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Wang Z, Yuan Z, Liu M, Liu Z, Leng P, Ding S, Guo J, Zhang J. Soft interface confined DNA walker for sensitive and specific detection of SARS-CoV-2 variants. Talanta 2024; 274:126009. [PMID: 38579420 DOI: 10.1016/j.talanta.2024.126009] [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: 01/04/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
Abstract
Nucleic acid detection is conducive to preventing the spread of COVID-19 pandemic. In this work, we successfully designed a soft interface confined DNA walker by anchoring hairpin reporter probes on cell membranes for the detection of SARS-CoV-2 variants. In the presence of target RNA, the cyclic self-assembly reaction occurred between hairpin probes H1 and H2, and the continuous walking of target RNA on cell membranes led to the gradual amplification of fluorescence signal. The enrichment of H1 on membranes and the unique fluidity of membranes promoted the collision efficiency between DNA strands in the reaction process, endowing this method with high sensitivity. In addition, the double-blind test of synthetic RNA in 5% normal human serum demonstrated the good stability and anti-interference in complex environment of this method, which exhibited great potential in clinical diagnostics.
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Affiliation(s)
- Zhangmin Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zuowei Yuan
- Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China
| | - Min Liu
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zhidong Liu
- Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China
| | - Ping Leng
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Jinlin Guo
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China
| | - Juan Zhang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China; Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing, 400021, China.
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2
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Zhu D, Zhao D, Hu Y, Wei T, Su T, Su S, Chao J, Wang L. Programmably engineered stochastic RNA nanowalker for ultrasensitive miRNA detection. Chem Commun (Camb) 2024; 60:6142-6145. [PMID: 38804211 DOI: 10.1039/d4cc01656d] [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: 05/29/2024]
Abstract
A programmably engineered stochastic RNA nanowalker powered by duplex-specific nuclease (DSN) is developed. By utilizing poly-adenine-based spherical nucleic acids (polyA-SNA) to accurately regulate the densities of DNA tracks, the nanowalker showcases its capability to identify miRNA-21, miRNA-486, and miRNA-155 with quick kinetics and attomolar sensitivity, positioning it as a promising option for cancer clinical surveillance.
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Affiliation(s)
- Dan Zhu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Dongxia Zhao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Yang Hu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Tianhui Wei
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Tong Su
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Shao Su
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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3
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Zhou X, Geng H, Shi P, Wang H, Zhang G, Cui Z, Lv S, Bi S. NIR-driven photoelectrochemical-fluorescent dual-mode biosensor based on bipedal DNA walker for ultrasensitive detection of microRNA. Biosens Bioelectron 2024; 247:115916. [PMID: 38104392 DOI: 10.1016/j.bios.2023.115916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Optical biosensors have become powerful tools for bioanalysis, but most of them are limited by optic damage, autofluorescence, as well as poor penetration ability of ultraviolet (UV) and visible (Vis) light. Herein, a near-infrared light (NIR)-driven photoelectrochemical (PEC)-fluorescence (FL) dual-mode biosensor has been proposed for ultrasensitive detection of microRNA (miRNA) based on bipedal DNA walker with cascade amplification. Fueled by toehold-mediated strand displacement (TMSD), the bipedal DNA walker triggered by target miRNA-21 is formed through catalytic hairpin assembly (CHA), which can efficiently move along DNA tracks on CdS nanoparticles (CdS NPs)-modified fluorine doped tin oxide (FTO) electrode, resulting in the introduction of upconversion nanoparticles (UCNPs) on electrode surface. Under 980 nm laser irradiation, the UCNPs serve as the energy donor to emit UV/Vis light and excite CdS NPs to generate photocurrent for PEC detection, while the upconversion luminescence (UCL) at 803 nm is monitored for FL detection. This PEC-FL dual-mode biosensor has achieved the ultrasensitive and accurate analysis of miRNA-21 in human serum and different gynecological cancer cells. Overall, the proposed dual-mode biosensor can not only couple the inherent features of each single-mode biosensor but also provide mutual authentication of testing results, which opens up a new avenue for early diagnosis of miRNA-related diseases in clinic.
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Affiliation(s)
- Xuemin Zhou
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; Department of Ultrasonic Medicine, Binzhou Medical University Hospital, Binzhou, 256603, PR China
| | - Hongyan Geng
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China
| | - Pengfei Shi
- College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China; Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, PR China
| | - Huijie Wang
- College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China
| | - Guofang Zhang
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China
| | - Zhumei Cui
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China.
| | - Shuzhen Lv
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China.
| | - Sai Bi
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China.
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Zhao S, Jia Y, Wang A, Yang J, Yang L. Dual-mode DNA walker-based optical fiber biosensor for ultrasensitive detection of microRNAs. Biosens Bioelectron 2023; 239:115613. [PMID: 37607447 DOI: 10.1016/j.bios.2023.115613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/06/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023]
Abstract
We present a novel dual-mode DNA-walker based optical fiber biosensor (DMDW-Opt biosensor) for sensitive assay of micro-RNAs in bio-samples. In the sensor system, we develop a new strategy for the cascade amplification, DNA-walker/rolling cycle amplification (RCA), by the use of the residue track of the walker. The strategy can significantly improve the response of the sensor and avoid any tedious operation procedure. Dual-mode readouts, i.e., fluorescence and chemiluminescence, are measured independently without interfering with each other to achieve reliable and accurate analysis. Optical fibers with the surface modified by gold nanoparticles are utilized as the support for fabrication of the sensor, which would be benefit for developing miniaturized and portable sensing devices. The performance of the proposed method is evaluated by using micro-RNAs (MiR-155 and MiR-21) as the analytical target. The method is successfully applied for accurate determination of micoRNAs in human serum and MCF-7 cells. Our method can perform sensitive assays of MiR-155 with limit-of-detection as low as 97.72 fM and 11.22 fM, MiR-21 with limit-of-detection as low as 107.15 fM and 8.32 fM for the fluorescence- and the chemiluminescence-readout respectively, and the biosensor exhibits excellent specificity, reproducibility and storage stability, indicating its valuable potential applications for sensing trace-amount targets in complicated real samples.
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Affiliation(s)
- Siqi Zhao
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Yaxue Jia
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Anping Wang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Jinlan Yang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Li Yang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China.
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5
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Ma H, Chen L, Lv J, Yan X, Li Y, Xu G. The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology. Chem Commun (Camb) 2023; 59:10330-10342. [PMID: 37615403 DOI: 10.1039/d3cc02597g] [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: 08/25/2023]
Abstract
DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.
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Affiliation(s)
- Hongmin Ma
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Long Chen
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Jingnan Lv
- The Second Affiliated People's Hospital of Soochow University, Suzhou 215008, China
| | - Xiaoyu Yan
- Guang'an Vocational & Technical College, Sichuan 638000, China
| | - Yonghao Li
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Guoxin Xu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
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6
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Li L, Liu S, Zhang C, Guo Z, Shao S, Deng X, Liu Q. Recent Advances in DNA-Based Cell Surface Engineering for Biological Applications. Chemistry 2022; 28:e202202070. [PMID: 35977912 DOI: 10.1002/chem.202202070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Indexed: 12/14/2022]
Abstract
Due to its excellent programmability and biocompatibility, DNA molecule has unique advantages in cell surface engineering. Recent progresses provide a reliable and feasible way to engineer cell surfaces with diverse DNA molecules and DNA nanostructures. The abundant form of DNA nanostructures has greatly expanded the toolbox of DNA-based cell surface engineering and gave rise to a variety of novel and fascinating applications. In this review, we summarize recent advances in DNA-based cell surface engineering and its biological applications. We first introduce some widely used methods of immobilizing DNA molecules on cell surfaces and their application features. Then we discuss the approaches of employing DNA nanostructures and dynamic DNA nanotechnology as elements for creating functional cell surfaces. Finally, we review the extensive biological applications of DNA-based cell surface engineering and discuss the challenges and prospects of DNA-based cell surface engineering.
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Affiliation(s)
- Lexun Li
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Shuang Liu
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Chunjuan Zhang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Zhenzhen Guo
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Shuxuan Shao
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Xiaodan Deng
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
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7
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DNA walker for signal amplification in living cells. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Zhou Y, Wang Z, Zhang S, Deng L. An ultrasensitive fluorescence detection template of pathogenic bacteria based on dual catalytic hairpin DNA Walker@Gold nanoparticles enzyme-free amplification. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 277:121259. [PMID: 35489113 DOI: 10.1016/j.saa.2022.121259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/02/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Integrating the advantages of catalytic hairpin components and multi-foot DNA walker, we designed a 16S rRNA detection probe template for pathogen bacteria, which utilizes DNA ligation quencher and dual catalytic hairpin@DNA walker to induce signal recovery. The dual catalytic hairpin@DNA walker uses the walking position of the target on the AuNP as a foothold to promote the reaction, so that the biosensing of the low-abundance target sequence can induce signal recovery. During the entire experiment, no enzyme is required, which can avoid the limitation of enzyme degradation under unfavorable conditions and the inability to detect the target. Most importantly, the detection template has the advantages of high sensitivity, and its detection limit is significantly better than that of single hairpin DNA walker probe. As the detection system can sensitively and rapidly detect its targeted bacteria and not rely on any enzyme and sophisticated instrumentation, it has great potential for sensitive and specific pathogenic bacteria detection.
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Affiliation(s)
- Yan Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, PR China
| | - Zefeng Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, PR China
| | - Shengnan Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, PR China
| | - Le Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, PR China.
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Catalytic hairpin assembly as cascade nucleic acid circuits for fluorescent biosensor: design, evolution and application. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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