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Mao H, Yu L, Tu M, Wang S, Zhao J, Zhang H, Cao Y. Recent Advances on the Metal-Organic Frameworks-Based Biosensing Methods for Cancer Biomarkers Detection. Crit Rev Anal Chem 2024; 54:1273-1289. [PMID: 35980613 DOI: 10.1080/10408347.2022.2111197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sensitive and selective detection of cancer biomarkers is crucial for early diagnosis and treatment of cancer, one of the most dangerous diseases in the world. Metal-organic frameworks (MOFs), a class of hybrid porous materials fabricated through the assembly of metal ions/clusters and organic ligands, have attracted increasing attention in the sensing of cancer biomarkers, due to the advantages of adjustable size, high porosity, large surface area and ease of modification. MOFs have been utilized to not only fabricate active sensing interfaces but also arouse a variety of measurable signals. Several representative analytical technologies have been applied in MOF-based biosensing strategies to ensure high detection sensitivity toward cancer biomarkers, such as fluorescence, electrochemistry, electrochemiluminescence, photochemistry and colorimetric methods. In this review, we summarized recent advances on MOFs-based biosensing strategies for the detection of cancer biomarkers in recent three years based on the categories of metal nodes, and aimed to provide valuable references for the development of innovative biosensing platform for the purpose of clinical diagnosis.
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Affiliation(s)
- Huiru Mao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, China
| | - Longmei Yu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
| | - Ming Tu
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shuning Wang
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, China
| | - Jing Zhao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, China
| | - Haiyun Zhang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
| | - Ya Cao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, China
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Chen Q, Xia X, Liang Z, Zuo T, Xu G, Wei F, Yang J, Hu Q, Zhao Z, Tang BZ, Cen Y. Self-Assembled DNA Nanospheres Driven by Carbon Dots for MicroRNAs Imaging in Tumor via Logic Circuit. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310728. [PMID: 38229573 DOI: 10.1002/smll.202310728] [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: 11/21/2023] [Revised: 12/26/2023] [Indexed: 01/18/2024]
Abstract
DNA nanostructures with diverse biological functions have made significant advancements in biomedical applications. However, a universal strategy for the efficient production of DNA nanostructures is still lacking. In this work, a facile and mild method is presented for self-assembling polyethylenimine-modified carbon dots (PEI-CDs) and DNA into nanospheres called CANs at room temperature. This makes CANs universally applicable to multiple biological applications involving various types of DNA. Due to the ultra-small size and strong cationic charge of PEI-CDs, CANs exhibit a dense structure with high loading capacity for encapsulated DNA while providing excellent stability by protecting DNA from enzymatic hydrolysis. Additionally, Mg2+ is incorporated into CANs to form Mg@CANs which enriches the performance of CANs and enables subsequent biological imaging applications by providing exogenous Mg2+. Especially, a DNAzyme logic gate system that contains AND and OR Mg@CANs is constructed and successfully delivered to tumor cells in vitro and in vivo. They can be specifically activated by endogenic human apurinic/apyrimidinic endonuclease 1 and recognize the expression levels of miRNA-21 and miRNA-155 at tumor sites by logic biocomputing. A versatile pattern for delivery of diverse DNA and flexible logic circuits for multiple miRNAs imaging are developed.
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Affiliation(s)
- Qiutong Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Xinyi Xia
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Zhigang Liang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Tongshan Zuo
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Guanhong Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Fangdi Wei
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Jing Yang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Qin Hu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Zheng Zhao
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, P. R. China
| | - Ben Zhong Tang
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, P. R. China
| | - Yao Cen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
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3
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Xie B, Du S, He H, Gao H, Zhang J, Fu H, Liao Y. Photoactivated Controlled Dnazyme Platform for on-Demand Activation Sensitive Electrochemiluminescence mRNA Analysis. Anal Chem 2024; 96:8682-8688. [PMID: 38757179 DOI: 10.1021/acs.analchem.4c00866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Programming ultrasensitive and stimuli-responsive DNAzyme-based probes holds great potential for on-demand biomarker detection. Here, an optically triggered DNAzyme platform was reported for on-demand activation-sensitive electrochemiluminescence (ECL) c-myc mRNA analysis. In this design, the sensing and recognition function of the split DNAzyme (SDz) probe was silent by engineering a blocking sequence containing a photocleavable linker (PC-linker) group at a defined site that could be indirectly cleaved by 302 nm ultraviolet (UV) light. When the SDz probes were assembled on the Au nanoparticles and potassium (K) element doped graphitic carbon nitride nanosheet (K-doped g-C3N4) covered electrode, UV light activation induces the configurational switching and consequently the formation of an active DNAzyme probe with the help of target c-myc mRNA, allowing the cleavage of the substrate strand by magnesium ions (Mg2+). Thus, the release of a ferrocene (Fc)-labeled DNAzyme 2 strand contributed to an extreme ECL signal recovery. In the meantime, the released target c-myc mRNA combined another inactive SDz motif to form active DNAzyme and repeat the cyclic cleavage reaction, resulting in the signal amplification. Furthermore, according to the responses toward two other designed nPC-SDz and m-SDz probes, we demonstrated that controlled UV light mediated photoactivation of the DNAzyme biosensor "on demand" effectively constrained the ECL signal to the mRNA of interest. Moreover, false positive signals could also be avoided due to such a photoactivation design with UV light. Therefore, this study provided a simple methodology that may be broadly applicable for investigating the mRNA-associated physiological events that were difficult to access using traditional DNAzyme probes.
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Affiliation(s)
- Benting Xie
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, Institute of Applied Chemistry, China West Normal University, Nanchong, Sichuan 637000, China
| | - Shimao Du
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, Institute of Applied Chemistry, China West Normal University, Nanchong, Sichuan 637000, China
| | - Haonan He
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, Institute of Applied Chemistry, China West Normal University, Nanchong, Sichuan 637000, China
| | - Hejun Gao
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, Institute of Applied Chemistry, China West Normal University, Nanchong, Sichuan 637000, China
| | - Juan Zhang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, Institute of Applied Chemistry, China West Normal University, Nanchong, Sichuan 637000, China
| | - Hongquan Fu
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, Institute of Applied Chemistry, China West Normal University, Nanchong, Sichuan 637000, China
| | - Yunwen Liao
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, Institute of Applied Chemistry, China West Normal University, Nanchong, Sichuan 637000, China
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Yang H, Chen D, Zhang Y, Yuan P, Xie N, Dai Z. MiRNA and mRNA-Controlled Double-Cascaded Amplifying Circuit Nanosensor for Accurate Discrimination of Breast Cancers in Living Cells, Animals, and Organoids. Anal Chem 2024; 96:4154-4162. [PMID: 38426698 DOI: 10.1021/acs.analchem.3c05085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Metastasis is the leading cause of death in patients with breast cancer. Detecting high-risk breast cancer, including micrometastasis, at an early stage is vital for customizing the right and efficient therapies. In this study, we propose an enzyme-free isothermal cascade amplification-based DNA logic circuit in situ biomineralization nanosensor, HDNAzyme@ZIF-8, for simultaneous imaging of multidimensional biomarkers in live cells. Taking miR-21 and Ki-67 mRNA as the dual detection targets achieved sensitive logic operations and molecular recognition through the cascade hybridization chain reaction and DNAzyme. The HDNAzyme@ZIF-8 nanosensor has the ability to accurately differentiate breast cancer cells and their subtypes by comparing their relative fluorescence intensities. Of note, our nanosensor can also achieve visualization within breast cancer organoids, faithfully recapitulating the functional characteristics of parental tumor. Overall, the combination of these techniques offers a universal strategy for detecting cancers with high sensitivity and holds vast potential in clinical cancer diagnosis.
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Affiliation(s)
- Huihui Yang
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
| | - Dong Chen
- Department of Thyroid and Breast Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Yanfei Zhang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Peixiu Yuan
- College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Ni Xie
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
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Chen Y, Song Y, Wang X, Tang H, Li C. Genetically engineered virus-like particle-armoured and multibranched DNA scaffold-corbelled ultra-sensitive hierarchical hybridization chain reaction for targeting-enhanced imaging in living biosystems under spatiotemporal light powering. Biosens Bioelectron 2024; 247:115943. [PMID: 38141440 DOI: 10.1016/j.bios.2023.115943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
Although nucleic acids-based fluorescent biosensors, exemplified by the hybridization chain reaction (HCR), have exhibited promise as an imaging tool for detecting disease-related biomolecular makers in living biosystems, they still face certain challenges. These include the need for improved sensitivity, poor bio-targeting capability, the absence of signal enrichment interface and the uncontrollable biosensing initiation. Herein, we present a range of effective solutions. First, a stacking design resembling building blocks is used to construct a special hierarchical HCR (termed H-HCR), for which a hierarchical bridge is employed to graft multiunit HCR products. Furthermore, the H-HCR components are encapsulated into a virus-like particle (VLP) endowed with a naturally peptide-mediated targeting unit through genetic engineering of plasmids, after which the biosensor can specifically identify cancer cytomembranes. By further creating a multibranched DNA scaffold to enrich the H-HCR produced detection signals, the biosensor's analyte recognition module is inserted with a photocleavage-linker, allowing that the biosensing process can be spatiotemporally initiated via a light-powered behavior. Following these innovations, this genetically engineered VLP-armoured and multibranched DNA-scaffold-corbelled H-HCR demonstrates an ultra-sensitive and specific biosensing performance to a cancer-associated microRNA marker (miRNA-155). Beyond the worthy in vitro analysis, our method is also effective in performing imaging assays for such low-abundance analyte in living cells and even bodies, thus providing a roust platform for disease diagnosis.
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Affiliation(s)
- Yaling Chen
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Yongyao Song
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China; Institute of Infection, Immunology and Tumor Microenvironment, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Xiaomei Wang
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China; Institute of Infection, Immunology and Tumor Microenvironment, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, PR China.
| | - Hongwu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Chengyu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China.
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6
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Hu X, Qiu D, Jiang Q, Xu Q, Li J. Cu 2+-doped zeolitic imidazolate frameworks and gold nanoparticle (AuNPs@ZIF-8/Cu) nanocomposites enable label-free and highly sensitive electrochemical detection of oral cancer-related biomarkers. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:615-623. [PMID: 38197313 DOI: 10.1039/d3ay01918g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
It is of great significance to accurately and sensitively detect oral cancer-related biomarkers (ORAOV 1) for the early diagnosis of oral cancer. Present here is a novel electrochemical biosensor based on Cu2+-doped zeolitic imidazolate frameworks and gold nanoparticle (AuNPs@ZIF-8/Cu) nanocomposites and a one-step strand displacement reaction for label-free, simple and sensitive detection of ORAOV 1 in saliva. It is worth noting that AuNPs@ZIF-8/Cu nanocomposites show large electrochemically effective surface area, good electrical conductivity and electrocatalytic activity due to the synergistic effect of metal nanoparticles (MNPs) and ZIF-8. Consequently, the newly developed electrochemical sensor displays a wide linear range of 0.1-104 pM and a low limit of detection (LOD) of 63 fM. Meanwhile, the electrochemical biosensor can distinguish single base mismatch. The relative standard deviation (RSD) of intra-assays and inter-assays is 1.46% and 1.76%, respectively, and the peak current values decline by 9.20% with a RSD value of 1.35% after being stored at 4 °C for 7 days, suggesting that the newly designed electrochemical sensor exhibits good selectivity, reproducibility and stability to detect ORAOV 1. More importantly, this novel electrochemical sensor is found to be applicable for detecting ORAOV 1 in human saliva samples with a satisfactory result. The RSD values range from 1.15% to 1.77%, and the recoveries range from 95.46% to 112.98%.
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Affiliation(s)
- Xueting Hu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, P. R. China.
| | - Dengxue Qiu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, P. R. China.
| | - Qi Jiang
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, P. R. China.
| | - Qin Xu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, P. R. China.
| | - Jing Li
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, P. R. China.
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Yang C, Wang K, Liang G, Tian S, Peng J, Mo L, Lin W. A versatile MOF-derived theranostic for dual-miRNA controlled accurate cancer cell recognition and photodynamic therapy. Talanta 2023; 265:124805. [PMID: 37331042 DOI: 10.1016/j.talanta.2023.124805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
Precise detection and monitoring of microRNAs (miRNAs) in living tumor cells is significant for the prompt diagnosis of cancer and provides important information for treatment of cancer. A significant challenge is developing methods for imaging different miRNAs simultaneously to further enhance diagnostic and treatment accuracy. In this work, a versatile MOF-derived theranostic system (DAPM) was constructed using photosensitive metal-organic frameworks (PMOF, PM) and a DNA AND logic gate (DA). The DAPM exhibited excellent biostability and enabled sensitive detection of miR-21 and miR-155, achieving a low limit of detection (LOD) for miR-21 (89.10 pM) and miR-155 (54.02 pM). The DAPM probe generated a fluorescence signal in tumor cells where miR-21 and miR-155 co-existed, demonstrating the enhanced ability of tumor cell recognition. Additionally, the DAPM achieved efficient ROS generation and concentration-dependent cytotoxicity under light irradiation, providing effective photodynamic therapy for anti-tumors. The proposed DAPM theranostic system enables accurate cancer diagnosis, and provides spatial and temporal information for PDT.
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Affiliation(s)
- Chan Yang
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China
| | - Kun Wang
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China
| | - Guohan Liang
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China
| | - Shuo Tian
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China
| | - Juanjuan Peng
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China
| | - Liuting Mo
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China
| | - Weiying Lin
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China.
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Zhu X, Xu J, Ling G, Zhang P. Tunable metal-organic frameworks assist in catalyzing DNAzymes with amplification platforms for biomedical applications. Chem Soc Rev 2023; 52:7549-7578. [PMID: 37817667 DOI: 10.1039/d3cs00386h] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Various binding modes of tunable metal organic frameworks (MOFs) and functional DNAzymes (Dzs) synergistically catalyze the emergence of abundant functional nanoplatforms. Given their serial variability in formation, structural designability, and functional controllability, Dzs@MOFs tend to be excellent building blocks for the precise "intelligent" manufacture of functional materials. To present a clear outline of this new field, this review systematically summarizes the progress of Dz integration into MOFs (MOFs@Dzs) through different methods, including various surface infiltration, pore encapsulation, covalent binding, and biomimetic mineralization methods. Atomic-level and time-resolved catalytic mechanisms for biosensing and imaging are made possible by the complex interplay of the distinct molecular structure of Dzs@MOF, conformational flexibility, and dynamic regulation of metal ions. Exploiting the precision of DNAzymes, MOFs@Dzs constructed a combined nanotherapy platform to guide intracellular drug synthesis, photodynamic therapy, catalytic therapy, and immunotherapy to enhance gene therapy in different ways, solving the problems of intracellular delivery inefficiency and insufficient supply of cofactors. MOFs@Dzs nanostructures have become excellent candidates for biosensing, bioimaging, amplification delivery, and targeted cancer gene therapy while emphasizing major advancements and seminal endeavors in the fields of biosensing (nucleic acid, protein, enzyme activity, small molecules, and cancer cells), biological imaging, and targeted cancer gene delivery and gene therapy. Overall, based on the results demonstrated to date, we discuss the challenges that the emerging MOFs@Dzs might encounter in practical future applications and briefly look forward to their bright prospects in other fields.
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Affiliation(s)
- Xiaoguang Zhu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Jiaqi Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Guixia Ling
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Peng Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
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9
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Yadav A, Patil R, Dutta S. Advanced Self-Powered Biofuel Cells with Capacitor and Nanogenerator for Biomarker Sensing. ACS APPLIED BIO MATERIALS 2023; 6:4060-4080. [PMID: 37787456 DOI: 10.1021/acsabm.3c00640] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Self-powered biofuel cells (BFCs) have evolved for highly sensitive detection of biomarkers such as noncodon micro ribonucleic acids (miRNAs) in the presence of interfering substrates. Self-charging supercapacitive BFCs for in vivo and in vitro cellular microenvironments represent the most prevalent sensing mechanism for diagnosis. Therefore, self-powered biosensing (SPB) with a capacitor and contact separation with a triboelectric nanogenerator (TENG) offers electrochemical and colorimetric dual-mode detection via improved electrical signal intensity. In this review, we discuss three major components: stretchable self-powered BFC design, miRNA sensing, and impedance spectroscopy. A specific focus is given to 1) assembling of sensors for biomarkers, 2) electrical output signal intensification, and 3) role of supercapacitors and nanogenerators in SPBs. We outline the key features of stretchable SPBs and the sequence of miRNA sensing by SPBs. We have emphasized the need of a supercapacitor and nanogenerator for SPBs in the context of advanced assembly of the sensing unit. Finally, we outline the role of impedance spectroscopy in the detection and estimation of biomarkers. We highlight key challenges in SPBs for biomarker sensing, which needs improved sensing accuracy, integration strategies of electrochemical biosensing for in vitro and in vivo microenvironments, and the impact of miRNA sensing on cancer diagnostics. This article attempts a specific focus on the accuracy and limitations of sensing unit for miRNA biomarkers and associated tool for boosting electrical signal intensity for a potential big step further.
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Affiliation(s)
- Anubha Yadav
- Electrochemical Energy & Sensor Research Laboratory Amity Institute of Click Chemistry Research & Studies, Amity University, Sector 125, Noida 201301, Uttar Pradesh, India
| | - Rahul Patil
- Electrochemical Energy & Sensor Research Laboratory Amity Institute of Click Chemistry Research & Studies, Amity University, Sector 125, Noida 201301, Uttar Pradesh, India
| | - Saikat Dutta
- Electrochemical Energy & Sensor Research Laboratory Amity Institute of Click Chemistry Research & Studies, Amity University, Sector 125, Noida 201301, Uttar Pradesh, India
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10
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Wei K, He M, Zhang J, Zhao C, Nie C, Zhang T, Liu Y, Chen T, Jiang J, Chu X. A DNA Logic Circuit Equipped with a Biological Amplifier Loaded into Biomimetic ZIF-8 Nanoparticles Enables Accurate Identification of Specific Cancers In Vivo. Angew Chem Int Ed Engl 2023; 62:e202307025. [PMID: 37615278 DOI: 10.1002/anie.202307025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/11/2023] [Accepted: 08/23/2023] [Indexed: 08/25/2023]
Abstract
DNA logic circuits (DLC) enable the accurate identification of specific cell types, such as cancer cells, but they face the challenges of weak output signals and a lack of competent platforms that can efficiently deliver DLC components to the target site in the living body. To address these issues, we rationally introduced a cascaded biological amplifier module based on the Primer Exchange Reaction inspired by electronic circuit amplifier devices. As a paradigm, three abnormally expressed Hela cell microRNAs (-30a, -17, and -21) were chosen as "AND" gate inputs. DLC response to these inputs was boosted by the amplifier markedly enhancing the output signal. More importantly, the encapsulation of DLC and amplifier components into ZIF-8 nanoparticles resulted in their efficient delivery to the target site, successfully distinguishing the Hela tumor subtype from other tumors in vivo. Thus, we envision that this strategy has great potential for clinical cancer diagnosis.
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Affiliation(s)
- Kaiji Wei
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Mengyun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Juan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Chuan Zhao
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Cunpeng Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Tong Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yi Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Tingting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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11
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Yu L, Wang Y, Sun Y, Tang Y, Xiao Y, Wu G, Peng S, Zhou X. Nanoporous Crystalline Materials for the Recognition and Applications of Nucleic Acids. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2305171. [PMID: 37616525 DOI: 10.1002/adma.202305171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Nucleic acid plays a crucial role in countless biological processes. Hence, there is great interest in its detection and analysis in various fields from chemistry, biology, to medicine. Nanoporous crystalline materials exhibit enormous potential as an effective platform for nucleic acid recognition and application. These materials have highly ordered and uniform pore structures, as well as adjustable surface chemistry and pore size, making them good carriers for nucleic acid extraction, detection, and delivery. In this review, the latest developments in nanoporous crystalline materials, including metal organic frameworks (MOFs), covalent organic frameworks (COFs), and supramolecular organic frameworks (SOFs) for nucleic acid recognition and applications are discussed. Different strategies for functionalizing these materials are explored to specifically identify nucleic acid targets. Their applications in selective separation and detection of nucleic acids are highlighted. They can also be used as DNA/RNA sensors, gene delivery agents, host DNAzymes, and in DNA-based computing. Other applications include catalysis, data storage, and biomimetics. The development of novel nanoporous crystalline materials with enhanced biocompatibility has opened up new avenues in the fields of nucleic acid analysis and therapy, paving the way for the development of sensitive, selective, and cost-effective diagnostic and therapeutic tools with widespread applications.
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Affiliation(s)
- Long Yu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yuhao Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuqing Sun
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongling Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuxiu Xiao
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Gaosong Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Shuang Peng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
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12
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Chen YL, Sun X, He JW, Xin MK, Liu D, Li CY. Light-Driven and Metal-Organic Framework Synergetic Loaded DNA Tetrahedral Amplifier for Exonuclease III-Powered All-in-One Biosensing and Chemotherapy in Live Biosystems. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37410886 DOI: 10.1021/acsami.3c06626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
As a result of inaccurate biosensing and difficult synergetic loading, it is challenging to further impel DNA amplifiers to perform therapeutic application. Herein, we introduce some innovative solutions. First, a smart light-driven biosensing concept based on embedding nucleic acid modules with a simple photocleavage-linker is proposed. In this system, the target identification component is exposed on irradiation with ultraviolet light, thus avoiding an always-on biosensing response during biological delivery. Further, in addition to providing controlled spatiotemporal behavior and precise biosensing information, a metal-organic framework is used for the synergetic loading of doxorubicin in the internal pores, whereafter a rigid DNA tetrahedron-sustained exonuclease III-powered biosensing system is attached to prevent drug leakage and enhance resistance to enzymatic degradation. By selecting a next-generation breast cancer correlative noncoding microRNA biomarker (miRNA-21) as a model low-abundance analyte, a highly sensitive in vitro detection ability even allowing to distinguish single-base mismatching is demonstrated. Moreover, the all-in-one DNA amplifier shows excellent bioimaging competence and good chemotherapy efficacy in live biosystems. These findings will drive research into the use of DNA amplifiers in diagnosis and therapy integrated fields.
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Affiliation(s)
- Ya-Ling Chen
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Xiaoming Sun
- School of Basic Medical Sciences, Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, P. R. China
| | - Jing-Wei He
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Meng-Kun Xin
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Da Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Cheng-Yu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
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13
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Du S, Xie B, Gao H, Zhang J, Fu H, Liao F, Liao Y. Self-Powered DNAzyme Walker Enables Dual-Mode Biosensor Construction for Electrochemiluminescence and Electrochemical Detection of MicroRNA. Anal Chem 2023; 95:7006-7013. [PMID: 37083199 DOI: 10.1021/acs.analchem.3c00546] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Herein, an electrochemiluminescence (ECL) and electrochemical (EC) dual-mode biosensor platform with a self-powered DNAzyme walking machine was established for accurate and sensitive detection of miRNA-21. By employing a magnesium ion (Mn2+)-dependent DNAzyme cleavage cycling reaction, the walking machine was built by assembling DNAzyme walking strands and ferrocene (Fc)-labeled substrate strands on the Au nanoparticles and graphitic carbon nitride nanosheet (g-C3N4 NS)-covered electrode. The DNAzyme walking strand was first prohibited by a blocker strand. After the addition of target miRNA-21 and Mn2+, the DNAzyme walker could be activated and produce autonomous movements along the electrode track fueled by Mn2+-dependent DNAzyme-catalyzed substrate cleavage without additional energy supply. Notably, each walking step resulted in the cleavage of a substrate strand and the release of a Fc-labeled DNA strand fragment, allowing us to acquire an extreme ECL signal recovery of g-C3N4 inhibited by Fc. Meanwhile, numerous Fc-labeled DNA fragments escaped from the surface of the electrode, directly producing an obvious decrease in the square wave voltammetry (SWV) signal from Fc on the same sensing platform. This work not only avoided difficultly assembling various signal indicators but also significantly improved the sensitivity through using self-powered DNAzyme-walker amplification. Moreover, the proposed design employed the same reaction to produce two signal output modes, which could eliminate the interference from diverse reactive pathways on the outcome to mutually improve the accuracy. Therefore, the dual-mode miRNA-21 biosensor exhibited wide detection ranges of 100 aM to 100 nM with low detection limits of 54.3 and 78.6 aM by ECL and SWV modes, respectively, which provided an efficient and universal biosensing approach with extensive applications in early disease diagnosis and bioanalysis.
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Affiliation(s)
- Shimao Du
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Benting Xie
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Hejun Gao
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Juan Zhang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Hongquan Fu
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Fang Liao
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Yunwen Liao
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
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14
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Shi L, Tang Q, Yang B, Liu W, Li B, Yang C, Jin Y. Logic-Gates of Gas Pressure for Portable, Intelligent and Multiple Analysis of Metal Ions. Anal Chem 2023; 95:5702-5709. [PMID: 36939344 DOI: 10.1021/acs.analchem.2c05677] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
DNA logic gates have shown outstanding magic in intelligent biology applications, but it remains challenging to construct a portable, affordable and convenient DNA logic gate. Herein, logic gates of gas pressure were innovatively developed for multiplex analysis of metal ions. Hg2+ and Ag+ were input to interact specifically with the respective mismatched base pairs, which activated DNA extension reaction by polymerase and led to the enrichment of platinum nanoparticles for catalyzing the decomposition of peroxide hydrogen. Thus, the gas pressure obtained from a sealed well was used as output for detecting or identifying metal ions. Hg2+ and Ag+ were sensitively and selectively detected, and the assay of the real samples was also satisfactory. Based on this, DNA logic gates, including YES, NOT, AND, OR, NAND, NOR, INHIBIT, and XOR were successfully established using a portable and hand-held gas pressure meter as detector. So, the interactions between DNA and metal ions were intelligently transferred into the output of gas pressure, which made metal ions to be detected portably and identified intelligently. Given the remarkable merits of simplicity, logic operation, and portable output, the metal ion-driven DNA logic gate of gas pressure provides a promising way for intelligent and portable biosensing.
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Affiliation(s)
- Lu Shi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Qiaorong Tang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Bing Yang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Wei Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Baoxin Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Chaoyong Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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15
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Yan Y, Zhou F, Wang Q, Huang Y. A sensitive electrochemical biosensor for quinolones detection based on Cu2+-modulated signal amplification. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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16
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Wang J, Wang K, Peng H, Zhang Z, Yang Z, Song M, Jiang G. Entropy-Driven Three-Dimensional DNA Nanofireworks for Simultaneous Real-Time Imaging of Telomerase and MicroRNA in Living Cells. Anal Chem 2023; 95:4138-4146. [PMID: 36790864 DOI: 10.1021/acs.analchem.2c05200] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Real-time monitoring of different types of intracellular tumor-related biomarkers is of key importance for the identification of tumor cells. However, it is hampered by the low abundance of biomarkers, inefficient free diffusion of reactants, and complex cytoplasmic milieu. Herein, we present a stable and general method for in situ imaging of microRNA-21 and telomerase utilizing simple highly integrated dual tetrahedral DNA nanostructures (TDNs) that can naturally enter cells, which could initiate to form the three-dimensional (3D) higher-order DNA superstructures (DNA nanofireworks, DNFs) through a reliable target-triggered entropy-driven strand displacement reaction in living cells for remarkable signal amplification. Importantly, the excellent biostability, biocompatibility, and sensitivity of this approach benefited from (i) the precise multidirectional arrangement of probes with a pure DNA structure and (ii) the local target concentration enhanced by the spatially confined microdomain inside the DNFs. This strategy provides a pivotal molecular toolbox for broad applications such as biomedical imaging and early precise cancer diagnosis.
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Affiliation(s)
- Jin Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Kaixuan Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.,School of Water, Energy, and Environment, Cranfield University, Cranfield, Milton Keynes MK43 0AL, U.K
| | - Hanyong Peng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco- Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhen Zhang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zhugen Yang
- School of Water, Energy, and Environment, Cranfield University, Cranfield, Milton Keynes MK43 0AL, U.K
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco- Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco- Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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17
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Qi M, Shi P, Zhang X, Cui S, Liu Y, Zhou S, Zhang Q. Reconfigurable DNA triplex structure for pH responsive logic gates †. RSC Adv 2023; 13:9864-9870. [PMID: 36998523 PMCID: PMC10043996 DOI: 10.1039/d3ra00536d] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The DNA triplex is a special DNA structure often used as a logic gate substrate due to its high stability, programmability, and pH responsiveness. However, multiple triplex structures with different C−G−C+ proportions must be introduced into existing triplex logic gates due to the numerous logic calculations involved. This requirement complicates circuit design and results in many reaction by-products, greatly restricting the construction of large-scale logic circuits. Thus, we designed a new reconfigurable DNA triplex structure (RDTS) and constructed the pH-responsive logic gates through its conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. The use of these logic calculations necessitates fewer substrates, further enhancing the extensibility of the logic circuit. This result is expected to promote the development of the triplex in molecular computing and facilitate the completion of large-scale computing networks. We constructed pH-responsive logic gates through substrate conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. Our logic gates necessitate fewer substrates when two types of logic calculations are needed.![]()
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Affiliation(s)
- Mingxuan Qi
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Shuang Cui
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
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18
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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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19
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Dong Z, Xu X, Ni J, Li Y, An K, Meng L, Wu H. Cruciate DNA probes for amplified multiplexed imaging of microRNAs in living cells. J Mater Chem B 2022; 11:204-210. [PMID: 36504047 DOI: 10.1039/d2tb02027k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The real-time imaging of low-abundance tumor-related microRNAs (miRNAs) in living cells holds great potential for early clinical diagnosis of cancers. However, the relatively low detection sensitivity and possible false-positive signals of a probe in complex cellular matrices remain critical challenges for accurate RNA detection. Herein, we developed a novel aptamer-functionalized cruciate DNA probe that enabled amplified multiple miRNA imaging in living cells via catalytic hairpin assembly (CHA). The cross-shaped design of the cruciate DNA probe improved the stability against nucleases and acted as a modular scaffold for CHA circuits for efficient delivery into tumor cells. The cruciate DNA probe allowed self-assembly through thermal annealing and displayed excellent performance for sensitive miRNA detection in vitro. The cruciate DNA probe could be internalized into nucleolin-overexpressed cells specifically via cell-targeting of the AS1411 aptamer, achieving amplified fluorescence imaging and quantitative evaluation of the expression of miRNAs in living cells. Through the simultaneous detection of intracellular multiple miRNAs, the developed cruciate DNA probe could provide more accurate information and reduce the chances of false positive signals for cancer diagnosis. This approach offers a new opportunity for promoting the development of miRNA-related biomedical research and tumor diagnostic applications.
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Affiliation(s)
- Zhe Dong
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.,State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Xizhu Xu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Jing Ni
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Yuancheng Li
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Kang An
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Ling Meng
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Han Wu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
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20
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Yan C, Shi G, Chen J. Fluorescent Detection of Two Pesticides Based on CRISPR-Cas12a and Its Application for the Construction of Four Molecular Logic Gates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12700-12707. [PMID: 36128975 DOI: 10.1021/acs.jafc.2c04548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An intelligent detection platform was developed through molecular logic gate operation based on CRISPR-Cas12a and signal amplification circuits using two kinds of pesticides [acetamiprid (ACE) and atrazine (ATR)] as inputs. The pesticide-aptamer bindings activate the signal amplification process to produce numerous double-stranded DNA, which can be identified by CRISPR-Cas12a. Under the optimal assay conditions, the sensor exhibits excellent analytical performance, with the detection limits for ACE and ATR of 2.5 and 0.2 pM, respectively. The practicality of the platform was verified by testing pesticide concentrations in food samples. Several molecular logic gates (OR, AND, XOR, and INHIBIT) were constructed using "0" and "1" to encode the target pesticides and the fluorescence readout. The logic detection platform with simple operation, high sensitivity, and multiple logic functions is promising to become a powerful sensing system for the intelligent assay of different pesticides in food samples.
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Affiliation(s)
- Chong Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, People's Republic of China
| | - Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, People's Republic of China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, People's Republic of China
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21
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Li D, Zhao T, Chen J, Shi J, Wang J, Yin Y, Chen S, Xu S, Luo X. Spatiotemporally Controlled Ultrasensitive Molecular Imaging Using a DNA Computation-Mediated DNAzyme Platform. Anal Chem 2022; 94:14467-14474. [PMID: 36194489 DOI: 10.1021/acs.analchem.2c03532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Programming ultrasensitive and stimuli-responsive DNAzyme-based probes that contain logic gate biocomputation hold great potential for precise molecular imaging. In this work, a DNA computation-mediated DNAzyme platform that can be activated by 808 nm NIR light and target c-MYC was designed for spatiotemporally controlled ultrasensitive AND-gated molecular imaging. Particularly, the sensing and recognition function of the traditional DNAzyme platform was inhibited by introducing a blocking sequence containing a photo-cleavable linker (PC-linker) that can be indirectly cleaved by 808 nm NIR light and thus enables the AND-gated molecular imaging. According to the responses toward three designed SDz, nPC-SDz, and m-SDz DNAzyme probes, the fluorescence recovery in diverse cell lines (MCF-7, HeLa, and L02) and inhibitor-treated cells was investigated to confirm the AND-gated sensing mechanism. It is worth noting that thanks to the strand displacement amplification and the ability of gold nanopyramids (Au NBPs) to enhance fluorescence, the fluorescence intensity increased by ∼7.9 times and the detection limit decreased by nearly 40.5 times. Moreover, false positive signals can be also excluded due to such AND-gated design. Furthermore, such a designed "AND-gate" sensing manner can also be applied to spatiotemporally controlled ultrasensitive in vivo molecular imaging, indicating its promising potential in precise biological molecular imaging.
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Affiliation(s)
- Dan Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Tingting Zhao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Jing Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Jiaheng Shi
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Junhao Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Yue Yin
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Shuwei Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Shenghao Xu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
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22
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Recent advance of RNA aptamers and DNAzymes for MicroRNA detection. Biosens Bioelectron 2022; 212:114423. [DOI: 10.1016/j.bios.2022.114423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 02/02/2023]
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23
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Liu JX, Sun XM, Liu D, Liu YH, Li CY. Smart NIR light-gated CRISPR/Cas12a fluorescent biosensor with boosted biological delivery and trans-cleavage activity for high-performance in vivo operation. Biosens Bioelectron 2022; 216:114646. [DOI: 10.1016/j.bios.2022.114646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/29/2022] [Accepted: 08/17/2022] [Indexed: 11/02/2022]
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24
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A high-integrated DNA biocomputing platform for MicroRNA sensing in living cells. Biosens Bioelectron 2022; 207:114183. [PMID: 35303538 DOI: 10.1016/j.bios.2022.114183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/31/2022]
Abstract
DNA logic computing has captured increasing interest due to its ability to assemble programmable DNA computing elements for disease diagnosis, gene regulation, and targeted therapy. In this work, we developed an aptamer-equipped high-integrated DNA biocomputing platform (HIDBP-A) with a dual-recognition function that enabled cancer cell targeting. Dual microRNAs were the input signals and can perform AND logic operations. Compared to the free DNA biocomputing platform (FDBP), the integration of all computing elements into the same DNA tetrahedron greatly improved logic computing speed and efficiency owing to the confinement effect reflected by the high local concentration of computing elements. As a proof of concept, the utilization of microRNA as the input signal was beneficial for improving the scalability and flexibility of the sequence design of the logic nano-platform. Given that the different microRNAs were over-expressed in cancer cells, this new HIDBP-A has great promise in accurate diagnosis and logic-controlled disease treatment.
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25
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Huang Z, Wang X, Wu Z, Jiang JH. Recent Advances on DNAzyme-Based Sensing. Chem Asian J 2022; 17:e202101414. [PMID: 35156764 DOI: 10.1002/asia.202101414] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/09/2022] [Indexed: 11/08/2022]
Abstract
DNAzymes are functional nucleic acid with catalytic activity. Owing to the high sensitivity, excellent programmability, and flexible obtainment through in vitro selection, RNA-cleaving DNAzymes have attracted increasing interest in developing DNAzyme-based sensors. In this review, we summarize the recent advances on DNAzyme-based sensing applications. We initially conclude two general strategies to expand the library of DNAzymes, in vitro selection to discover new DNAzymes towards different targets of interest and chemical modifications to endue the existing DNAzymes with new function or properties. We then discuss the recent applications of DNAzyme-based sensors for the detection of a variety of important biomolecules both in vitro and in vivo . Finally, perspectives on the challenges and future directions in the development of DNAzyme-based sensors are provided.
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Affiliation(s)
- Zhimei Huang
- Hunan University, College of Chemistry and Chemical Engineering, CHINA
| | - Xiangnan Wang
- Hunan University of Technology and Business, College of Science, CHINA
| | - Zhenkun Wu
- Hunan University, State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics and College of Chemistry and Chemical Engineering, South of Lushan Road, 410082, Changsha, CHINA
| | - Jian-Hui Jiang
- Hunan University, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering, CHINA
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26
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Chen Y, Shi S. Advances and prospects of dynamic DNA nanostructures in biomedical applications. RSC Adv 2022; 12:30310-30320. [PMID: 36337940 PMCID: PMC9590593 DOI: 10.1039/d2ra05006d] [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] [Received: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
With the rapid development of DNA nanotechnology, the emergence of stimulus-responsive dynamic DNA nanostructures (DDNs) has broken many limitations of static DNA nanostructures, making precise, remote, and reversible control possible. DDNs are intelligent nanostructures with certain dynamic behaviors that are capable of responding to specific stimuli. The responsible stimuli of DDNs include exogenous metal ions, light, pH, etc., as well as endogenous small molecules such as GSH, ATP, etc. Due to the excellent stimulus responsiveness and other superior physiological characteristics of DDNs, they are now widely used in biomedical fields. For example, they can be applied in the fields of biosensing and bioimaging, which are able to detect biomarkers with greater spatial and temporal precision to help disease diagnosis and live cell physiological function studies. Moreover, they are excellent intelligent carriers for drug delivery in treating cancer and other diseases, achieving controlled release of drugs. And they can promote tissue regeneration and regulate cellular behaviors. Although some challenges need further study, such as the practical value in clinical applications, DDNs have shown great potential applications in the biomedical field. With the rapid development of DNA nanotechnology, the emergence of stimulus-responsive dynamic DNA nanostructures (DDNs) has great potential applications in the biomedical field.![]()
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Affiliation(s)
- Yiling Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan UniversityChengdu 610041P. R. China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan UniversityChengdu 610041P. R. China
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