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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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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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Ma X, Suo T, Zhao F, Shang Z, Chen Y, Wang P, Li B. Integrating CRISPR/Cas12a with strand displacement amplification for the ultrasensitive aptasensing of cadmium(II). Anal Bioanal Chem 2023; 415:2281-2289. [PMID: 36952025 DOI: 10.1007/s00216-023-04650-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/26/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023]
Abstract
Cadmium ion (Cd(II)) is a pernicious environmental pollutant that has been shown to contaminate agricultural lands, accumulate through the food chain, and seriously threaten human health. At present, Cd(II) monitoring is dependent on centralized instruments, necessitating the development of rapid and on-site detection platforms. Against this backdrop, the present study reports on the development of a fluorometric aptasensor designed to target Cd(II), which is achieved through the integration of strand displacement amplification (SDA) and CRISPR/Cas12a. In the absence of Cd(II), the aptamer initiates SDA, resulting in the generation of a profusion of ssDNA that activates Cas12a, leading to a substantial increase in fluorescence output. Conversely, the presence of Cd(II) curtails the SDA efficiency, culminating in a significant reduction in fluorescence output. The proposed approach has been demonstrated to enable the selective detection of Cd(II) at concentrations of 60 pM, with the performance of the aptasensor validated in real water and rice samples. The proposed platform based on aptamer-target interaction holds immense promise as a signal-amplified and precise method for the detection of Cd(II) and has the potential to transform current hazard detection practices in food samples.
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Affiliation(s)
- Xiaochen Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, CAS, Beijing, 100101, China
| | - Tiying Suo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
- Nanjing Jiangbei New Area Biopharmaceutical Public Platform Co., Ltd., Nanjing, 211899, China
| | - Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Zhaoyang Shang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yue Chen
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, 211166, China.
| | - Pei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
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Li B, Wang Q, Sohail M, Zhang X, He H, Lin L. Facilitating the determination of microcystin toxins with bio-inspired sensors. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Cheng X, Li Y, Kou J, Liao D, Zhang W, Yin L, Man S, Ma L. Novel non-nucleic acid targets detection strategies based on CRISPR/Cas toolboxes: A review. Biosens Bioelectron 2022; 215:114559. [DOI: 10.1016/j.bios.2022.114559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 07/07/2022] [Indexed: 12/26/2022]
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The regulatory role of AP-2β in monoaminergic neurotransmitter systems: insights on its signalling pathway, linked disorders and theragnostic potential. Cell Biosci 2022; 12:151. [PMID: 36076256 PMCID: PMC9461128 DOI: 10.1186/s13578-022-00891-7] [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: 06/20/2022] [Accepted: 08/28/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractMonoaminergic neurotransmitter systems play a central role in neuronal function and behaviour. Dysregulation of these systems gives rise to neuropsychiatric and neurodegenerative disorders with high prevalence and societal burden, collectively termed monoamine neurotransmitter disorders (MNDs). Despite extensive research, the transcriptional regulation of monoaminergic neurotransmitter systems is not fully explored. Interestingly, certain drugs that act on these systems have been shown to modulate central levels of the transcription factor AP-2 beta (AP-2β, gene: TFAP2Β). AP-2β regulates multiple key genes within these systems and thereby its levels correlate with monoamine neurotransmitters measures; yet, its signalling pathways are not well understood. Moreover, although dysregulation of TFAP2Β has been associated with MNDs, the underlying mechanisms for these associations remain elusive. In this context, this review addresses AP-2β, considering its basic structural aspects, regulation and signalling pathways in the controlling of monoaminergic neurotransmitter systems, and possible mechanisms underpinning associated MNDS. It also underscores the significance of AP-2β as a potential diagnostic biomarker and its potential and limitations as a therapeutic target for specific MNDs as well as possible pharmaceutical interventions for targeting it. In essence, this review emphasizes the role of AP-2β as a key regulator of the monoaminergic neurotransmitter systems and its importance for understanding the pathogenesis and improving the management of MNDs.
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Advances in improvement strategies of digital nucleic acid amplification for pathogen detection. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116568] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Sohail M, Qin L, Li S, Chen Y, Zaman MH, Zhang X, Li B, Huang H. Molecular reporters for CRISPR/Cas: from design principles to engineering for bioanalytical and diagnostic applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Sohail M, Xie S, Zhang X, Li B. Methodologies in visualizing the activation of CRISPR/Cas: The last mile in developing CRISPR-Based diagnostics and biosensing – A review. Anal Chim Acta 2022; 1205:339541. [DOI: 10.1016/j.aca.2022.339541] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
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Ding R, Chen Y, Wang Q, Wu Z, Zhang X, Li B, Lin L. Recent advances in quantum dots-based biosensors for antibiotic detection. J Pharm Anal 2021; 12:355-364. [PMID: 35811614 PMCID: PMC9257440 DOI: 10.1016/j.jpha.2021.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/21/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Affiliation(s)
- Rui Ding
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yue Chen
- School of Nursing, Nanjing Medical University, Nanjing, 211166, China
| | - Qiusu Wang
- School of Environment, Nanjing Normal University, Nanjing, 210023, China
| | - Zhengzhang Wu
- Jiangsu Conat Biological Products Co., Ltd., Taixing, Jiangsu, 225400, China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
- Corresponding author.
| | - Lei Lin
- School of Environment, Nanjing Normal University, Nanjing, 210023, China
- Corresponding author. .
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An exonuclease protection and CRISPR/Cas12a integrated biosensor for the turn-on detection of transcription factors in cancer cells. Anal Chim Acta 2021; 1165:338478. [PMID: 33975701 DOI: 10.1016/j.aca.2021.338478] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Transcription factors (TFs) are critical proteins that regulate the expression of genes, and the abnormal change of TFs levels is directly related to physical dysfunctions. Herein, we developed a clustered regularly interspaced short palindromic repeats (CRISPR)-based biosensor for the measurement of TFs level with the assistance of exonuclease protection assay. A dsDNA (activator) with the ability to activate Cas12a was engineered to contain TFs binding domain, and the binding between TFs and the activator can protect the dsDNA from being digested by exonuclease III (Exo III). The reserved activator then triggered a CRISPR/Cas12a reporting reaction to produce fluorescent signal for detection. In the detection of nuclear factor-kappa B (NF-κB) p50 subunit, the limit of detection of 0.2 pM and limit of quantification of 0.6 pM were obtained respectively, and the performance of this biosensor has been challenged by cell nucleoprotein extracts. Additionally, this method can be applied in the screening and evaluation of TFs inhibitors, calculating the IC50 of oridonin. Integrating merits including high sensitivity, low cost, and good portability, this method may enrich the arsenal for TFs-related applications.
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Hernández-Rodríguez JF, Rojas D, Escarpa A. Electrochemical Sensing Directions for Next-Generation Healthcare: Trends, Challenges, and Frontiers. Anal Chem 2020; 93:167-183. [PMID: 33174738 DOI: 10.1021/acs.analchem.0c04378] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juan F Hernández-Rodríguez
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, Faculty of Sciences, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Daniel Rojas
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, Faculty of Sciences, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain.,Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Alberto Escarpa
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, Faculty of Sciences, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain.,Chemical Research Institute Andres M. del Rio, University of Alcalá, E-28871 Madrid, Spain
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