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Gao MH, Yang XH, Tang JH, Zhou XM, Lei YM, Zhuo Y. Selective Activation of Cascade Assembly Amplification for DNA Methyltransferase Detection Using a Double-Loop Interlocked DNA Circuit. Anal Chem 2024. [PMID: 39024185 DOI: 10.1021/acs.analchem.4c02498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Precise and reliable monitoring of DNA adenine methyltransferase (Dam) activity is essential for disease diagnosis and biological analysis. However, existing techniques for detecting Dam activity often rely on specific DNA recognition probes that are susceptible to DNA degradation and exhibit limited target sensitivity and specificity. In this study, we designed and engineered a stable and dynamic DNA nanodevice called the double-loop interlocked DNA circuit (DOOR) that enables the sensitive and selective monitoring of Dam activity in complex biological environments. The DOOR incorporates two interlocked specialized sequences: a palindromic sequence for Dam identification and an initiator sequence for signal amplification. In the presence of Dam, the DOOR is cleaved by double-stranded DNA phosphodiesterase I endonuclease, generating massive double-stranded DNA (dsDNA) units. These units can self-assemble into a long dsDNA scaffold, thereby enhancing the subsequent reaction kinetics. The dsDNA scaffold further triggers a hyperbranched hybrid chain reaction to produce a fluorescent 3D DNA nanonet, enabling more precise monitoring of the Dam activity. The DOOR device exhibits excellent sensitivity, specificity, and stability, rendering it a powerful tool for studying DNA methylation in various biological processes and diseases.
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Affiliation(s)
- Mao-Hua Gao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xiao-Hong Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Ave, Beibei, Chongqing 400714, China
| | - Jia-Hao Tang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xue-Mei Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yan-Mei Lei
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Chongqing 400715, P. R. China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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Quazi MZ, Choi JH, Kim M, Park N. DNA and Nanomaterials: A Functional Combination for DNA Sensing. ACS APPLIED BIO MATERIALS 2024; 7:778-786. [PMID: 38270150 DOI: 10.1021/acsabm.3c01190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Recent decades have experienced tough situations due to the lack of reliable diagnostic facilities. The most recent cases occurred during the pandemic, where researchers observed the lack of diagnostic facilities with precision. Microorganisms and viral disease's ability to escape diagnosis has been a global challenge. DNA always has been a unique moiety with a strong and precise base-paired structure. DNA in human and foreign particles makes identification possible through base pairing. Since then, researchers have focused heavily on designing diagnostic assays targeting DNA in particular. Moreover, DNA nanotechnology has contributed vastly to designing composite nanomaterials by combining DNA/nucleic acids with functional nanomaterials and inorganic nanoparticles exploiting their physicochemical properties. These nanomaterials often exhibit unique or enhanced properties due to the synergistic activity of the many components. The capabilities of DNA and additional nanomaterials have shown the combination of robust and advanced tailoring of biosensors. Preceding findings state that the conventional strategies have exhibited certain limitations such as a low range of target detection, less biodegradability, subordinate half-life, and high susceptibility to microenvironments; however, a DNA-nanomaterial-based biosensor has overcome these limitations meaningfully. Additionally, the unique properties of nucleic acids have been studied extensively due to their high signal conduction abilities. Here, we review recent studies on DNA-nanomaterial-based biosensors, their mechanism of action, and improved/updated strategies in vivo and in situ. Furthermore, this review highlights the recent methodologies on DNA utilization to exploit the interfacial properties of nanomaterials in DNA sensing. Lastly, the review concludes with the limitations/challenges and future directions.
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Affiliation(s)
- Mohzibudin Z Quazi
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Jang Hyeon Choi
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Minchul Kim
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Nokyoung Park
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
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Wang Z, Liu M, Lin H, Zhu G, Dong Z, Wu N, Fan Y, Xu G, Chang L, Wang Y. An Ion Concentration Polarization Microplatform for Efficient Enrichment and Analysis of ctDNA. ACS NANO 2024; 18:2872-2884. [PMID: 38236597 DOI: 10.1021/acsnano.3c07137] [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: 01/19/2024]
Abstract
Strategies for rapid, effective nucleic acid processing hold tremendous significance to the clinical analysis of circulating tumor DNA (ctDNA), a family of important markers indicating tumorigenesis and metastasis. However, traditional techniques remain challenging to achieve efficient DNA enrichment, further bringing about complicated operation and limited detection sensitivity. Here, we developed an ion concentration polarization microplatform that enabled highly rapid, efficient enrichment and purification of ctDNA from a variety of clinical samples, including serum, urine, and feces. The platform demonstrated efficiently separating and enriching ctDNA within 30 s, with a 100-fold improvement over traditional methods. Integrating an on-chip isothermal amplification module, the platform further achieved 100-fold enhanced sensitivity in ctDNA detection, which significantly eliminated false-negative results in the serum or urine samples due to the low abundance of ctDNA. Such a simple-designed platform offers a user-friendly yet powerful diagnosis technique with a wide applicability, ranging from early tumor diagnosis to infection screening.
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Affiliation(s)
- Zhiying Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Ming Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Haocheng Lin
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Guiying Zhu
- School of Biomedical Engineering/Med-X, Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Zaizai Dong
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yubo Fan
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Gaolian Xu
- School of Biomedical Engineering/Med-X, Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Shanghai Sci-Tech InnoCenter for Infection & Immunity, Shanghai, 200000, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
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Liu B, Wang F, Chao J. Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing. SENSORS (BASEL, SWITZERLAND) 2023; 23:3313. [PMID: 36992023 PMCID: PMC10051322 DOI: 10.3390/s23063313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.
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Affiliation(s)
- Bing Liu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Fan Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin 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), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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Jiang W, Han L, Li G, Yang Y, Shen Q, Fan B, Wang Y, Yu X, Sun Y, He S, Du H, Miao J, Wang Y, Jia L. Baits-trap chip for accurate and ultrasensitive capture of living circulating tumor cells. Acta Biomater 2023; 162:226-239. [PMID: 36940769 DOI: 10.1016/j.actbio.2023.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/17/2023] [Accepted: 03/13/2023] [Indexed: 03/22/2023]
Abstract
Accurate analysis of living circulating tumor cells (CTCs) plays a crucial role in cancer diagnosis and prognosis evaluation. However, it is still challenging to develop a facile method for accurate, sensitive, and broad-spectrum isolation of living CTCs. Herein, inspired by the filopodia-extending behavior and clustered surface-biomarker of living CTCs, we present a unique baits-trap chip to achieve accurate and ultrasensitive capture of living CTCs from peripheral blood. The baits-trap chip is designed with the integration of nanocage (NCage) structure and branched aptamers. The NCage structure could "trap" the extended filopodia of living CTCs and resist the adhesion of filopodia-inhibited apoptotic cells, thus realizing the accurate capture (∼95% accuracy) of living CTCs independent of complex instruments. Using an in-situ rolling circle amplification (RCA) method, branched aptamers were easily modified onto the NCage structure, and served as "baits" to enhance the multi-interactions between CTC biomarker and chips, leading to ultrasensitive (99%) and reversible cell capture performance. The baits-trap chip successfully detects living CTCs in broad-spectrum cancer patients and achieves high diagnostic sensitivity (100%) and specificity (86%) of early prostate cancer. Therefore, our baits-trap chip provides a facile, accurate, and ultrasensitive strategy for living CTC isolation in clinical. STATEMENT OF SIGNIFICANCE: A unique baits-trap chip integrated with precise nanocage structure and branched aptamers was developed for the accurate and ultrasensitive capture of living CTCs. Compared with the current CTC isolation methods that are unable to distinguish CTC viability, the nanocage structure could not only "trap" the extended-filopodia of living CTCs, but also resist the adhesion of filopodia-inhibited apoptotic cells, thus realizing the accurate capture of living CTCs. Additionally, benefiting from the "baits-trap" synergistic effects generated by aptamer modification and nanocage structure, our chip achieved ultrasensitive, reversible capture of living CTCs. Moreover, this work provided a facile strategy for living CTC isolation from the blood of patients with early-stage and advanced cancer, exhibiting high consistency with the pathological diagnosis.
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Affiliation(s)
- Wenning Jiang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Lulu Han
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China.
| | - Guorui Li
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Ying Yang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Qidong Shen
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Bo Fan
- Department of Urology, The Second Hospital Affiliated of Dalian Medical University, Dalian 116023, P. R. China
| | - Yuchao Wang
- Department of Urology, The Second Hospital Affiliated of Dalian Medical University, Dalian 116023, P. R. China
| | - Xiaomin Yu
- Department of Oncology, The Dalian Municipal Central Hospital Affiliated of Dalian University of Technology, Dalian 116033, P.R. China
| | - Yan Sun
- Department of Oncology, The Dalian Municipal Central Hospital Affiliated of Dalian University of Technology, Dalian 116033, P.R. China
| | - Shengxiu He
- Department of Oncology, The Dalian Municipal Central Hospital Affiliated of Dalian University of Technology, Dalian 116033, P.R. China
| | - Huakun Du
- Department of Oncology, The Dalian Municipal Central Hospital Affiliated of Dalian University of Technology, Dalian 116033, P.R. China
| | - Jian Miao
- Hepatobiliary Pancreatic Surgery II, The Second Hospital Affiliated of Dalian Medical University, Dalian 116023, P. R. China
| | - Yuefeng Wang
- Hepatobiliary Pancreatic Surgery II, The Second Hospital Affiliated of Dalian Medical University, Dalian 116023, P. R. China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China.
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Wen X, Pu H, Liu Q, Guo Z, Luo D. Circulating Tumor DNA-A Novel Biomarker of Tumor Progression and Its Favorable Detection Techniques. Cancers (Basel) 2022; 14:6025. [PMID: 36551512 PMCID: PMC9775401 DOI: 10.3390/cancers14246025] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/20/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Cancer is the second leading cause of death in the world and seriously affects the quality of life of patients. The diagnostic techniques for tumors mainly include tumor biomarker detection, instrumental examination, and tissue biopsy. In recent years, liquid technology represented by circulating tumor DNA (ctDNA) has gradually replaced traditional technology with its advantages of being non-invasive and accurate, its high specificity, and its high sensitivity. ctDNA may carry throughout the circulatory system through tumor cell necrosis, apoptosis, circulating exosome secretion, etc., carrying the characteristic changes in tumors, such as mutation, methylation, microsatellite instability, gene rearrangement, etc. In this paper, ctDNA mutation and methylation, as the objects to describe the preparation process before ctDNA analysis, and the detection methods of two gene-level changes, including a series of enrichment detection techniques derived from PCR, sequencing-based detection techniques, and comprehensive detection techniques, are combined with new materials. In addition, the role of ctDNA in various stages of cancer development is summarized, such as early screening, diagnosis, molecular typing, prognosis prediction, recurrence monitoring, and drug guidance. In summary, ctDNA is an ideal biomarker involved in the whole process of tumor development.
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Affiliation(s)
- Xiaosha Wen
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, China
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Huijie Pu
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, China
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Quan Liu
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Zifen Guo
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Dixian Luo
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
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