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Wang Z, Zhang R, Liu S, Zhang W, Han J, Bu H. Thermodynamic Allosteric Switch-Actuated 3D DNA Nanomachine for Ultrasensitive Electrochemical/Fluorescent Dual-Mode Biosensing of a Transcription Factor. ACS APPLIED BIO MATERIALS 2024; 7:1073-1080. [PMID: 38215043 DOI: 10.1021/acsabm.3c01018] [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: 01/14/2024]
Abstract
Herein, we reported an innovative thermodynamic allosteric switch-actuated 3D DNA nanomachine for selective, sensitive, and accurate electrochemical (EC)/fluorescent (FL) dual-mode biosensing of a microphthalmia-associated transcription factor (MITF). The thermodynamic allosteric switch was ingeniously customized as a hairpin probe (HP) that was in dynamic equilibrium but rapidly interconverting conformations. At the "inactive state", the MITF-binding region and the switch part were "sequestered". Upon the introduction of MITF, an MITF-HP complex promptly formed, and the equilibrium of HP thermodynamically inclined from the "inactive state" toward the "active state" conformation. Immediately, the exposed switch on HP effectively actuated the 3D DNA nanomachine and synchronously produced the restriction site for Nb.BbvCI nicking endonuclease. After the autonomous conveying of the 3D DNA nanomachine by means of the high-efficiency circularly nicking endonuclease signal amplification (NESA), not only was MB-S1 in the supernatant used for FL measurements but also MB-SP/MNs/S2 in the precipitate was adapted for EC analysis, significantly improving the utilization of output products derived from the 3D DNA nanomachine. Accordingly, benefiting from the efficient DNA nanomachine signal amplification manner and the self-calibration function of a dual-mode bioassay, the constructed biosensor exhibits superior sensitivity and accuracy for MITF determination.
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Affiliation(s)
- Zhen Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
| | - Rongrong Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Shuning Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
| | - Wen Zhang
- School of Chemical Engineering, Xi'an University, Xi'an 710065, China
| | - Jing Han
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Huaiyu Bu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
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Qu H, Fan C, Chen M, Zhang X, Yan Q, Wang Y, Zhang S, Gong Z, Shi L, Li X, Liao Q, Xiang B, Zhou M, Guo C, Li G, Zeng Z, Wu X, Xiong W. Recent advances of fluorescent biosensors based on cyclic signal amplification technology in biomedical detection. J Nanobiotechnology 2021; 19:403. [PMID: 34863202 PMCID: PMC8645109 DOI: 10.1186/s12951-021-01149-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022] Open
Abstract
The cyclic signal amplification technology has been widely applied for the ultrasensitive detection of many important biomolecules, such as nucleic acids, proteins, enzymes, adenosine triphosphate (ATP), metal ions, exosome, etc. Due to their low content in the complex biological samples, traditional detection methods are insufficient to satisfy the requirements for monitoring those biomolecules. Therefore, effective and sensitive biosensors based on cyclic signal amplification technology are of great significance for the quick and simple diagnosis and treatment of diseases. Fluorescent biosensor based on cyclic signal amplification technology has become a research hotspot due to its simple operation, low cost, short time, high sensitivity and high specificity. This paper introduces several cyclic amplification methods, such as rolling circle amplification (RCA), strand displacement reactions (SDR) and enzyme-assisted amplification (EAA), and summarizes the research progress of using this technology in the detection of different biomolecules in recent years, in order to provide help for the research of more efficient and sensitive detection methods.
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Affiliation(s)
- Hongke Qu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Mingjian Chen
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Qijia Yan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shanshan Zhang
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lei Shi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Bo Xiang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Xu Wu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
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Huang C, Xu X, Jiang D, Jiang W. Binding mediated MNAzyme signal amplification strategy for enzyme-free and label-free detection of DNA-binding proteins. Anal Chim Acta 2021; 1166:338560. [PMID: 34022996 DOI: 10.1016/j.aca.2021.338560] [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: 10/04/2020] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
A novel MNAzyme signal amplification strategy was developed for enzyme-free and label-free detection of DNA-binding proteins. This strategy relied on the binding-mediated MNAzyme cleavage and G-quadruplex-based light-up fluorescence switch. Three DNA sequences were designed to construct the MNAzyme in which DNA1 (including half binding site of the target protein and a toehold sequence) and DNA2 (including another half binding site of the target protein and one MNAzyme partzyme) firstly hybridized. The target protein recognized the binding sites on DNA1-DNA2 hybrid to form a stable protein-DNA1-DNA2 conjugates. Then, the MNAzyme was assembled with the presence of DNA3 which contained another MNAzyme partzyme and the complementary sequence of DNA1. The active MNAzyme cleaved DNA4 to release the G-quadruplex that was locked in the stem of DNA4. Finally, N-methyl mesoporphyrin IX (NMM) was inserted into the released G-quadruplex structure and the fluorescence signal was turned on. Taking nuclear factor-κB p50 (NF-κB p50) as the model, the limit of detection was low to 0.14 nM. Furthermore, the sequence-specific recognition of NF-κB p50 with DNA displayed excellent selectivity and specificity. The results in present work showed that this strategy will be a promising tool for DNA-binding proteins analysis in biomedical exploration and clinical diagnosis.
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Affiliation(s)
- Chao Huang
- Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China
| | - Xiaowen Xu
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China
| | - Dafeng Jiang
- Department of Physical and Chemical Testing, Shandong Center for Food Safety Risk Assessment, Shandong Center for Disease Control and Prevention, 250014, Jinan, PR China.
| | - Wei Jiang
- Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China; School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China.
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Chen Y, Yan X, Yang W, Wang J, Lu Q, Li B, Zhu W, Zhou X. A signal transduction approach for multiplexed detection of transcription factors by integrating DNA nanotechnology, multi-channeled isothermal amplification, and chromatography. J Chromatogr A 2020; 1624:461148. [PMID: 32376029 DOI: 10.1016/j.chroma.2020.461148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 12/16/2022]
Abstract
The variation patterns of transcription factors (TFs) provide direct information for the states of cell populations, which is of significance for biomedical research and clinical diagnostics. Herein, we show that through multi-channeled isothermal amplification, it is feasible to connect DNA-based signal transduction with chromatography for multiplexed detection of TFs. The described system is referred to as "PAC" which includes three major steps: (i) Protection, which uses DNA-modified magnetic beads to capture TFs and converts the capturing event into triggering signal; (ii) Amplification, which receives the triggering signal and generate DNA reporters through multi-channeled extension and nicking of oligonucleotides; and (iii) Chromatography, which separates and detects the DNA reporters in liquid chromatography. The quantitative detection of five essential TFs includes p50, p53, AP-1, MITF, and c-Myc is realized in a multiplexed manner, with the lowest detection limit of 0.5 pM. PAC can also provide effective means to measure the above five TFs in real samples, including cultured cells, xenograft tumors, and blood-based liquid biopsy. This study not only established a solution for multiplexed measurement of TFs for molecular diagnostics, but also paved avenue for bridging the gap between DNA nanotechnology and chromatography.
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Affiliation(s)
- Yue Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China; School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Xiaoqiang Yan
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Wei Yang
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Jing Wang
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Qiaoyun Lu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
| | - Wanying Zhu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China.
| | - Xuemin Zhou
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China.
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