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Chen Y, Liu Z, Zhang B, Wu H, Lv X, Zhang Y, Lin Y. Biomedical Utility of Non-Enzymatic DNA Amplification Reaction: From Material Design to Diagnosis and Treatment. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2404641. [PMID: 39152925 DOI: 10.1002/smll.202404641] [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: 06/06/2024] [Revised: 08/04/2024] [Indexed: 08/19/2024]
Abstract
Nucleic acid nanotechnology has become a promising strategy for disease diagnosis and treatment, owing to remarkable programmability, precision, and biocompatibility. However, current biosensing and biotherapy approaches by nucleic acids exhibit limitations in sensitivity, specificity, versatility, and real-time monitoring. DNA amplification reactions present an advantageous strategy to enhance the performance of biosensing and biotherapy platforms. Non-enzymatic DNA amplification reaction (NEDAR), such as hybridization chain reaction and catalytic hairpin assembly, operate via strand displacement. NEDAR presents distinct advantages over traditional enzymatic DNA amplification reactions, including simplified procedures, milder reaction conditions, higher specificity, enhanced controllability, and excellent versatility. Consequently, research focusing on NEDAR-based biosensing and biotherapy has garnered significant attention. NEDAR demonstrates high efficacy in detecting multiple types of biomarkers, including nucleic acids, small molecules, and proteins, with high sensitivity and specificity, enabling the parallel detection of multiple targets. Besides, NEDAR can strengthen drug therapy, cellular behavior control, and cell encapsulation. Moreover, NEDAR holds promise for constructing assembled diagnosis-treatment nanoplatforms in the forms of pure DNA nanostructures and hybrid nanomaterials, which offer utility in disease monitoring and precise treatment. Thus, this paper aims to comprehensively elucidate the reaction mechanism of NEDAR and review the substantial advancements in NEDAR-based diagnosis and treatment over the past five years, encompassing NEDAR-based design strategies, applications, and prospects.
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Affiliation(s)
- Ye Chen
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Zhiqiang Liu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Bowen Zhang
- Department of Prosthodontics, Tianjin Stomatological Hospital, School of Medicine, Nankai University, Tianjin, 300041, P. R. China
- Tianjin Key Laboratory of Oral and Maxillofacial Function Reconstruction, Tianjin, 300041, P. R. China
| | - Haoyan Wu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Xiaoying Lv
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yuxin Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, 610041, P. R. China
- National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
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Yuan H, Hu J, Ge QQ, Liu WJ, Ma F, Zhang CY. Construction of a Spatial-Confined Self-Stacking Catalytic Circuit for Rapid and Sensitive Imaging of Piwi-Interacting RNA in Living Cells. NANO LETTERS 2024; 24:8732-8740. [PMID: 38958407 DOI: 10.1021/acs.nanolett.4c02230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Piwi-interacting RNAs (piRNAs) are small noncoding RNAs that repress transposable elements to maintain genome integrity. The canonical catalytic hairpin assembly (CHA) circuit relies on random collisions of free-diffused reactant probes, which substantially slow down reaction efficiency and kinetics. Herein, we demonstrate the construction of a spatial-confined self-stacking catalytic circuit for rapid and sensitive imaging of piRNA in living cells based on intramolecular and intermolecular hybridization-accelerated CHA. We rationally design a 3WJ probe that not only accelerates the reaction kinetics by increasing the local concentration of reactant probes but also eliminates background signal leakage caused by cross-entanglement of preassembled probes. This strategy achieves high sensitivity and good specificity with shortened assay time. It can quantify intracellular piRNA expression at a single-cell level, discriminate piRNA expression in tissues of breast cancer patients and healthy persons, and in situ image piRNA in living cells, offering a new approach for early diagnosis and postoperative monitoring.
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Affiliation(s)
- Huimin Yuan
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Jinping Hu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Qi-Qin Ge
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Wen-Jing Liu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
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Gong X, Li R, Zhang J, Zhang P, Jiang Z, Hu L, Liu X, Wang Y, Wang F. Scaling up of a Self-Confined Catalytic Hybridization Circuit for Robust microRNA Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400517. [PMID: 38613838 PMCID: PMC11165520 DOI: 10.1002/advs.202400517] [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: 01/14/2024] [Revised: 03/27/2024] [Indexed: 04/15/2024]
Abstract
The precise regulation of cellular behaviors within a confined, crowded intracellular environment is highly amenable in diagnostics and therapeutics. While synthetic circuitry system through a concatenated chemical reaction network has rarely been reported to mimic dynamic self-assembly system. Herein, a catalytic self-defined circuit (CSC) for the hierarchically concatenated assembly of DNA domino nanostructures is engineered. By incorporating pre-sealed symmetrical fragments into the preying hairpin reactants, the CSC system allows the hierarchical DNA self-assembly via a microRNA (miRNA)-powered self-sorting catalytic hybridization reaction. With minimal strand complexity, this self-sustainable CSC system streamlined the circuit component and achieved localization-intensified cascaded signal amplification. Profiting from the self-adaptively concatenated hybridization reaction, a reliable and robust method has been achieved for discriminating carcinoma tissues from the corresponding para-carcinoma tissues. The CSC-sustained self-assembly strategy provides a comprehensive and smart toolbox for organizing various hierarchical DNA nanostructures, which may facilitate more insights for clinical diagnosis and therapeutic assessment.
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Affiliation(s)
- Xue Gong
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityCollege of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education)Chongqing Key Laboratory of Green Catalysis Materials and TechnologyCollege of ChemistryChongqing Normal UniversityChongqing401331P. R. China
| | - Ruomeng Li
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityCollege of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Jiajia Zhang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education)Chongqing Key Laboratory of Green Catalysis Materials and TechnologyCollege of ChemistryChongqing Normal UniversityChongqing401331P. R. China
| | - Pu Zhang
- College of PharmacyChongqing Medical UniversityChongqing400016P. R. China
| | - Zhongwei Jiang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education)Chongqing Key Laboratory of Green Catalysis Materials and TechnologyCollege of ChemistryChongqing Normal UniversityChongqing401331P. R. China
| | - Lianzhe Hu
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education)Chongqing Key Laboratory of Green Catalysis Materials and TechnologyCollege of ChemistryChongqing Normal UniversityChongqing401331P. R. China
| | - Xiaoqing Liu
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityCollege of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Yi Wang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education)Chongqing Key Laboratory of Green Catalysis Materials and TechnologyCollege of ChemistryChongqing Normal UniversityChongqing401331P. R. China
| | - Fuan Wang
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityCollege of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
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He J, Shang X, Long M, Yang C, Zhang Y, Li M, Yuan R, Xu W. Fluorescence Biosensing Based on Bifurcated DNA Scaffold-Aggregated Ag Nanocluster via Responsive Conformation Switch of Quasi-Molecular Beacon. Anal Chem 2024; 96:3480-3488. [PMID: 38351592 DOI: 10.1021/acs.analchem.3c05108] [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: 02/28/2024]
Abstract
To address the limitations of typical hairpin-structural molecular beacons, exploring the ability of a quasi-molecular beacon (qMB) to create label-free fluorescence biosensors is intriguing and remains a challenge. Herein, we propose the first example of modular qMB with the feature of a stimulation-responsive conformation switch to develop an aggregated Ag nanocluster (aAgNC) in a bifurcated DNA scaffold for fluorescently sensing a specific initiator (I*). This qMB was well designed to program four functional modules: I*-recognizable element adopting metastable stem-loop bihairpin structure and two DNA splits (exposed C3GT4 and locked C4AC4T) of aAgNC template that is separated by a tunable hairpin spacer for the customized combination of selective recognition and signaling readout. When presenting I* in an assay route, the specific hybridization induces the directional disassembly of the bihairpin unit, on which the qMB is configurationally switched to liberate the locked split. Thus, the bifurcated parent template pair of C3GT4/C4AC4T is proximal, affording in situ nucleation and clustering of emissive aAgNC. By collecting the fluorescence signal, the quantitative detection of I* is achieved. Benefiting from the ingenious programming of qMB, the recognizing and signaling integration actuates the construction of a facile and convenient fluorescent biosensor featuring rapid reaction kinetics, a wide linear range, high sensitivity, and specificity. This would provide a new paradigm to exploit versatile qMB-based biosensing platforms via stimulation-responsive conformation switches for developing various DNA-scaffolded Ag clusters.
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Affiliation(s)
- Jiayang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xin Shang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Min Long
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Chunli Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yuqing Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Mengdie Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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Zhu J, Peng L, Jehan S, Wang H, Chen X, Zhao S, Zhou W. Activable Photodynamic DNA Probe with an "AND" Logic Gate for Precision Skin Cancer Therapy. RESEARCH (WASHINGTON, D.C.) 2024; 7:0295. [PMID: 38269029 PMCID: PMC10807844 DOI: 10.34133/research.0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/10/2023] [Indexed: 01/26/2024]
Abstract
Photodynamic therapy (PDT) has emerged as a promising approach for squamous cell carcinoma treatment but hindered by tumor hypoxia, acquired resistance, phototoxicity, and so on. To address these issues, we developed a smart strategy utilizing activable photosensitizers delivered by an aptamer-functionalized DNA probe (ADP). The ADP incorporated an AS1411 aptamer for tumor targeting and a linear antisense oligonucleotide (ASO) for recognition of Survivin mRNA. In the absence of the target, PDT remained quenched, thereby avoiding phototoxicity during circulation and nonselective distribution. With the aid of the aptamer, ADP achieved selective targeting of tumors. Upon internalization, ADP targeted recognized Survivin mRNA, triggering PDT activation, and releasing ASO to down-regulate Survivin expression and reverse tumor resistance. Consequently, the activable photosensitizers exhibited an "AND" logic gate, combining tumor-targeting delivery and tumor-related gene activation, thus enhancing its specificity. Additionally, the incorporation of hemin into the ADP provided catalase activity, converting tumor-abundant H2O2 into O2, thereby ameliorating tumor hypoxia. The resulting functionalized G-quadruplex/hemin-DNA probe complex demonstrated targeted delivery and activation, minimized side effects, and enhanced PDT efficacy in both xenograft tumor-bearing mice and patient-derived xenograft models. This study offers a unique and promising platform for efficient and safe PDT, thus holding great potential for future clinical translation and improved cancer therapy.
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Affiliation(s)
- Jiaojiao Zhu
- Xiangya School of Pharmaceutical Sciences,
Central South University, Changsha, Hunan 410013, China
| | - Lanyuan Peng
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital,
Central South University, Changsha, Hunan 410008, China
| | - Shah Jehan
- Xiangya School of Pharmaceutical Sciences,
Central South University, Changsha, Hunan 410013, China
- Department of Vascular Surgery,
The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Haiyang Wang
- Department of Vascular Surgery,
The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Xiang Chen
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital,
Central South University, Changsha, Hunan 410008, China
| | - Shuang Zhao
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital,
Central South University, Changsha, Hunan 410008, China
- Furong Laboratory, Changsha, Hunan, China
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences,
Central South University, Changsha, Hunan 410013, China
- Key Laboratory of Biological Nanotechnology of National Health Commission, Changsha, Hunan 410008, China
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