. R. China
| | - Jingyan Zhang
- School of Pharmacy; East China University of Science and Technology; No. 130 Meilong Road, Xuhui District Shanghai 200237 P. R. China
- Department of Biochemistry, Molecular Biology, and Biophysics, and the Center for Metals in Biocatalysis; University of Minnesota; Minneapolis, MN 55455 USA
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49
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Alizadeh N, Salimi A, Hallaj R. Hemin/G-Quadruplex Horseradish Peroxidase-Mimicking DNAzyme: Principle and Biosensing Application. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 170:85-106. [DOI: 10.1007/10_2017_37] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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50
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Integrating Deoxyribozymes into Colorimetric Sensing Platforms. SENSORS 2016; 16:s16122061. [PMID: 27918487 PMCID: PMC5191042 DOI: 10.3390/s16122061] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.
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