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He Y, Wang Q, Zhang Q, Wang Y, Jiang Y, Zhao Q, Liu X, Wang F. A Methyl-Engineered DNAzyme for Endogenous Alkyltransferase Monitoring and Self-Sufficient Gene Regulation. SMALL METHODS 2024:e2401160. [PMID: 39295467 DOI: 10.1002/smtd.202401160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Revised: 08/30/2024] [Indexed: 09/21/2024]
Abstract
The on-demand gene regulation is crucial for extensively exploring specific gene functions and developing personalized gene therapeutics, which shows great promise in precision medicines. Although some nucleic acid-based gene regulatory tools (antisense oligonucleotides and small interfering RNAs) are devised for achieving on-demand activation, the introduction of chemical modifications may cause undesired side effects, thereby impairing the gene regulatory efficacy. Herein, a methyl-engineered DNAzyme (MeDz) is developed for the visualization of endogenous alkyltransferase (AGT) and the simultaneous self-sufficiently on-demand gene regulation. The catalytic activity of DNAzyme can be efficiently blocked by O6-methylguanine (O6MeG) modification and specifically restored via the AGT-mediated DNA-repairing pathway. This simply designed MeDz is demonstrated to reveal AGT of varying expression levels in different cells, opening the possibility to explore the AGT-related biological processes. Moreover, the AGT-guided MeDz exhibits cell-selective regulation on the human early growth response-1 (EGR-1) gene, with efficient gene repression in breast cancer cells and low effectiveness in normal cells. The proposed MeDz offers an attractive strategy for on-demand gene regulation, displaying great potential in biomedical applications.
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Affiliation(s)
- Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Qing Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Qingqing Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Yifei Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuqian Jiang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Provincial Clinical Research Center for Intestinal and Colorectal Diseases, Hubei Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Provincial Clinical Research Center for Intestinal and Colorectal Diseases, Hubei Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, 430071, China
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2
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Rath WH, Göstl R, Herrmann A. Mechanochemical Activation of DNAzyme by Ultrasound. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306236. [PMID: 38308193 PMCID: PMC10885644 DOI: 10.1002/advs.202306236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/11/2024] [Indexed: 02/04/2024]
Abstract
Controlling the activity of DNAzymes by external triggers is an important task. Here a temporal control over DNAzyme activity through a mechanochemical pathway with the help of ultrasound (US) is demonstrated. The deactivation of the DNAzyme is achieved by hybridization to a complementary strand generated through rolling circle amplification (RCA), an enzymatic polymerization process. Due to the high molar mass of the resulting polynucleic acids, shear force can be applied on the RCA strand through inertial cavitation induced by US. This exerts mechanical force and leads to the cleavage of the base pairing between RCA strand and DNAzyme, resulting in the recovery of DNAzyme activity. This is the first time that this release mechanism is applied for the activation of catalytic nucleic acids, and it has multiple advantages over other stimuli. US has higher penetration depth into tissues compared to light, and it offers a more specific stimulus than heat, which has also limited use in biological systems due to cell damage caused by hyperthermia. This approach is envisioned to improve the control over DNAzyme activity for the development of reliable and specific sensing applications.
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Affiliation(s)
- Wolfgang H. Rath
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
- DWI – Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
| | - Robert Göstl
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
- DWI – Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
| | - Andreas Herrmann
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
- DWI – Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
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3
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Yan J, Ma X, Liang D, Ran M, Zheng D, Chen X, Zhou S, Sun W, Shen X, Zhang H. An autocatalytic multicomponent DNAzyme nanomachine for tumor-specific photothermal therapy sensitization in pancreatic cancer. Nat Commun 2023; 14:6905. [PMID: 37903795 PMCID: PMC10616286 DOI: 10.1038/s41467-023-42740-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023] Open
Abstract
Multicomponent deoxyribozymes (MNAzymes) have great potential in gene therapy, but their ability to recognize disease tissue and further achieve synergistic gene regulation has rarely been studied. Herein, Arginylglycylaspartic acid (RGD)-modified Distearyl acylphosphatidyl ethanolamine (DSPE)-polyethylene glycol (PEG) (DSPE-PEG-RGD) micelle is prepared with a DSPE hydrophobic core to load the photothermal therapy (PTT) dye IR780 and the calcium efflux pump inhibitor curcumin. Then, the MNAzyme is distributed into the hydrophilic PEG layer and sealed with calcium phosphate through biomineralization. Moreover, RGD is attached to the outer tail of PEG for tumor targeting. The constructed nanomachine can release MNAzyme and the cofactor Ca2+ under acidic conditions and self-assemble into an active mode to cleave heat shock protein (HSP) mRNA by consuming the oncogene miRNA-21. Silencing miRNA-21 enhances the expression of the tumor suppressor gene PTEN, leading to PTT sensitization. Meanwhile, curcumin maintains high intracellular Ca2+ to further suppress HSP-chaperone ATP by disrupting mitochondrial Ca2+ homeostasis. Therefore, pancreatic cancer is triple-sensitized to IR780-mediated PTT. The in vitro and in vivo results show that the MNAzyme-based nanomachine can strongly regulate HSP and PTEN expression and lead to significant pancreatic tumor inhibition under laser irradiation.
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Affiliation(s)
- Jiaqi Yan
- Joint Centre of Translational Medicine, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Xiaodong Ma
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Danna Liang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Meixin Ran
- Joint Centre of Translational Medicine, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Dongdong Zheng
- Department of Ultrasound, Fudan University Shanghai Cancer Center, Shanghai, 200032, PR China
| | - Xiaodong Chen
- Joint Centre of Translational Medicine, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shichong Zhou
- Department of Ultrasound, Fudan University Shanghai Cancer Center, Shanghai, 200032, PR China
| | - Weijian Sun
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
| | - Xian Shen
- Joint Centre of Translational Medicine, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Hongbo Zhang
- Joint Centre of Translational Medicine, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
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4
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Cui M, Zhang D, Wang Q, Chao J. An intelligent, autocatalytic, DNAzyme biocircuit for amplified imaging of intracellular microRNAs. NANOSCALE 2023; 15:578-587. [PMID: 36533380 DOI: 10.1039/d2nr05165f] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
DNAzymes hold great promise as transducing agents for the analysis of intracellular biomarkers. However, their low intracellular delivery efficiency and limited signal amplification capability (including an additional supply of cofactors) hinder their application in low-abundance biomarker analysis. Herein, a general strategy to design an intelligent, autocatalytic, DNAzyme biocircuit is developed for amplified microRNA imaging in living cells. The DNAzyme biocircuit is constructed based on a nanodevice composed of catalytic hairpin assembly (CHA) and DNAzyme biocatalytic functional units, sustained by Au nanoparticles (AuNPs) and MnO2 nanosheets (CD/AM nanodevices). Once the CD/AM nanodevices are endocytosed by cells, the MnO2 nanosheets are reduced by intracellular glutathione (GSH), which not only releases the different units of the DNAzyme circuit, but also generates the cofactor Mn2+ for DNAzyme autocatalysis. The intracellular analytes could trigger the coordinated cross-activation of CHA and autocatalytic DNAzymes on AuNPs, enabling reliable and accurate detection of miRNAs in living cells. This intelligent autocatalytic multilayer DNAzyme biocircuit can effectively avoid signal leakage and obtain high amplification gain, expanding the application of programmable complex DNA nanocircuits in biosensing, nanomaterial assembly, and biomedicine.
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Affiliation(s)
- Meirong Cui
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
| | - Dan Zhang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
| | - Qingfu Wang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
| | - Jie Chao
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
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5
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Yang P, Zhou R, Hu J, Du L, Li F, Chen J, Hou X. Lanthanide Encoded Logically Gated Micromachine for Simultaneous Detection of Nucleic Acids and Proteins by Elemental Mass Spectrometry. Anal Chem 2022; 94:17746-17750. [PMID: 36480455 DOI: 10.1021/acs.analchem.2c04494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA-based logic computing potentially for analysis of biomarker inputs and generation of oligonucleotide signal outputs is of great interest to scientists in diverse areas. However, its practical use for sensing of multiple biomarkers is limited by the universality and robustness. Based on a proximity assay, a lanthanide encoded logically gated micromachine (LGM-Ln) was constructed in this work, which is capable of responding to multiplex inputs in biological matrices. Under the logic function controls triggered by inputs and a Boolean "AND" algorithm, it is followed by an amplified "ON" signal to indicate the analytes (inputs). In this logically gated sensing system, the whole computational process does not involve strand displacement in an intermolecular reaction, and a threshold-free design is employed to generate the 0 and 1 computation via intraparticle cleavage, which facilitates the computation units and makes the "computed values" more reliable. By simply altering the affinity ligands for inputs' biorecognition, LGM-Ln can also be extended to multi-inputs mode and produce the robust lanthanide encoded outputs in the whole human serum for sensing nucleic acids (with the detection limit of 10 pM) and proteins (with the detection limit of 20 pM). Compared with a logically gated micromachine encoded with fluorophores, the LGM-Ln has higher resolution and no spectral overlaps for multiple inputs, thus holding great promise in multiplex analyses and clinical diagnosis.
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Affiliation(s)
- Peng Yang
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, China.,Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Rongxing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Hu
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Lijie Du
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Junbo Chen
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xiandeng Hou
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China.,Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
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6
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Xiao X, Chen M, Zhang Y, Li L, Peng Y, Li J, Zhou W. Hemin-incorporating DNA nanozyme enabling catalytic oxygenation and GSH depletion for enhanced photodynamic therapy and synergistic tumor ferroptosis. J Nanobiotechnology 2022; 20:410. [PMID: 36109814 PMCID: PMC9479271 DOI: 10.1186/s12951-022-01617-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Photodynamic therapy (PDT) has emerged as a promising tumor treatment method via light-triggered generation of reactive oxygen species (ROS) to kill tumor cells. However, the efficacy of PDT is usually restricted by several biological limitations, including hypoxia, excess glutathione (GSH) neutralization, as well as tumor resistance. To tackle these issues, herein we developed a new kind of DNA nanozyme to realize enhanced PDT and synergistic tumor ferroptosis. The DNA nanozyme was constructed via rolling circle amplification, which contained repeat AS1411 G quadruplex (G4) units to form multiple G4/hemin DNAzymes with catalase-mimic activity. Both hemin, an iron-containing porphyrin cofactor, and chlorine e6 (Ce6), a photosensitizer, were facilely inserted into G4 structure with high efficiency, achieving in-situ catalytic oxygenation and photodynamic ROS production. Compared to other self-oxygen-supplying tools, such DNA nanozyme is advantageous for high biological stability and compatibility. Moreover, the nanostructure could achieve tumor cells targeting internalization and intranuclear transport of Ce6 by virtue of specific nucleolin binding of AS1411. The nanozyme could catalyze the decomposition of intracellular H2O2 into oxygen for hypoxia relief as evidenced by the suppression of hypoxia-inducible factor-1α (HIF-1α), and moreover, GSH depletion and cell ferroptosis were also achieved for synergistic tumor therapy. Upon intravenous injection, the nanostructure could effectively accumulate into tumor, and impose multi-modal tumor therapy with excellent biocompatibility. Therefore, by integrating the capabilities of O2 generation and GSH depletion, such DNA nanozyme is a promising nanoplatform for tumor PDT/ferroptosis combination therapy.
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Affiliation(s)
- Xiaoxiong Xiao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Min Chen
- Department of Thoracic Surgery, The Second People's Hospital of Huaihua City, Huaihua, China
| | - Yuchen Zhang
- Department of Pharmacy, Yichun People's Hospital, Yichun, Jiangxi, China
| | - Liang Li
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Ying Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Junyu Li
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, China.
| | - Wenhu Zhou
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China.
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7
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Jiao Y, Shang Y, Li N, Ding B. DNA-based enzymatic systems and their applications. iScience 2022; 25:104018. [PMID: 35313688 PMCID: PMC8933709 DOI: 10.1016/j.isci.2022.104018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA strands with unique secondary structures can catalyze various chemical reactions and mimic natural enzymes with the assistance of cofactors, which have attracted much research attention. At the same time, the emerging DNA nanotechnology provides an efficient platform to organize functional components of the enzymatic systems and regulate their catalytic performances. In this review, we summarize the recent progress of DNA-based enzymatic systems. First, DNAzymes (Dzs) are introduced, and their versatile utilities are summarized. Then, G-quadruplex/hemin (G4/hemin) Dzs with unique oxidase/peroxidase-mimicking activities and representative examples where these Dzs served as biosensors are explicitly elaborated. Next, the DNA-based enzymatic cascade systems fabricated by the structural DNA nanotechnology are depicted. In addition, the applications of catalytic DNA nanostructures in biosensing and biomedicine are included. At last, the challenges and the perspectives of the DNA-based enzymatic systems for practical applications are also discussed.
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8
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Harding BI, Pollak NM, Stefanovic D, Macdonald J. Complexing deoxyribozymes with RNA aptamers for detection of the small molecule theophylline. Biosens Bioelectron 2022; 198:113774. [PMID: 34823962 DOI: 10.1016/j.bios.2021.113774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 10/17/2021] [Accepted: 11/05/2021] [Indexed: 11/28/2022]
Abstract
Biointegrative information processing systems offer a great advantage to autonomous biodevices, as their capacity for biological computation provides the ability to sense the state of more complex environments and better integrate with downstream biological regulation systems. Deoxyribozymes (DNAzymes) and aptamers are of interest to such computational biosensing systems due to the enzymatic properties of DNAzymes and the ligand-inducible conformational structures of aptamers. Herein, we describe a novel method for providing ligand-responsive allosteric control to a DNAzyme using an RNA aptamer. We designed a NOT-logic-compliant E6 DNAzyme to be complementary to an RNA aptamer targeting theophylline, such that the aptamer competitively interacted with either theophylline or the DNAzyme, and disabled the DNAzyme only when theophylline concentration was below a given threshold. Out of our seven designed "complexing aptazymes," three demonstrated effective theophylline-responsive allosteric regulation (2.84 ± 3.75%, 4.97 ± 2.92%, and 8.91 ± 4.19% activity in the absence of theophylline; 46.29 ± 3.36%, 50.70 ± 10.15%, and 61.26 ± 6.18% activity in the presence of theophylline). Moreover, the same three complexing aptazymes also demonstrated the ability to semi-quantitatively determine the concentration of theophylline present in solution, successfully discriminating between therapeutically ineffective (<20 μM), safe (20-100 μM), and toxic (>100 μM) theophylline concentrations. Our method of using an RNA aptamer for ligand-responsive allosteric control of a DNAzyme expands the way aptamers can be configured for biosensing, and suggests a pathway for embedding DNAzymes to provide enhanced information processing and control of biological systems.
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Affiliation(s)
- Bradley I Harding
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia; School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Nina M Pollak
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia; School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia; CSIRO Synthetic Biology Future Science Platform, GPO Box 1700, Canberra, Australian Capital Territory, 2601, Australia
| | - Darko Stefanovic
- Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, United States; Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, United States; Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, United States
| | - Joanne Macdonald
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia; School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia.
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Gao Y, Zhang S, Wu C, Li Q, Shen Z, Lu Y, Wu ZS. Self-Protected DNAzyme Walker with a Circular Bulging DNA Shield for Amplified Imaging of miRNAs in Living Cells and Mice. ACS NANO 2021; 15:19211-19224. [PMID: 34854292 DOI: 10.1021/acsnano.1c04260] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Abnormal expression of miRNAs is often detected in various human cancers. DNAzyme machines combined with gold nanoparticles (AuNPs) hold promise for detecting specific miRNAs in living cells but show short circulation time due to the fragility of catalytic core. Using miRNA-21 as the model target, by introducing a circular bulging DNA shield into the middle of the catalytic core, we report herein a self-protected DNAzyme (E) walker capable of fully stepping on the substrate (S)-modified AuNP for imaging intracellular miRNAs. The DNAzyme walker exhibits 5-fold enhanced serum resistance and more than 8-fold enhanced catalytic activity, contributing to the capability to image miRNAs much higher than commercial transfection reagent and well-known FISH technique. Diseased cells can accurately be distinguished from healthy cells. Due to its universality, DNAzyme walker can be extended for imaging other miRNAs only by changing target binding domain, indicating a promising tool for cancer diagnosis and prognosis.
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Affiliation(s)
- Yansha Gao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Songbai Zhang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- College of Chemistry and Materials Engineering, Hunan University of Arts and Science, Changde 415000, China
| | - Chengwei Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Qian Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
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10
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Lee CY, Liao CH, Fang NM, Hsieh YZ. DNAzyme-Amplified Label-Free Biosensor for the Simple and Sensitive Detection of Pyrophosphatase. BIOSENSORS 2021; 11:422. [PMID: 34821638 PMCID: PMC8615721 DOI: 10.3390/bios11110422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The level of pyrophosphatase (PPase) expression has been suggested as a potential biomarker of various cancers, and its prognostic value has been evaluated in patients suffering from lung cancer, colorectal cancer, and hyperthyroidism. However, the detection of PPase usually needs specific materials that require complicated, time-consuming reactions with restricted linear range and sensitivity, limiting their application in early clinical diagnosis. Herein, we developed a DNAzyme-based biosensor for the detection of PPase. In the presence of PPase, pyrophosphate (PPi) and Cu2+ ions released from the PPi-Cu2+-PPi complex induce the cleavage of the DNAzyme and the corresponding substrate. An apurinic/apyrimidinic (AP) site was elaborately designed within substrates that could encase the fluorophore 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND). The fluorescence of ATMND was initially quenched but restored when the DNAzyme/substrate complex was hydrolyzed with the release of ATMND. In this way, the PPase activity can be estimated by detecting the increased fluorescence of the released ATMND. Under optimized conditions, the activity of PPase could be analyzed at concentrations from 0.5 to 1000 mU, with the lowest detectable concentration being 0.5 mU. This work lays a foundation for developing a DNAzyme-amplified fluorescent biosensor with a high sensitivity, a wide linear range, and single-step operation for use as an easy diagnostic for PPase analysis.
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Affiliation(s)
- Cheng-Yu Lee
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (C.-Y.L.); (C.-H.L.); (N.-M.F.)
| | - Chi-Hsiang Liao
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (C.-Y.L.); (C.-H.L.); (N.-M.F.)
| | - Nei-Mei Fang
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (C.-Y.L.); (C.-H.L.); (N.-M.F.)
| | - You-Zung Hsieh
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (C.-Y.L.); (C.-H.L.); (N.-M.F.)
- Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
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11
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Wang W, Shen Y, Wang F, Liu Y, Liu X. Bio-inspired dynamic biomolecule assembling for fine regulation of protein activity. Chem Commun (Camb) 2021; 57:11205-11208. [PMID: 34622901 DOI: 10.1039/d1cc03926a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A versatile approach for the fine control of DNA-based hierarchical assembly via dual stimuli and two assembly strategies is developed. Moreover, with a reasonable design of functional thrombin aptamer structures on the formed DNA nanoassembly, it can achieve precise regulation of thrombin activity.
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Affiliation(s)
- Wenxiao Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China. .,College of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, P. R. China
| | - Yu Shen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China.
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China.
| | - Ying Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China.
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China.
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12
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Xi Y, Xie X, Peng Y, Liu P, Ding J, Zhou W. DNAzyme-adsorbed polydopamine@MnO 2 core-shell nanocomposites for enhanced photothermal therapy via the self-activated suppression of heat shock protein 70. NANOSCALE 2021; 13:5125-5135. [PMID: 33651054 DOI: 10.1039/d0nr08845e] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Photothermal therapy (PTT) is a promising tumor treatment modality, but its efficacy is strictly hindered by abnormally upregulated heat shock proteins (HSPs) in tumor cells under heat stress. Herein, we developed a flower-like MnO2-coated polydopamine (PDA@MnO2) core-shell nanoplatform with the surface adsorption of HSP70-silencing DNAzyme (DZ) for enhanced PPT. The PDA core acted as a robust photothermal agent, and also as a reductant to allow the surface growth of MnO2via an in situ reduction of KMnO4. The MnO2 shell enabled a rapid and efficient adsorption of DZ, and more importantly, acted as a metal reservoir to release Mn2+ in response to intracellular stimuli for the in situ activation of DZ, which addressed the key limitation of DZ for biological applications, i.e., metal-dependent activity. As a result, HSP70 was remarkably suppressed for improved PTT efficacy upon laser irradiation, which was explicitly demonstrated both in vitro and in vivo. Upon intravenous injection, the nanosystem could effectively accumulate in the tumor, and impose potent PTT for complete tumor elimination via inducing tumor cell apoptosis, but without any noticeable toxicity. This work provides a promising nanosystem for enhanced PTT via silencing resistance-related genes, and offers ideas for the design of self-activated gene therapy platforms using DZ.
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Affiliation(s)
- Yang Xi
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China.
| | - Xin Xie
- School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Ying Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China.
| | - Peng Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China.
| | - Jinsong Ding
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China.
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China. and Academician Workstation, Changsha Medical University, Changsha 410219, China
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13
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Chen C, Wu R, Wang B. Development of a neuron model based on DNAzyme regulation. RSC Adv 2021; 11:9985-9994. [PMID: 35423534 PMCID: PMC8695483 DOI: 10.1039/d0ra10515e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/02/2021] [Indexed: 12/25/2022] Open
Abstract
Neural networks based on DNA molecular circuits play an important role in molecular information processing and artificial intelligence systems. In fact, some DNA molecular systems can become dynamic units with the assistance of DNAzymes. The complex DNA circuits can spontaneously induce corresponding feedback behaviors when their inputs changed. However, most of the reported DNA neural networks have been implemented by the toehold-mediated strand displacement (TMSD) method. Therefore, it was important to develop a method to build a neural network utilizing the TMSD mechanism and adding a mechanism to account for modulation by DNAzymes. In this study, we designed a model of a DNA neuron controlled by DNAzymes. We proposed an approach based on the DNAzyme modulation of neuronal function, combing two reaction mechanisms: DNAzyme digestion and TMSD. Using the DNAzyme adjustment, each component simulating the characteristics of neurons was constructed. By altering the input and weight of the neuron model, we verified the correctness of the computational function of the neurons. Furthermore, in order to verify the application potential of the neurons in specific functions, a voting machine was successfully implemented. The proposed neuron model regulated by DNAzymes was simple to construct and possesses strong scalability, having great potential for use in the construction of large neural networks.
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Affiliation(s)
- Cong Chen
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University Dalian 116622 China
| | - Ranfeng Wu
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University Dalian 116622 China
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14
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Li Y, Liu J. Highly Specific Recognition of Guanosine Using Engineered Base-Excised Aptamers. Chemistry 2020; 26:13644-13651. [PMID: 32700427 DOI: 10.1002/chem.202001835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/20/2020] [Indexed: 12/18/2022]
Abstract
Purines and their derivatives are highly important molecules in biology for nucleic acid synthesis, energy storage, and signaling. Although many DNA aptamers have been obtained for binding adenine derivatives such as adenosine, adenosine monophosphate, and adenosine triphosphate, success for the specific binding of guanosine has been limited. Instead of performing new aptamer selections, we report herein a base-excision strategy to engineer existing aptamers to bind guanosine. Both a Na+ -binding aptamer and the classical adenosine aptamer have been manipulated as base-excising scaffolds. A total of seven guanosine aptamers were designed, of which the G16-deleted Na+ aptamer showed the highest bindng specificity and affinity for guanosine with an apparent dissociation constant of 0.78 mm. Single monophosphate difference in the target molecule was also recognizable. The generality of both the aptamer scaffold and excised site were systematically studied. Overall, this work provides a few guanosine binding aptamers by using a non-SELEX method. It also provides deeper insights into the engineering of aptamers for molecular recognition.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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15
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Zhou R, Hu C, Jin Y, Zhang J, Du H, Yang P, Chen J, Hou X, Cheng N. Spatially Constrained DNA Nanomachines To Accelerate Kinetics in Response to External Input: Design and Bioanalysis. Anal Chem 2020; 92:8909-8916. [PMID: 32521999 DOI: 10.1021/acs.analchem.0c00802] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cells take advantage of the spatial organization to accelerate the reaction kinetics of diverse components within a crowded intracellular environment. Inspired by this, we hereby designed a principle of spatial constraint to overcome limitations of response kinetics in DNAzyme-powered DNA nanomachines. First, we proposed the type-1 of spatially constrained DNA nanomachines (scDN-1) by co-localizing the aptamer probe and power unit (DNAzyme), allowing the DNA nanomachines to accomplish faster cyclic cleavage of DNAzyme as intramolecular reactions. To expand the scDN into the clinical practice, Type 2 spatially constrained DNA nanomachines (scDN-2) with constrained antibody probes were then constructed through Holliday junction assembly, which increased the effective local concentration to obtain the improved kinetics. With an accelerated response kinetics, this design principle allows DNA nanomachines to accomplish the response to tumor markers in real patients' samples within 30 min, significantly broadening the bioanalytical applications of DNA nanomachines to clinical practice.
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Affiliation(s)
- Rongxing Zhou
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Changjia Hu
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yanwen Jin
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jie Zhang
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Huan Du
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Peng Yang
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Junbo Chen
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xiandeng Hou
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Nansheng Cheng
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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16
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Safdar S, Lammertyn J, Spasic D. RNA-Cleaving NAzymes: The Next Big Thing in Biosensing? Trends Biotechnol 2020; 38:1343-1359. [PMID: 32473751 DOI: 10.1016/j.tibtech.2020.04.012] [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: 03/02/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023]
Abstract
Nucleic acid enzymes (NAzymes) are nucleic acid molecules with catalytic activity. A subset, the RNA-cleaving NAzyme, is characterized by its substrate of choice: an RNA unit. These enzymes have been used for diverse applications, including biosensor development, akin to their protein counterparts. Owing to their function as both biorecognition elements and signal generators, robust bioassays based entirely on NAzyme molecules have been developed. Additionally, unique mechanisms for integration with other biorecognition elements and signal generation methods have been explored to realize ultrasensitive, specific, and user-friendly biosensors. Furthermore, NAzyme-based bioassays have already broken into the in vitro diagnostics market, with more promise in the pipeline.
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Affiliation(s)
- Saba Safdar
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium.
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
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17
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Cui MR, Li XL, Xu JJ, Chen HY. Acid-Switchable DNAzyme Nanodevice for Imaging Multiple Metal Ions in Living Cells. ACS APPLIED MATERIALS & INTERFACES 2020; 12:13005-13012. [PMID: 32100993 DOI: 10.1021/acsami.0c00987] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Metal-assisted deoxyribozyme catalysis (DNAzyme) has been a general platform for constructing highly sensitive and selective detection sensors of metal ions. However, the "always on" mode of the traditional DNAzyme sensors greatly limits their application in the visual analysis of endogenous metal ions in a complex physiological microenvironment. To overcome this obstacle, a smart acid-switchable DNAzyme nanodevice is designed to control the DNAzyme activity in living cells and achieve simultaneous visualization of metal ions (Zn2+ and Pb2+) in situ. This nanodevice is built on DNAzyme precursors (DPs) and acid-switchable DNA (SW-DNA), precisely responding to pH variations in the range of 4.5-7.0, and the state of the three-strand hybridization of DPs successfully renders the DNAzymes inactive before being transported into cells. Once the nanodevice is taken up into living cells, the SW-DNA will change the configuration from linear to triplex in the acidic intracellular compartments (lysosomes, pH ∼4.5 to 5.0) and then the strands hybridized with the SW-DNA are liberated and subsequently react with DPs to form the active DNAzyme, which can further realize multi-imaging of intracellular metal ions. Moreover, this strategy has broad prospects as a powerful platform for constructing various acid-switchable nanodevices for visual analysis of multiple biomolecules in living cells.
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Affiliation(s)
- Mei-Rong Cui
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Xiang-Ling Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Life Science and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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18
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Minero GAS, Bagnasco M, Fock J, Tian B, Garbarino F, Hansen MF. Automated on-chip analysis of tuberculosis drug-resistance mutation with integrated DNA ligation and amplification. Anal Bioanal Chem 2020; 412:2705-2710. [PMID: 32157358 DOI: 10.1007/s00216-020-02568-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/24/2020] [Accepted: 03/02/2020] [Indexed: 01/14/2023]
Abstract
Detection of a single base mutation in Mycobacterium tuberculosis DNA can provide fast and highly specific diagnosis of antibiotic-resistant tuberculosis. Mutation-specific ligation of padlock probes (PLPs) on the target followed by rolling circle amplification (RCA) is highly specific, but challenging to integrate in a simple microfluidic device due to the low temperature stability of the phi29 polymerase and the interference of phi29 with the PLP annealing and ligation. Here, we utilized the higher operation temperature and temperature stability of Equiphi29 polymerase to simplify the integration of the PLP ligation and RCA steps of an RCA assay in two different strategies performed at uniform temperature. In strategy I, PLP annealing took place off-chip and the PLP ligation and RCA were performed in one pot and the two reactions were clocked by a change of the temperature. For a total assay time of about 1.5 h, we obtained a limit of detection of 2 pM. In strategy II, the DNA ligation mixture and the RCA mixture were separated into two chambers on a microfluidic disc. After on-disc PLP annealing and ligation, the disc was spun to mix reagents and initiate RCA. For a total assay time of about 2 h, we obtained a limit of detection of 5 pM. Graphical abstract.
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Affiliation(s)
- Gabriel Antonio S Minero
- Department of Health Technology, DTU Health Tech, Technical University of Denmark, Building 345C, 2800, Kongens Lyngby, Denmark.
| | - Martina Bagnasco
- Department of Health Technology, DTU Health Tech, Technical University of Denmark, Building 345C, 2800, Kongens Lyngby, Denmark
| | - Jeppe Fock
- BluSense Diagnostics ApS, Fruebjergvej 3, DK-2100, Copenhagen, Denmark
| | - Bo Tian
- Department of Health Technology, DTU Health Tech, Technical University of Denmark, Building 345C, 2800, Kongens Lyngby, Denmark
| | - Francesca Garbarino
- Department of Health Technology, DTU Health Tech, Technical University of Denmark, Building 345C, 2800, Kongens Lyngby, Denmark
| | - Mikkel F Hansen
- Department of Health Technology, DTU Health Tech, Technical University of Denmark, Building 345C, 2800, Kongens Lyngby, Denmark.
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19
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Mitra M, Mahapatra M, Dutta A, Chattopadhyay PK, Deb M, Deb Roy JS, Roy C, Banerjee S, Singha NR. Light-Emitting Multifunctional Maleic Acid- co-2-( N-(hydroxymethyl)acrylamido)succinic Acid- co- N-(hydroxymethyl)acrylamide for Fe(III) Sensing, Removal, and Cell Imaging. ACS OMEGA 2020; 5:3333-3345. [PMID: 32118148 PMCID: PMC7045568 DOI: 10.1021/acsomega.9b03536] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/28/2020] [Indexed: 05/04/2023]
Abstract
The intrinsically fluorescent highly hydrophilic multifunctional aliphatic terpolymer, maleic acid (MA)-co-2-(N-(hydroxymethyl)acrylamido)succinic acid (NHASA)-co-N-(hydroxymethyl)acrylamide (NHMA), that is, 1, was designed and synthesized via C-C/N-C-coupled in situ allocation of a fluorophore monomer, that is, NHASA, composed of amido and carboxylic acid functionalities in the polymerization of two nonemissive MA and NHMA. The scalable and reusable intrinsically fluorescent biocompatible 1 was suitable for sensing and high-performance adsorptive exclusion of Fe(III), along with the imaging of Madin-Darby canine kidney cells. The structure of 1, in situ fluorophore monomer, aggregation-induced enhanced emission, cell-imaging ability, and superadsorption mechanism were studied via microstructural analyses using 1H/13C NMR, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, atomic absorption spectroscopy, ultraviolet-visible spectroscopy, thermogravimetric analysis, dynamic light scattering, high-resolution transmission electron microscopy, solid-state fluorescence, fluorescence lifetime, and fluorescence imaging, along with measuring kinetics, isotherms, and thermodynamic parameters. The location, electronic structures, and geometries of the fluorophore and absorption and emission properties of 1 were investigated using density functional theory and natural transition orbital analyses. The limit of detection and the maximum adsorption capacity were 2.45 × 10-7 M and 542.81 mg g-1, respectively.
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Affiliation(s)
- Madhushree Mitra
- Department
of Leather Technology, Government College of Engineering and Leather
Technology (Post Graduate), Maulana Abul
Kalam Azad University of Technology, Salt Lake City, Kolkata 700106, West Bengal, India
| | - Manas Mahapatra
- Advanced
Polymer Laboratory, Department of Polymer Science and Technology,
Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata 700106, West
Bengal, India
| | - Arnab Dutta
- Advanced
Polymer Laboratory, Department of Polymer Science and Technology,
Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata 700106, West
Bengal, India
| | - Pijush Kanti Chattopadhyay
- Department
of Leather Technology, Government College of Engineering and Leather
Technology (Post Graduate), Maulana Abul
Kalam Azad University of Technology, Salt Lake City, Kolkata 700106, West Bengal, India
| | - Mousumi Deb
- Advanced
Polymer Laboratory, Department of Polymer Science and Technology,
Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata 700106, West
Bengal, India
| | - Joy Sankar Deb Roy
- Advanced
Polymer Laboratory, Department of Polymer Science and Technology,
Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata 700106, West
Bengal, India
| | - Chandan Roy
- Department
of Leather Technology, Government College of Engineering and Leather
Technology (Post Graduate), Maulana Abul
Kalam Azad University of Technology, Salt Lake City, Kolkata 700106, West Bengal, India
- Advanced
Polymer Laboratory, Department of Polymer Science and Technology,
Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata 700106, West
Bengal, India
| | - Snehasis Banerjee
- Department
of Chemistry, Government College of Engineering and Leather Technology
(Post Graduate), Maulana Abul Kalam Azad
University of Technology, Salt Lake City, Kolkata 700106, West Bengal, India
| | - Nayan Ranjan Singha
- Advanced
Polymer Laboratory, Department of Polymer Science and Technology,
Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata 700106, West
Bengal, India
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20
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Yang P, Deng P, Du H, Hou X, Zhang J, Chen J, Hou X, Zhou R. Building an anti-interfering DNAzyme-powered micromachine resistant to being inhibited by biological matrices. Chem Commun (Camb) 2020; 56:2658-2661. [PMID: 32022034 DOI: 10.1039/c9cc08515g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A DNAzyme-powered micromachine with anti-interfering properties and displaying resistance to being inhibited by biological matrices was built.
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Affiliation(s)
- Peng Yang
- Analytical & Testing Center
- Sichuan University
- 29 Wangjiang Road
- Chengdu
- China
| | - Ping Deng
- Nephrology Division
- the Third Affiliated Hospital of Sun Yat-sen University
- Guangzhou
- China
| | - Huan Du
- Analytical & Testing Center
- Sichuan University
- 29 Wangjiang Road
- Chengdu
- China
| | - Xin Hou
- Key Lab of Green Chem & Tech of MOE, and College of Chemistry, Sichuan University
- Chengdu
- China
| | - Jie Zhang
- Biliary Surgical Department of West China Hospital
- Sichuan University
- Chengdu
- China
| | - Junbo Chen
- Analytical & Testing Center
- Sichuan University
- 29 Wangjiang Road
- Chengdu
- China
| | - Xiandeng Hou
- Analytical & Testing Center
- Sichuan University
- 29 Wangjiang Road
- Chengdu
- China
| | - Rongxing Zhou
- Biliary Surgical Department of West China Hospital
- Sichuan University
- Chengdu
- China
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21
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Mahapatra M, Dutta A, Roy JSD, Mitra M, Mahalanobish S, Sanfui MDH, Banerjee S, Chattopadhyay PK, Sil PC, Singha NR. Fluorescent Terpolymers via In Situ Allocation of Aliphatic Fluorophore Monomers: Fe(III) Sensor, High-Performance Removals, and Bioimaging. Adv Healthc Mater 2019; 8:e1900980. [PMID: 31664786 DOI: 10.1002/adhm.201900980] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/21/2019] [Indexed: 12/22/2022]
Abstract
Herein, purely aliphatic intrinsically fluorescent terpolymers, i.e., 1 and 2, are synthesized through one-pot solution polymerization via N-H functionalized and multi C-C/C-N coupled in situ protrusion of fluorescent monomers using two nonemissive monomers. These scalable terpolymers are suitable for highly selective Fe(III) sensing, high-performance exclusion of Fe(III), logic function and the imaging of normal mammalian Madin-Darby canine kidney and human osteosarcoma cancer cell lines. The structures of terpolymers, in situ attachment of fluorescent monomers, clusteroluminescence, adsorption-mechanism, and cell-imaging abilities are understood via unadsorbed and/or adsorbed microstructural analyses using 1 H/13 C NMR, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, UV-vis spectroscopy, atomic absorption spectroscopy, thermogravimetric analysis, high-resolution transmission electron microscopy, dynamic light scattering, fluorescence imaging, and fluorescence lifetime. The geometries, electronic structures, location of fluorophores, and singlet-singlet absorption and emission of terpolymers are examined using density functional theory (DFT) and time-dependent DFT. For the precise identification of fluorophores, transition from occupied natural transition orbitals (NTOs) to unoccupied NTOs is computed. For 1/2, limit of detection (LOD) values and adsorption capacities are 6.0 × 10-7 /8.0 × 10-7 m and 147.82/120.56 mg g-1 at pHi = 7.0 and 303 K, respectively. The overall properties of 1 are more advantageous compared to 2 in sensing, cell imaging, and adsorptive exclusion of Fe(III).
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Affiliation(s)
- Manas Mahapatra
- Advanced Polymer LaboratoryDepartment of Polymer Science and TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Arnab Dutta
- Advanced Polymer LaboratoryDepartment of Polymer Science and TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Joy Sankar Deb Roy
- Advanced Polymer LaboratoryDepartment of Polymer Science and TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Madhushree Mitra
- Department of Leather TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Sushweta Mahalanobish
- Division of Molecular MedicineBose Institute P‐1/12, CIT Scheme VII M Kolkata 700054 West Bengal India
| | - MD Hussain Sanfui
- Advanced Polymer LaboratoryDepartment of Polymer Science and TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Snehasis Banerjee
- Department of ChemistryGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Pijush Kanti Chattopadhyay
- Department of Leather TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Parames C. Sil
- Division of Molecular MedicineBose Institute P‐1/12, CIT Scheme VII M Kolkata 700054 West Bengal India
| | - Nayan Ranjan Singha
- Advanced Polymer LaboratoryDepartment of Polymer Science and TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
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22
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Li C, Xue C, Wang J, Luo M, Shen Z, Wu ZS. Oriented Tetrahedron-Mediated Protection of Catalytic DNA Molecular-Scale Detector against in Vivo Degradation for Intracellular miRNA Detection. Anal Chem 2019; 91:11529-11536. [DOI: 10.1021/acs.analchem.9b00860] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Congcong Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Fujian Engineering Research Center for Drug and Diagnoses-Treat of Photodynamic Therapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Chang Xue
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Fujian Engineering Research Center for Drug and Diagnoses-Treat of Photodynamic Therapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Jue Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, People’s Republic of China
| | - Mengxue Luo
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Fujian Engineering Research Center for Drug and Diagnoses-Treat of Photodynamic Therapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, People’s Republic of China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Fujian Engineering Research Center for Drug and Diagnoses-Treat of Photodynamic Therapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, People’s Republic of China
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23
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Wang S, Ding J, Zhou W. An aptamer-tethered, DNAzyme-embedded molecular beacon for simultaneous detection and regulation of tumor-related genes in living cells. Analyst 2019; 144:5098-5107. [PMID: 31373344 DOI: 10.1039/c9an01097a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Simultaneous detection and regulation of tumor-related genes presents a promising strategy for early diagnosis and treatment of cancer, but achieving this has been a huge challenge for both chemical and biomedical communities. Towards this objective, we have devised a novel aptamer-tethered, DNAzyme-embedded molecular beacon (MB) for multiple functions in cancer cells. In this design, a tumor targeting aptamer was employed to specifically deliver the sensor into cancer cells for target gene detection, and an RNA-cleaving DNAzyme was embedded to realize gene regulation. Both aptamer-tethering and DNAzyme-embedding had little influence on the sensor performance, with a detection limit of ∼2 nM and high specificity. After delivering into tumor cells, our device could monitor the tumor-related genes by producing detectable fluorescence signals, and regulate the gene expression at both mRNA and protein levels as evidenced by the RT-PCR and western blot analyses. This study provides a simple and efficient strategy to rationally combine various functional nucleic acids for multi-functional applications in living cells, which hold great potential for cancer diagnosis and therapy.
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Affiliation(s)
- Shengfeng Wang
- Xiangya School of Pharmaceutical Sciences, State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410013, China. and Department of Pharmacy, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
| | - Jinsong Ding
- Xiangya School of Pharmaceutical Sciences, State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410013, China.
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410013, China.
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24
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Du H, Yang P, Hou X, Zhou R, Hou X, Chen J. Expanding DNA nanomachine functionality through binding-induced DNA output for application in clinical diagnosis. Chem Commun (Camb) 2019; 55:3610-3613. [PMID: 30843913 DOI: 10.1039/c9cc01228a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Herein, we describe two homogeneous conversion systems that can convert protein recognition into the release of predesigned output DNA for the activation of DNA nanomachines.
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Affiliation(s)
- Huan Du
- College of Chemistry
- Sichuan University
- Chengdu
- China
| | - Peng Yang
- Analytical & Testing Centre
- Sichuan University
- Chengdu
- China
| | - Xin Hou
- College of Chemistry
- Sichuan University
- Chengdu
- China
| | - Rongxing Zhou
- Biliary Surgical Department
- West China Hospital
- Sichuan University
- Chengdu
- China
| | - Xiandeng Hou
- College of Chemistry
- Sichuan University
- Chengdu
- China
- Analytical & Testing Centre
| | - Junbo Chen
- Analytical & Testing Centre
- Sichuan University
- Chengdu
- China
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25
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Yang K, Wang H, Ma N, Zeng M, Luo H, He D. Programmable Target-Initiated DNAzyme Walker Walking along a Spatially Isolated and Highly Hybridizable Substrate Track on a Nanoparticle Surface. ACS APPLIED MATERIALS & INTERFACES 2018; 10:44546-44553. [PMID: 30489066 DOI: 10.1021/acsami.8b16408] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Synthetic DNA machines that operate on the nanoscale three-dimensional (3D) track have attracted rapidly increasing interest because of their potential in biocomputing, drug delivery, and biosensing applications. Current nanoscale 3D DNA tracks are typically created by self-assembling thiolated oligonucleotides at gold nanoparticle (AuNP) surfaces via the strong Au-S chemistry. However, it remains challenging to accurately control the conformation and orientation of the 3D DNA track on AuNP surfaces and finely adjust the hybridization ability of the 3D track. Herein, we describe for the first time a polyadenine (polyA)-based, spatially isolated 3D DNA track, on which a target-initiated DNAzyme walker moves by a burnt-bridge mechanism with improved efficiency and processivity. PolyA serves as an anchoring block for preferential binding with the AuNP surface, and the appended substrate block adopts an upright conformation that favors the hybridization and subsequent DNAzyme-mediated cleavage. The operation of this target-initiated DNAzyme walker was monitored in real time and at a single-particle level. We tested the cleavage efficiency of 3D substrates with various polyA block lengths, which displayed that the DNAzyme activity was remarkably improved as compared with a thiol-based 3D track. We also explored bioanalytical applications of this DNAzyme nanomachine by movement-triggered cascade signal amplification.
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Affiliation(s)
- Ke Yang
- Hunan Key Laboratory Cultivation Base of the Research and Development of Novel Pharmaceutical Preparations, Department of Human Anatomy, Histology and Embryology , Changsha Medical University , Changsha 410219 , China
| | - Huizhen Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | - Ning Ma
- Hunan Key Laboratory Cultivation Base of the Research and Development of Novel Pharmaceutical Preparations, Department of Human Anatomy, Histology and Embryology , Changsha Medical University , Changsha 410219 , China
| | - Ming Zeng
- Hunan Key Laboratory Cultivation Base of the Research and Development of Novel Pharmaceutical Preparations, Department of Human Anatomy, Histology and Embryology , Changsha Medical University , Changsha 410219 , China
| | - Huaiqing Luo
- Hunan Key Laboratory Cultivation Base of the Research and Development of Novel Pharmaceutical Preparations, Department of Human Anatomy, Histology and Embryology , Changsha Medical University , Changsha 410219 , China
| | - Dinggeng He
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences , Hunan Normal University , Changsha 410081 , China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China
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26
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Kumar S, Jain S, Dilbaghi N, Ahluwalia AS, Hassan AA, Kim KH. Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications. Trends Biochem Sci 2018; 44:190-213. [PMID: 30559045 DOI: 10.1016/j.tibs.2018.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023]
Abstract
DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes is expected to open the door to several healthcare applications. Therefore, a significant portion of this review is dedicated to various biological applications of DNAzymes, such as sensing, therapeutics, and nanodevices. In addition, discussion is further extended to the barriers encountered for the real-life application of these DNAzymes to provide a foundation for future research.
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Affiliation(s)
- Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India; Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA.
| | - Shikha Jain
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | | | - Ashraf Aly Hassan
- Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
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27
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Tian B, Han Y, Wetterskog E, Donolato M, Hansen MF, Svedlindh P, Strömberg M. MicroRNA Detection through DNAzyme-Mediated Disintegration of Magnetic Nanoparticle Assemblies. ACS Sens 2018; 3:1884-1891. [PMID: 30188122 DOI: 10.1021/acssensors.8b00850] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA-assembled nanoparticle superstructures offer numerous bioresponsive properties that can be utilized for point-of-care diagnostics. Functional DNA sequences such as deoxyribozymes (DNAzymes) provide novel bioresponsive strategies and further extend the application of DNA-assembled nanoparticle superstructures. In this work, we describe a microRNA detection biosensor that combines magnetic nanoparticle (MNP) assemblies with DNAzyme-assisted target recycling. The DNA scaffolds of the MNP assemblies contain substrate sequences for DNAzyme and can form cleavage catalytic structures in the presence of target DNA or RNA sequences, leading to rupture of the scaffolds and disintegration of the MNP assemblies. The target sequences are preserved during the cleavage reaction and release into the suspension to trigger the digestion of multiple DNA scaffolds. The high local concentration of substrate sequences in the MNP assemblies reduces the diffusion time for target recycling. The concentration of released MNPs, which is proportional to the concentration of the target, can be quantified by a 405 nm laser-based optomagnetic sensor. For the detection of let-7b in 10% serum, after 1 h of isothermal reaction at 50 °C, we found a linear detection range between 10 pM and 100 nM with a limit of detection of 6 pM. For the quantification of DNA target in buffer solution, a limit of detection of 1.5 pM was achieved. Compared to protein enzyme-based microRNA detection methods, the proposed DNAzyme-based biosensor has an increased stability, a reduced cost and a possibility to be used in living cells, all of which are valuable features for biosensing applications.
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Affiliation(s)
- Bo Tian
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech,
Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Yuanyuan Han
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
| | - Erik Wetterskog
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
| | - Marco Donolato
- BluSense Diagnostics, Fruebjergvej 3, DK-2100 Copenhagen, Denmark
| | - Mikkel Fougt Hansen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech,
Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Peter Svedlindh
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
| | - Mattias Strömberg
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
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28
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Meng Y, Liu P, Zhou W, Ding J, Liu J. Bioorthogonal DNA Adsorption on Polydopamine Nanoparticles Mediated by Metal Coordination for Highly Robust Sensing in Serum and Living Cells. ACS NANO 2018; 12:9070-9080. [PMID: 30130385 DOI: 10.1021/acsnano.8b03019] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
DNA-functionalized nanomaterials, such as various 2D materials, metal oxides, and gold nanoparticles, have been extensively explored as biosensors. However, their practical applications for selective sensing and imaging in biological samples remain challenging due to interference from the sample matrix. Bioorthogonal chemistry has allowed specific reactions in cells, and we want to employ this concept to design nanomaterials that can selectively adsorb DNA but not proteins or other abundant biomolecules. In this work, DNA oligonucleotides were found to be adsorbed on polydopamine nanoparticles (PDANs) via polyvalent metal-mediated coordination, and such adsorption bioorthogonally resisted DNA displacement by various biological ligands, showing better performance compared to graphene oxide and metal oxide nanoparticles for DNA detection. Using DNA/PDANs as biosensors, a detection limit of <1 nM target DNA was achieved in serum and other biological samples, and imaging of cancer-related microRNA in cells was demonstrated. The DNA binding mechanism on PDAN was further studied by ligand displacement experiments and X-ray photoelectron spectroscopy characterization, which demonstrated the critical role of polyvalent metal ions to bridge DNA with PDANs. This work provides fundamental insights into the biointerface science of PDANs with DNA, which can benefit applications in biosensor design, directed assembly of nanomaterials, bioimaging, and drug delivery.
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Affiliation(s)
- Yingcai Meng
- Xiangya School of Pharmaceutical Sciences , Central South University , Changsha , Hunan 410013 , China
| | - Peng Liu
- Xiangya School of Pharmaceutical Sciences , Central South University , Changsha , Hunan 410013 , China
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences , Central South University , Changsha , Hunan 410013 , China
| | - Jinsong Ding
- Xiangya School of Pharmaceutical Sciences , Central South University , Changsha , Hunan 410013 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario , Canada , N2L 3G1
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29
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Manochehry S, McConnell EM, Tram KQ, Macri J, Li Y. Colorimetric Detection of Uranyl Using a Litmus Test. Front Chem 2018; 6:332. [PMID: 30140672 PMCID: PMC6095041 DOI: 10.3389/fchem.2018.00332] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/16/2018] [Indexed: 01/10/2023] Open
Abstract
Ingestion of water containing toxic contaminants above levels deemed safe for human consumption can occur unknowingly since numerous common contaminants in drinking water are colorless and odorless. Uranyl is particularly problematic as it has been found at dangerous levels in sources of drinking water. Detection of this heavy metal-ion species in drinking water currently requires sending a sample to a laboratory where trained personnel use equipment to perform the analysis and turn-around times can be long. A pH-responsive colorimetric biosensor was developed to enable detection of uranyl in water which coupled the uranyl-specific 39E DNAzyme as a recognition element, and an enzyme capable of producing a pH change as the reporter element. The rapid colorimetric assay presented herein can detect uranyl in lake and well water at concentrations relevant for environmental monitoring, as demonstrated by the detection of uranyl at levels below the limits set for drinking water by major regulatory agencies including the World Health Organization (30 μg/L). This simple and inexpensive DNAzyme-based assay enabled equipment-free visual detection of 15 μg/L uranyl, using both solution-based and paper-based pH-dependent visualization strategies.
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Affiliation(s)
- Sepehr Manochehry
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
| | - Erin M. McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
| | - Kha Q. Tram
- Department of Chemistry and Chemical Biology, McMaster UniversityHamilton, ON, Canada
| | - Joseph Macri
- Department of Pathology and Molecular Medicine, McMaster UniversityHamilton, ON, Canada
- Hamilton Regional Laboratory Medicine ProgramHamilton, ON, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster UniversityHamilton, ON, Canada
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30
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Liu P, Wang S, Liu X, Ding J, Zhou W. Platinated graphene oxide: A nanoplatform for efficient gene-chemo combination cancer therapy. Eur J Pharm Sci 2018; 121:319-329. [PMID: 29906508 DOI: 10.1016/j.ejps.2018.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/13/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023]
Abstract
Cisplatin (CisPt) is one of the most effective antitumor drugs against a wide range of solid cancers, and recent studies have indicated that combination of CisPt and RNA interference (RNAi) agents would effectively enhance therapeutic index, while the development of simple yet robust dual-delivery systems still remains a challenge. Here, we demonstrated that platinated graphene oxide is an excellent platform to achieve such goal. Nano-Graphene oxide (NGO) was easily platinated by CisPt, and the resulting CisPt/NGO was characterized by several aspects. As a proof-of-concept, an antisense microRNA-21 (Anti-miR-21) was employed as a potential RNAi agent. While most previous work functionalized NGO with cationic polymers for gene delivery, we demonstrated that platinated NGO is a potent carrier to load Anti-miR-21 with improved capacity and adsorption stability. With Anti-miR-21 loading, the system displayed significantly enhanced cytotoxicity to cancer cells, suggesting a synergistic effect. Finally, the underlying mechanism of the improved efficacy was explored, which can be ascribed to the cell apoptosis induced by Anti-miR-21 for gene silencing. This work demonstrated platinated graphene oxide as an effective nanocarrier to co-deliver CisPt and gene therapy for the treatment of cancer.
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Affiliation(s)
- Peng Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Shengfeng Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China; Department of Pharmacy, the Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
| | - Xuanjun Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Jinsong Ding
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China.
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31
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Li L, Ma X, Dong W, Miao P, Tang Y. Electrochemical Determination of Ca 2+ Based On Recycling Formation of Highly Selective DNAzyme and Gold Nanoparticle-Mediated Amplification. Bioconjug Chem 2018. [PMID: 29528621 DOI: 10.1021/acs.bioconjchem.8b00096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Calcium ion (Ca2+) plays a critical and indispensable role in many physiological and biochemical processes in the human body. In this report, we demonstrate a novel electrochemical method for the determination of the Ca2+ level aided by three functional DNA probes and gold nanoparticles (AuNPs). It affords high selectivity in sensing Ca2+ over other metal cations, which is due to the adoption of the DNAzyme at the electrode interface with exceptionally high binding ability. This method also integrates recycling formation of DNAzyme and AuNPs-mediated amplification; thus, high sensitivity is promised. Therefore, this work provides a favorable way to probe Ca2+ for biomedical applications.
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Affiliation(s)
- Li Li
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
| | - Xiaoyi Ma
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China.,University of Science and Technology of China , Hefei 230026 , People's Republic of China
| | - Wenfei Dong
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China.,University of Science and Technology of China , Hefei 230026 , People's Republic of China
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
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32
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33
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Chen J, Zuehlke A, Deng B, Peng H, Hou X, Zhang H. A Target-Triggered DNAzyme Motor Enabling Homogeneous, Amplified Detection of Proteins. Anal Chem 2017; 89:12888-12895. [PMID: 29099172 DOI: 10.1021/acs.analchem.7b03529] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We report here the concept of a self-powered, target-triggered DNA motor constructed by engineering a DNAzyme to adapt into binding-induced DNA assembly. An affinity ligand was attached to the DNAzyme motor via a DNA spacer, and a second affinity ligand was conjugated to the gold nanoparticle (AuNP) that was also decorated with hundreds of substrate strands serving as a high-density, three-dimensional track for the DNAzyme motor. Binding of a target molecule to the two ligands induced hybridization between the DNAzyme and its substrate on the AuNP, which are otherwise unable to spontaneously hybridize. The hybridization of DNAzyme with the substrate initiates the cleavage of the substrate and the autonomous movement of the DNAzyme along the AuNP. Each moving step restores the fluorescence of a dye molecule, enabling monitoring of the operation of the DNAzyme motor in real time. A simple addition or depletion of the cofactor Mg2+ allows for fine control of the DNAzyme motor. The motor can translate a single binding event into cleavage of hundreds of substrates, enabling amplified detection of proteins at room temperature without the need for separation.
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Affiliation(s)
- Junbo Chen
- Analytical and Testing Center, Sichuan University , 29 Wangjiang Road, Chengdu, Sichuan 610064, China.,Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta T6G 2G3, Canada
| | - Albert Zuehlke
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta T6G 2G3, Canada
| | - Bin Deng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta T6G 2G3, Canada
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta T6G 2G3, Canada
| | - Xiandeng Hou
- Analytical and Testing Center, Sichuan University , 29 Wangjiang Road, Chengdu, Sichuan 610064, China.,College of Chemistry, Sichuan University , 29 Wangjiang Road, Chengdu, Sichuan 610064, China
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta T6G 2G3, Canada
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34
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Nakano SI, Watabe T, Sugimoto N. Modulation of Ribozyme and Deoxyribozyme Activities Using Tetraalkylammonium Ions. Chemphyschem 2017; 18:3614-3619. [DOI: 10.1002/cphc.201700882] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/13/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry; Faculty of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20, Minatojima-minamimachi, Chuo-ku Kobe 650-0047 Japan
| | - Takaaki Watabe
- Department of Nanobiochemistry; Faculty of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20, Minatojima-minamimachi, Chuo-ku Kobe 650-0047 Japan
- Department of Chemistry; Faculty of Science and Engineering; Konan University; 8-9-1, Okamoto, Higashinada-ku Kobe 658-8501 Japan
| | - Naoki Sugimoto
- Department of Nanobiochemistry; Faculty of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20, Minatojima-minamimachi, Chuo-ku Kobe 650-0047 Japan
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; 7-1-20, Minatojima-minamimachi, Chuo-ku Kobe 650-0047 Japan
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35
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Wang L, Zhou H, Liu B, Zhao C, Fan J, Wang W, Tong C. Fluorescence Assay for Ribonuclease H Based on Nonlabeled Substrate and DNAzyme Assisted Cascade Amplification. Anal Chem 2017; 89:11014-11020. [DOI: 10.1021/acs.analchem.7b02899] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lanbo Wang
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
| | - Hongyan Zhou
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
| | - Bin Liu
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
| | - Chuan Zhao
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
| | - Jialong Fan
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
| | - Wei Wang
- TCM
and Ethnomedicine Innovation and Development Laboratory, Sino-Luxemburg
TCM Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Chunyi Tong
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
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36
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Wang J, Qin H, Wang F, Ren J, Qu X. Metal-Ion-Activated DNAzymes Used for Regulation of Telomerase Activity in Living Cells. Chemistry 2017. [DOI: 10.1002/chem.201702236] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jiasi Wang
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences; Beijing 100039 P. R. China
| | - Hongshuang Qin
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
| | - Faming Wang
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences; Beijing 100039 P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
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37
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Chen Z, He Q, Zhao M, Lin C, Luo F, Lin Z, Chen G. A fluorometric histidine biosensor based on the use of a quencher-labeled Cu(II)-dependent DNAzyme. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2425-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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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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39
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Xu W, Tian J, Luo Y, Zhu L, Huang K. A rapid and visual turn-off sensor for detecting copper (II) ion based on DNAzyme coupled with HCR-based HRP concatemers. Sci Rep 2017; 7:43362. [PMID: 28266536 PMCID: PMC5339725 DOI: 10.1038/srep43362] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/23/2017] [Indexed: 12/14/2022] Open
Abstract
To solve the requirement of on-site, rapid, and visual detection of copper (II) (Cu2+) in aqueous solution, a turn-off sensor for detecting copper (II) ion was developed based on Cu2+-dependent DNAzyme as the recognition element and hybridization chain reaction (HCR)-based horseradish peroxidase (HRP) concatemers as the signal amplifier and the signal report element. The detection unit, which was composed of the immobilized Cu2+-dependent DNAzyme coupled with HCR-based HRP concatemers via Waston-Crick base pairing, could catalyze hydrogen peroxide (H2O2) via TMB, generating obvious green color and turning yellow after sulfuric acid termination with optical absorption at 450 nm. Upon Cu2+ addition, the substrate strand of the Cu2+-dependent DNAzyme concatenated with the HCR-based HRP complex was irreversibly cleaved, efficiently causing dramatic reduction of the detection signal. Under optimal conditions, the detection signal decreased with the concentration of Cu2+ in 5 min, exhibiting a linear calibration from 0.05 to 3 μM with a detection limit of 8 nM. The sensor also displayed a high selectivity for Cu2+ given the specificity and anti-interference of the detection unit, and this system was applicable for monitoring Cu2+ in real water samples. Generally speaking, the proposed sensor exhibits good potential in environment surveys.
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Affiliation(s)
- 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
| | - Jingjing Tian
- Beijing Laboratory for Food Quality and Safety, College of Food Science and 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
| | - Longjiao Zhu
- 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
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40
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A microRNA-initiated DNAzyme motor operating in living cells. Nat Commun 2017; 8:14378. [PMID: 28262725 PMCID: PMC5343503 DOI: 10.1038/ncomms14378] [Citation(s) in RCA: 382] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 12/16/2016] [Indexed: 12/21/2022] Open
Abstract
Synthetic DNA motors have great potential to mimic natural protein motors in cells but the operation of synthetic DNA motors in living cells remains challenging and has not been demonstrated. Here we report a DNAzyme motor that operates in living cells in response to a specific intracellular target. The whole motor system is constructed on a 20 nm gold nanoparticle (AuNP) decorated with hundreds of substrate strands serving as DNA tracks and dozens of DNAzyme molecules each silenced by a locking strand. Intracellular interaction of a target molecule with the motor system initiates the autonomous walking of the motor on the AuNP. An example DNAzyme motor responsive to a specific microRNA enables amplified detection of the specific microRNA in individual cancer cells. Activated by specific intracellular targets, these self-powered DNAzyme motors will have diverse applications in the control and modulation of biological functions. Synthetic DNA nanomachines have been designed to perform a variety of tasks in vitro. Here, the authors build a nanomotor system that integrates a DNAzyme and DNA track on a gold nanoparticle, to facilitate cellular uptake, and apply it as a real-time miRNA imaging tool in living cells.
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41
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Abstract
DNAzymes are catalytically active DNA molecules that are obtained via in vitro selection. RNA-cleaving DNAzymes have attracted significant attention for both therapeutic and diagnostic applications due to their excellent programmability, stability, and activity. They can be designed to cleave a specific mRNA to down-regulate gene expression. At the same time, DNAzymes can sense a broad range of analytes. By combining these two functions, theranostic DNAzymes are obtained. This review summarizes the progress of DNAzyme for theranostic applications. First, in vitro selection of DNAzymes is briefly introduced, and some representative DNAzymes related to biological applications are summarized. Then, the applications of DNAzyme for RNA cleaving are reviewed. DNAzymes have been used to cleave RNA for treating various diseases, such as viral infection, cancer, inflammation and atherosclerosis. Several formulations have entered clinical trials. Next, the use of DNAzymes for detecting metal ions, small molecules and nucleic acids related to disease diagnosis is summarized. Finally, the theranostic applications of DNAzyme are reviewed. The challenges to be addressed include poor DNAzyme activity under biological conditions, mRNA accessibility, delivery, and quantification of gene expression. Possible solutions to overcome these challenges are discussed, and future directions of the field are speculated.
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42
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Diao W, Tang M, Ding X, Zhang Y, Yang J, Cheng W, Mo F, Wen B, Xu L, Yan Y. Electrochemical DNA biosensor based on MNAzyme-mediated signal amplification. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1910-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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43
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Yang Y, Huang J, Yang X, Quan K, Wang H, Ying L, Xie N, Ou M, Wang K. Aptazyme-Gold Nanoparticle Sensor for Amplified Molecular Probing in Living Cells. Anal Chem 2016; 88:5981-7. [PMID: 27167489 DOI: 10.1021/acs.analchem.6b00999] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To date, a few of DNAzyme-based sensors have been successfully developed in living cells; however, the intracellular aptazyme sensor has remained underdeveloped. Here, the first aptazyme sensor for amplified molecular probing in living cells is developed. A gold nanoparticle (AuNP) is modified with substrate strands hybridized to aptazyme strands. Only the target molecule can activate the aptazyme and then cleave and release the fluorophore-labeled substrate strands from the AuNP, resulting in fluorescence enhancement. The process is repeated so that each copy of target can cleave multiplex fluorophore-labeled substrate strands, amplifying the fluorescence signal. Results show that the detection limit is about 200 nM, which is 2 or 3 orders of magnitude lower than that of the reported aptamer-based adenosine triphosphate (ATP) sensors used in living cells. Furthermore, it is demonstrated that the aptazyme sensor can readily enter living cells and realize intracellular target detection.
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Affiliation(s)
- Yanjing Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, People's Republic of China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, People's Republic of China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, People's Republic of China
| | - Ke Quan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, People's Republic of China
| | - He Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, People's Republic of China
| | - Le Ying
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, People's Republic of China
| | - Nuli Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, People's Republic of China
| | - Min Ou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, People's Republic of China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, People's Republic of China
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44
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Zhou W, Zhang Y, Ding J, Liu J. In Vitro Selection in Serum: RNA-Cleaving DNAzymes for Measuring Ca2+ and Mg2+. ACS Sens 2016. [DOI: 10.1021/acssensors.5b00306] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Wenhu Zhou
- School
of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China 410013
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Yupei Zhang
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Jinsong Ding
- School
of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China 410013
| | - Juewen Liu
- School
of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China 410013
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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45
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Cui L, Peng R, Fu T, Zhang X, Wu C, Chen H, Liang H, Yang C, Tan W. Biostable L-DNAzyme for Sensing of Metal Ions in Biological Systems. Anal Chem 2016; 88:1850-5. [PMID: 26691677 PMCID: PMC4892185 DOI: 10.1021/acs.analchem.5b04170] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/22/2015] [Indexed: 12/13/2022]
Abstract
DNAzymes, an important type of metal ion-dependent functional nucleic acid, are widely applied in bioanalysis and biomedicine. However, the use of DNAzymes in practical applications has been impeded by the intrinsic drawbacks of natural nucleic acids, such as interferences from nuclease digestion and protein binding, as well as undesired intermolecular interactions with other nucleic acids. On the basis of reciprocal chiral substrate specificity, the enantiomer of D-DNAzyme, L-DNAzyme, could initiate catalytic cleavage activity with the same achiral metal ion as a cofactor. Meanwhile, by using the advantage of nonbiological L-DNAzyme, which is not subject to the interferences of biological matrixes, as recognition units, a facile and stable L-DNAzyme sensor was proposed for sensing metal ions in complex biological samples and live cells.
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Affiliation(s)
- Liang Cui
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Ruizi Peng
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Ting Fu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Xiaobing Zhang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Cuichen Wu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Center for Research at the Bio/Nano Interface, Health Cancer Center, University
of Florida, Gainesville, Florida 32611-7200, United States
| | - Huapei Chen
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Hao Liang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Chaoyong
James Yang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory
for Chemical Biology of Fujian Province, The MOE Key Laboratory of
Spectrochemical Analysis & Instrumentation, Department of Chemical
Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Center for Research at the Bio/Nano Interface, Health Cancer Center, University
of Florida, Gainesville, Florida 32611-7200, United States
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46
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Lv Y, Cui L, Peng R, Zhao Z, Qiu L, Chen H, Jin C, Zhang XB, Tan W. Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids. Anal Chem 2015; 87:11714-20. [PMID: 26505212 PMCID: PMC4898272 DOI: 10.1021/acs.analchem.5b02654] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Here, we propose an efficient strategy
for enzyme- and hairpin-free
nucleic acid detection called an entropy beacon (abbreviated as Ebeacon).
Different from previously reported DNA hybridization/displacement-based
strategies, Ebeacon is driven forward by increases in the entropy
of the system, instead of free energy released from new base-pair
formation. Ebeacon shows high sensitivity, with a detection limit
of 5 pM target DNA in buffer and 50 pM in cellular homogenate. Ebeacon
also benefits from the hairpin-free amplification strategy and zero-background,
excellent thermostability from 20 °C to 50 °C, as well as
good resistance to complex environments. In particular, based on the
huge difference between the breathing rate of a single base pair and
two adjacent base pairs, Ebeacon also shows high selectivity toward
base mutations, such as substitution, insertion, and deletion and,
therefore, is an efficient nucleic acid detection method, comparable
to most reported enzyme-free strategies.
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Affiliation(s)
- Yifan Lv
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Liang Cui
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Zilong Zhao
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Liping Qiu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida , Gainesville, Florida 32611-7200, United States
| | - Huapei Chen
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Cheng Jin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida , Gainesville, Florida 32611-7200, United States
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47
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Zhang N, Bing T, Liu X, Qi C, Shen L, Wang L, Shangguan D. Cytotoxicity of guanine-based degradation products contributes to the antiproliferative activity of guanine-rich oligonucleotides. Chem Sci 2015; 6:3831-3838. [PMID: 29218153 PMCID: PMC5707456 DOI: 10.1039/c4sc03949a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/04/2015] [Indexed: 01/03/2023] Open
Abstract
Guanine-rich oligonucleotides with lower nuclease resistance exhibited higher antiproliferative activity; guanine-based compounds showed highly concentration-dependent cytotoxicity.
Guanine-rich oligonucleotides (GROs) have attracted considerable attention as anticancer agents, because they exhibit cancer-selective antiproliferative activity and can form G-quadruplex structures with higher nuclease resistance and cellular uptake. Recently, a GRO, AS1411 has reached phase II clinical trials for acute myeloid leukemia and renal cell carcinoma. The antiproliferative activity of GROs has been associated with various protein targets; however the real mechanisms of action remain unclear. In this study, we showed evidence that antiproliferative activity of GROs (including AS1411) is mainly contributed by the cytotoxicity of their guanine-based degradation products, such as monophosphate deoxyguanosine (dGMP), deoxyguanosine (dG) and guanine. The GROs with lower nuclease resistance exhibited higher antiproliferative activity. Among nucleotides, nucleosides and nucleobases, only guanine-based compounds showed highly concentration-dependent cytotoxicity. Our results suggest that it is necessary to reconsider the cancer-selective antiproliferative activity of GROs. Since guanine-based compounds are endogenous substances in living organisms, systematic studies of the cytotoxicity of these compounds will provide new information for the understanding of certain diseases and offer useful information for drug design.
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Affiliation(s)
- Nan Zhang
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing , 100190 , China . ; ; Tel: +86-10-62528509.,University of the Chinese Academy of Sciences , Beijing 100049 , China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing , 100190 , China . ; ; Tel: +86-10-62528509
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing , 100190 , China . ; ; Tel: +86-10-62528509
| | - Cui Qi
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing , 100190 , China . ; ; Tel: +86-10-62528509
| | - Luyao Shen
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing , 100190 , China . ; ; Tel: +86-10-62528509.,University of the Chinese Academy of Sciences , Beijing 100049 , China
| | - Linlin Wang
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing , 100190 , China . ; ; Tel: +86-10-62528509
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing , 100190 , China . ; ; Tel: +86-10-62528509
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48
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Zeng S, Huang H, Huang Y, Liu X, Qin J, Zhao S, Chen ZF, Liang H. Label-free and amplified colorimetric assay of ribonuclease H activity and inhibition based on a novel enzyme-responsive DNAzyme cascade. RSC Adv 2015. [DOI: 10.1039/c5ra05712d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A simple, label-free and amplified colorimetric assay strategy based on a novel enzyme-responsive DNAzyme cascade is developed for assay of ribonuclease H activity and inhibition. This assay exhibits high sensitivity and selectivity.
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Affiliation(s)
- Shulan Zeng
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
| | - Huakui Huang
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
| | - Yong Huang
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
| | - Xiaoqian Liu
- College of Chemistry and Pharmacy
- Guangxi Normal University
- Guilin
- China
| | - Jian Qin
- College of Chemistry and Pharmacy
- Guangxi Normal University
- Guilin
- China
| | - Shulin Zhao
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
| | - Zhen-Feng Chen
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
| | - Hong Liang
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
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