1
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Peng JM, Liu H, Ying ZM. Rapid one-pot isothermal amplification reassembled of fluorescent RNA aptamer for SARS-CoV-2 detection. Talanta 2024; 276:126264. [PMID: 38761661 DOI: 10.1016/j.talanta.2024.126264] [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: 01/17/2024] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
The outbreak of SARS-CoV-2 poses a serious threat to human life and health. A rapid nucleic acid tests can effectively curb the spread of the disease. With the advantages of fluorescent RNA aptamers, low background and high sensitivity. A variety of fluorescent RNA aptamer sensors have been developed for the detection of nucleic acid. Here, we report a hypersensitive detection platform in which SARS-CoV-2 initiates RTF-EXPAR to amplify trigger fragments. This activation leads to the reassembled of the SRB2 fluorescent RNA aptamer, restoring its secondary structure for SR-DN binding and turn-on fluorescence. The platform completes the assay in 30 min and all reactions occur in one tube. The detection limit is as low as 116 aM. Significantly, the platform's quantitative analyses were almost identical to qPCR results in simulated tests of positive samples. In conclusion, the platform is sensitive, accurate and provides a new protocol for point-of-care testing of viruses.
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Affiliation(s)
- Jia-Min Peng
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Hao Liu
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Zhan-Ming Ying
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
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2
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Huang Z, Guo X, Ma X, Wang F, Jiang JH. Genetically encodable tagging and sensing systems for fluorescent RNA imaging. Biosens Bioelectron 2023; 219:114769. [PMID: 36252312 DOI: 10.1016/j.bios.2022.114769] [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: 07/31/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 10/06/2022]
Abstract
Live cell imaging of RNAs is crucial to interrogate their fundamental roles in various biological processes. The highly spatiotemporal dynamic nature of RNA abundance and localization has presented great challenges for RNA imaging. Genetically encodable tagging and sensing (GETS) systems that can be continuously produced in living systems have afforded promising tools for imaging and sensing RNA dynamics in live cells. Here we review the recent advances of GETS systems that have been developed for RNA tagging and sensing in live cells. We first describe the various GETS systems using MS2-bacteriophage-MS2 coat protein, pumilio homology domain and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9/13 for RNA labeling and tracking. The progresses of GETS systems for fluorogenic labeling and/or sensing RNAs by engineering light-up RNA aptamers, CRISPR-Cas9 systems and RNA aptamer stabilized fluorogenic proteins are then elaborated. The challenges and future perspectives in this field are finally discussed. With the continuing development, GETS systems will afford powerful tools to elucidate RNA biology in living systems.
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Affiliation(s)
- Zhimei Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Xiaoyan Guo
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Xianbo Ma
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
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3
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Zhang C, Zhang R, Liang C, Deng Y, Li Z, Deng Y, Tang BZ. Charge-elimination strategy for constructing RNA-selective fluorescent probe undisturbed by mitochondria. Biomaterials 2022; 291:121915. [DOI: 10.1016/j.biomaterials.2022.121915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/04/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
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4
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Zhou WJ, Li H, Zhang KK, Wang F, Chu X, Jiang JH. Genetically Encoded Sensor Enables Endogenous RNA Imaging with Conformation-Switching Induced Fluorogenic Proteins. J Am Chem Soc 2021; 143:14394-14401. [PMID: 34431301 DOI: 10.1021/jacs.1c07719] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genetically encoded molecular tools are crucial for live cell RNA imaging, and few are available for endogenous RNA imaging. We develop a new genetically encoded sensor using conformation switching RNA induced fluorogenic proteins that enable multicolor and signal-amplified imaging of endogenous RNAs. The sensor system is designed with an RNA sensing module and a degron-fused fluorescent protein reporter. Target RNA induces conformation switching of the RNA sensing module to form RNA aptamers that stabilize the degron-fused protein for fluorogenic imaging. This sensor is demonstrated for high-contrast imaging of survivin mRNA abundance and dynamics in live cells. Moreover, the sensor system is extended to a multicolor palette by screening fluorogenic proteins of distinct colors, and engineered into a signal amplifier using the split fluorescent protein design. The sensor is further exploited for imaging lncRNA MALAT-1 and its translocation dynamics during mitosis. Our sensor system can afford a valuable platform for RNA imaging in biomedical research and clinical theranostics.
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Affiliation(s)
- Wen-Jing Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Hua Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ke-Ke Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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5
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Fluorescent functional nucleic acid: Principles, properties and applications in bioanalyzing. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116292] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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6
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Kolpashchikov DM, Spelkov AA. Binary (Split) Light‐up Aptameric Sensors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201914919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dmitry M. Kolpashchikov
- Chemistry Department University of Central Florida Orlando FL 32816-2366 USA
- Burnett School of Biomedical Sciences University of Central Florida Orlando FL 32816 USA
| | - Alexander A. Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies ITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
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7
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Activatable CRISPR Transcriptional Circuits Generate Functional RNA for mRNA Sensing and Silencing. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Ying ZM, Wang F, Chu X, Yu RQ, Jiang JH. Activatable CRISPR Transcriptional Circuits Generate Functional RNA for mRNA Sensing and Silencing. Angew Chem Int Ed Engl 2020; 59:18599-18604. [PMID: 32633466 DOI: 10.1002/anie.202004751] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/26/2020] [Indexed: 12/11/2022]
Abstract
CRISPR-dCas9 systems that are precisely activated by cell-specific information facilitate the development of smart sensors or therapeutic strategies. We report the development of an activatable dCas9 transcriptional circuit that enables sensing and silencing of mRNA in living cells using hybridization-mediated structure switching for gRNA activation. The gRNA is designed with the spacer sequence blocked by a hairpin structure, and mRNA hybridization induces gRNA structure switching and activates the transcription of reporter RNA. An mRNA sensor developed using a light-up RNA reporter shows high sensitivity and fast-response imaging of survivin mRNA in cells under drug treatments and different cell lines. Furthermore, a feedback circuit is engineered by incorporating a small hairpin RNA in the reporter RNA, demonstrating a smart strategy for dynamic sensing and silencing of survivin with induced tumor cell apoptosis. This circuit illustrates a broadly applicable platform for the development of cell-specific sensing and therapeutic strategies.
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Affiliation(s)
- Zhan-Ming Ying
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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9
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Kolpashchikov DM, Spelkov AA. Binary (Split) Light-up Aptameric Sensors. Angew Chem Int Ed Engl 2020; 60:4988-4999. [PMID: 32208549 DOI: 10.1002/anie.201914919] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Indexed: 12/12/2022]
Abstract
This Minireview discusses the design and applications of binary (also known as split) light-up aptameric sensors (BLAS). BLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. When associated, the two strands form a dye-binding site, followed by an increase in fluorescence of the aptamer-bound dye. The design is cost-efficient because it uses short oligonucleotides and does not require conjugation of organic dyes with nucleic acids. In some applications, BLAS design is preferable over monolithic sensors because of simpler assay optimization and improved selectivity. RNA-based BLAS can be expressed in cells and used for the intracellular monitoring of biological molecules. BLAS have been used as reporters of nucleic acid association events in RNA nanotechnology and nucleic-acid-based molecular computation. Other applications of BLAS include the detection of nucleic acids, proteins, and cancer cells, and potentially they can be tailored to report a broad range of biological analytes.
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Affiliation(s)
- Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Alexander A Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation
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Bai J, Luo Y, Wang X, Li S, Luo M, Yin M, Zuo Y, Li G, Yao J, Yang H, Zhang M, Wei W, Wang M, Wang R, Fan C, Zhao Y. A protein-independent fluorescent RNA aptamer reporter system for plant genetic engineering. Nat Commun 2020; 11:3847. [PMID: 32737299 PMCID: PMC7395781 DOI: 10.1038/s41467-020-17497-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 07/02/2020] [Indexed: 02/05/2023] Open
Abstract
Reporter systems are routinely used in plant genetic engineering and functional genomics research. Most such plant reporter systems cause accumulation of foreign proteins. Here, we demonstrate a protein-independent reporter system, 3WJ-4 × Bro, based on a fluorescent RNA aptamer. Via transient expression assays in both Escherichia coli and Nicotiana benthamiana, we show that 3WJ-4 × Bro is suitable for transgene identification and as an mRNA reporter for expression pattern analysis. Following stable transformation in Arabidopsis thaliana, 3WJ-4 × Bro co-segregates and co-expresses with target transcripts and is stably inherited through multiple generations. Further, 3WJ-4 × Bro can be used to visualize virus-mediated RNA delivery in plants. This study demonstrates a protein-independent reporter system that can be used for transgene identification and in vivo dynamic analysis of mRNA.
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Affiliation(s)
- Jiuyuan Bai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yao Luo
- State Key Laboratory and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xin Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Shi Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Mei Luo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Meng Yin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yuanli Zuo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Guolin Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Junyu Yao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Hua Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Mingdi Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wei Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Maolin Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Rui Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Yun Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Shi H, Lei Y, Ge J, He X, Cui W, Ye X, Liu J, Wang K. A Simple, pH-Activatable Fluorescent Aptamer Probe with Ultralow Background for Bispecific Tumor Imaging. Anal Chem 2019; 91:9154-9160. [PMID: 31185714 DOI: 10.1021/acs.analchem.9b01828] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Activatable aptamer probes (AAPs) are promising in molecular imaging of tumors, but the reported shape-switching-dependent AAPs are still challenged by unsatisfied noise suppression, poor stability, and sophisticated sequence design. To address the problem, we constructed a pH-activatable aptamer probe (pH-AAP) by utilizing an acid-labile acetal linker as the responsive element to be fused with a tumor-targeted aptamer. Specifically, a Cy5-labeled aptamer was connected with the quencher BHQ2 through the acetal group, thus generating pH-AAP with quenched fluorescence. Due to the stable proximity of Cy5 to BHQ2, pH-AAP was found to have ultralow background with a quenching efficiency as high as 98%. In comparison with shape-switching-dependent AAPs, the noise suppression of pH-AAP was well maintained for a much longer time in both serum and mouse body, thus showing a robust fluorescence stability. By a combination of the fluorescence recovery induced by acid hydrolysis of acetal linkers and the tumor-targeted recognition of aptamers, pH-AAP could either specifically anchor the extracellular pH-activated signals on the target cell surface in an acidic tumor microenvironment or be activated by acidic lysosomes after it was internalized into target cells. As proof of concept, in vitro evaluation and in vivo imaging of A549 lung cancer cells were performed by using S6 aptamer as a demonstration. It was indicated that pH-AAP realized washing-free, bispecific, and contrast-enhanced tumor imaging. The strategy is simple and free of sequence modification, which promises to provide a universal platform for sensitive and precise tumor diagnosis.
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Affiliation(s)
- Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Yanli Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China.,School of Chemistry and Food Engineering , Changsha University of Science and Technology , Changsha 410076 , People's Republic of China
| | - Jia Ge
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Wensi Cui
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Xiaosheng Ye
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
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12
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Ying ZM, Yuan YY, Tu B, Tang LJ, Yu RQ, Jiang JH. A single promoter system co-expressing RNA sensor with fluorescent proteins for quantitative mRNA imaging in living tumor cells. Chem Sci 2019; 10:4828-4833. [PMID: 31160957 PMCID: PMC6509996 DOI: 10.1039/c9sc00458k] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/27/2019] [Indexed: 12/14/2022] Open
Abstract
Genetically encoded light-up RNA aptamers afford a valuable platform for developing RNA sensors toward live cell imaging. However, quantitative imaging of intracellular RNAs remains a grand challenge. Here we reported a novel genetically encoded RNA sensor strategy using a plasmid that expresses a splittable fusion of the RNA sensor and the GFP mRNA in an individual transcript using a single promoter system. This splittable fusion design enables synchronous co-expression of the RNA sensor with GFP mRNA while alleviates the interference with correct folding of RNA aptamers due to intramolecular hybridization. This single-promoter system is applied to ratiometric imaging of survivin mRNA in tumor cells. The results reveal that the ratiometric images dynamically correlated with survivin mRNA concentrations and allow quantitative imaging of survivin mRNA in different tumor cells. The RNA sensor strategy may provide a new paradigm for developing a robust imaging platform for quantitative mRNA studies in living cells.
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Affiliation(s)
- Zhan-Ming Ying
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Yue-Yan Yuan
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Bin Tu
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Li-Juan Tang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Ru-Qin Yu
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Jian-Hui Jiang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
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14
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15
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2019; 58:1266-1279. [PMID: 30102012 PMCID: PMC6391945 DOI: 10.1002/anie.201806482] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 12/16/2022]
Abstract
The cellular functions of RNA are not limited to their role as blueprints for protein synthesis. In particular, noncoding RNA, such as, snRNAs, lncRNAs, miRNAs, play important roles. With increasing numbers of RNAs being identified, it is well known that the transcriptome outnumbers the proteome by far. This emphasizes the great importance of functional RNA characterization and the need to further develop tools for these investigations, many of which are still in their infancy. Fluorescent light-up aptamers (FLAPs) are RNA sequences that can bind nontoxic, cell-permeable small-molecule fluorogens and enhance their fluorescence over many orders of magnitude upon binding. FLAPs can be encoded on the DNA level using standard molecular biology tools and are subsequently transcribed into RNA by the cellular machinery, so that they can be used as fluorescent RNA tags (FLAP-tags). In this Minireview, we give a brief overview of the fluorogens that have been developed and their binding RNA aptamers, with a special focus on published crystal structures. A summary of current and future cellular FLAP applications with an emphasis on the study of RNA-RNA and RNA-protein interactions using split-FLAP and Förster resonance energy transfer (FRET) systems is given.
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Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
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A label-free fluorescent aptasensor for the detection of Aflatoxin B1 in food samples using AIEgens and graphene oxide. Talanta 2019; 198:71-77. [PMID: 30876604 DOI: 10.1016/j.talanta.2019.01.078] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 01/13/2019] [Accepted: 01/18/2019] [Indexed: 01/08/2023]
Abstract
The detection of Aflatoxin B1 (AFB1) has attracted extensive attention for food safety is a worldwide public health problem. Herein, a novel, simple and label-free fluorescent aptasensor, based on quaternized tetraphenylethene salt (TPE-Z), graphene oxide (GO) and AFB1 aptamer, has been constructed to detect AFB1. In the presence of AFB1, AFB1 aptamer undergoes a conformational switch from single stranded structure to the AFB1/AFB1 aptamer complex upon target binding, which induces the release of TPE-Z/AFB1 aptamer from the surface of GO. Thus, the fluorescence of TPE-Z/AFB1 aptamer is recovered. The assay can be performed by simply mixing TPE-Z, AFB1 aptamer, the GO and the AFB1 samples with a detection limit of 0.25 ng/mL. It is highly selective against other aflatoxins in foods and its performance has been verified in food samples (corn, milk and rice) with known concentration AFB1.
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
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18
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Ying ZM, Xiao HY, Tang H, Yu RQ, Jiang JH. Light-up RNA aptamer enabled label-free protein detection via a proximity induced transcription assay. Chem Commun (Camb) 2018; 54:8877-8880. [PMID: 30043035 DOI: 10.1039/c8cc04498h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A novel proximity induced transcription assay for highly sensitive protein detection based on protein mediated ligation of a DNA template with the transcription of a light-up RNA aptamer for signal amplification has been developed.
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Affiliation(s)
- Zhan-Ming Ying
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
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