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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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Pham TG, Wu J. Recent advances in methods for live-cell RNA imaging. NANOSCALE 2024; 16:5537-5545. [PMID: 38414383 DOI: 10.1039/d4nr00129j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
As one of the most fundamental building blocks of life, RNA plays critical roles in diverse biological processes, from X chromosome inactivation, genome stability maintenance, to embryo development. Being able to visualize the localization and dynamics of RNA can provide critical insights into these fundamental processes. In this review, we provide an overview of current methods for live-cell RNA imaging with a focus on methods for visualizing RNA in living mammalian cells with single-molecule resolution.
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Affiliation(s)
- Tien G Pham
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Jiahui Wu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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3
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Ji X, Wang N, Wang J, Wang T, Huang X, Hao H. Non-destructive real-time monitoring and investigation of the self-assembly process using fluorescent probes. Chem Sci 2024; 15:3800-3830. [PMID: 38487216 PMCID: PMC10935763 DOI: 10.1039/d3sc06527h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 03/17/2024] Open
Abstract
Self-assembly has been considered as a strategy to construct superstructures with specific functions, which has been widely used in many different fields, such as bionics, catalysis, and pharmacology. A detailed and in-depth analysis of the self-assembly mechanism is beneficial for directionally and accurately regulating the self-assembly process of substances. Fluorescent probes exhibit unique advantages of sensitivity, non-destructiveness, and real-time self-assembly tracking, compared with traditional methods. In this work, the design principle of fluorescent probes with different functions and their applications for the detection of thermodynamic and kinetic parameters during the self-assembly process were systematically reviewed. Their efficiency, limitations and advantages are also discussed. Furthermore, the promising perspectives of fluorescent probes for investigating the self-assembly process are also discussed and suggested.
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Affiliation(s)
- Xiongtao Ji
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
| | - Na Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Jingkang Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Ting Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Xin Huang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Hongxun Hao
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
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4
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Yin C, Wu M, Sun Q, Su C, Cao S, Niu N, Chen L. Dual-functionalization of fluorescent carbon dots via cyclodextrin and aminosilane for visual detection of β-glucuronidase and bioimaging. Anal Chim Acta 2024; 1285:341996. [PMID: 38057046 DOI: 10.1016/j.aca.2023.341996] [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: 08/01/2023] [Revised: 10/08/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023]
Abstract
A sensitive method for the detection of β-glucuronidase was established using functionalized carbon dots (β-CD-SiCDs) as fluorescent probes. The β-CD-SiCDs were found to be obtained through in situ autopolymerization by mixing the solutions of methyldopa, mono-6-ethylenediamine-β-cyclodextrin and N-(β-aminoethyl)-γ-aminopropyltrimethoxysilane at room temperature. The method has the characteristics of low energy consumption, simple and rapid. β-CD-SiCDs exhibited green fluorescence at 515 nm emission with a quantum yield of 7.9 %. 4-nitrophenyl-β-D-glucuronide was introduced as a substrate for β-glucuronidase to generate p-nitrophenol. Subsequently, p-nitrophenol self-assembled with β-CD-SiCDs through host-guest recognition to form a stable inclusion complex, resulting in the fluorescence quenching of β-CD-SiCDs. The linear range of β-CD-SiCDs for detecting β-glucuronidase activity was 0.5-60 U L-1 with a detection limit of 0.14 U L-1. For on-site detection, gel reagents were prepared by a simple method and the images were visualized and quantified by taking advantage of smartphones, avoiding the use of large instrumentation. The constructed fluorescence sensing platform has the benefits of easy operation and time saving, and has been successfully used for the detection of β-glucuronidase activity in serum and cell imaging.
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Affiliation(s)
- Chenhui Yin
- College of Chemistry, Chemical Engineering and Resource Utilization, Key Laboratory of Forest Plant Ecology, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Meng Wu
- College of Chemistry, Chemical Engineering and Resource Utilization, Key Laboratory of Forest Plant Ecology, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Qijun Sun
- College of Chemistry, Chemical Engineering and Resource Utilization, Key Laboratory of Forest Plant Ecology, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Chenglin Su
- College of Chemistry, Chemical Engineering and Resource Utilization, Key Laboratory of Forest Plant Ecology, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Shuang Cao
- College of Chemistry, Chemical Engineering and Resource Utilization, Key Laboratory of Forest Plant Ecology, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Na Niu
- College of Chemistry, Chemical Engineering and Resource Utilization, Key Laboratory of Forest Plant Ecology, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Ligang Chen
- College of Chemistry, Chemical Engineering and Resource Utilization, Key Laboratory of Forest Plant Ecology, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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5
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Chen K, Wang Y. CRISPR/Cas systems for in situ imaging of intracellular nucleic acids: Concepts and applications. Biotechnol Bioeng 2023; 120:3446-3464. [PMID: 37641170 DOI: 10.1002/bit.28543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Accurate and precise localization of intracellular nucleic acids is crucial for regulating genetic information transcription and diagnosing diseases. Although intracellular nucleic acid imaging methods are available for various cell types, their widespread utilization is impeded by the intricate nature of the process and its exorbitant cost. Recently, numerous intracellular nucleic acid labeling techniques based on clustered regularly interspaced short palindromic repeats (CRISPR) have been established due to their modularity, flexibility, and specificity. In this work, we present various CRISPR methods that are currently employed for visualizing intracellular genomic sequences and RNA, based on their detection principles and application scenarios. Furthermore, we discuss the advantages and drawbacks of the existing CRISPR imaging methods, as well as future research directions. We anticipate that with continued refinement, more advanced CRISPR-based imaging techniques can be developed to better elucidate the localization and dynamics of intracellular nucleic acids, thereby providing a powerful tool for molecular biology research and clinical molecular pathology diagnosis.
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Affiliation(s)
- Kun Chen
- Department of Clinical Laboratory, Peking University Cancer Hospital & Institute, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Beijing, China
| | - Yufei Wang
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, NMPA Key Laboratory for Quality Control of In Vitro Diagnostics, Beijing Engineering Research Center of Immunological Reagents Clinical Research, Beijing, China
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6
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Jiang L, Xie X, Su N, Zhang D, Chen X, Xu X, Zhang B, Huang K, Yu J, Fang M, Bao B, Zuo F, Yang L, Zhang R, Li H, Huang X, Chen Z, Zeng Q, Liu R, Lin Q, Zhao Y, Ren A, Zhu L, Yang Y. Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells. Nat Methods 2023; 20:1563-1572. [PMID: 37723244 DOI: 10.1038/s41592-023-01997-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/08/2023] [Indexed: 09/20/2023]
Abstract
Fluorescent RNAs, aptamers that bind and activate small fluorogenic dyes, have provided a particularly attractive approach to visualizing RNAs in live cells. However, the simultaneous imaging of multiple RNAs remains challenging due to a lack of bright and stable fluorescent RNAs with bio-orthogonality and suitable spectral properties. Here, we develop the Clivias, a series of small, monomeric and stable orange-to-red fluorescent RNAs with large Stokes shifts of up to 108 nm, enabling the simple and robust imaging of RNA with minimal perturbation of the target RNA's localization and functionality. In combination with Pepper fluorescent RNAs, the Clivias enable the single-excitation two-emission dual-color imaging of cellular RNAs and genomic loci. Clivias can also be used to detect RNA-protein interactions by bioluminescent imaging both in live cells and in vivo. We believe that these large Stokes shift fluorescent RNAs will be useful tools for the tracking and quantification of multiple RNAs in diverse biological processes.
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Affiliation(s)
- Li Jiang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Xie
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ni Su
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Dasheng Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Fluorescence Diagnosis (Shanghai) Biotech Company Ltd, Shanghai, China
| | - Xianjun Chen
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Bibi Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Kaiyi Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
- Department of Orthopedics Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jingwei Yu
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Mengyue Fang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Fangting Zuo
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Lipeng Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Huiwen Li
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xinyi Huang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengda Chen
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qingmei Zeng
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Renmei Liu
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Department of Orthopedics Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Linyong Zhu
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
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7
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Fan Z, Dou CX, Tang LJ, Wang F, Jiang JH. Genetically Encoded RNA Sensors for Ratiometric and Multiplexed Imaging of Small Molecules in Living Cells. Anal Chem 2023; 95:14455-14464. [PMID: 37699117 DOI: 10.1021/acs.analchem.3c03027] [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: 09/14/2023]
Abstract
Genetically encoded sensors afford powerful tools for studying small molecules and metabolites in live cells. However, genetically encoded sensors with a general design remain to be developed. Here we develop genetically encoded RNA sensors with a modular design for ratiometric and multiplexed imaging of small molecules in live cells. The sensor utilizes aptazyme as a recognition module and the light-up RNA aptamer as a signal reporter. The conformation of light-up aptamers is abrogated by a blocking sequence, and aptazyme-mediated cleavage restores the correct conformation, delivering activated fluorescence for small molecule imaging. We first developed a genetically encoded ratiometric sensor using Mango aptamer as a reference and SRB2 as a reporter. It is shown that the sensor allows quantitative imaging and detection of theophylline in live cells. The generality of the design is further demonstrated for imaging other small molecules by replacing the aptazymes. Its ability for multiplexed imaging of small molecules is further explored via the integration of different small-molecule responsive aptazymes and light-up RNA aptamers. This modular design could offer a versatile platform for imaging diverse molecules in living cells.
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Affiliation(s)
- Ze Fan
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Cai-Xia Dou
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Li-Juan Tang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
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8
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Lee KH, Song J, Kim S, Han SR, Lee SW. Real-time monitoring strategies for optimization of in vitro transcription and quality control of RNA. Front Mol Biosci 2023; 10:1229246. [PMID: 37771458 PMCID: PMC10523567 DOI: 10.3389/fmolb.2023.1229246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
RNA-based therapeutics and vaccines are opening up new avenues for modern medicine. To produce these useful RNA-based reagents, in vitro transcription (IVT) is an important reaction that primarily determines the yield and quality of the product. Therefore, IVT condition should be well optimized to achieve high yield and purity of transcribed RNAs. To this end, real-time monitoring of RNA production during IVT, which allows for fine tuning of the condition, would be required. Currently, light-up RNA aptamer and fluorescent dye pairs are considered as useful strategies to monitor IVT in real time. Fluorophore-labeled antisense probe-based methods can also be used for real-time IVT monitoring. In addition, a high-performance liquid chromatography (HPLC)-based method that can monitor IVT reagent consumption has been developed as a powerful tool to monitor IVT reaction in near real-time. This mini-review briefly introduces some strategies and examples for real-time IVT monitoring and discusses pros and cons of IVT monitoring methods.
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Affiliation(s)
| | - Jaehwi Song
- R&D Center, Rznomics Inc., Seongnam, Republic of Korea
| | | | | | - Seong-Wook Lee
- R&D Center, Rznomics Inc., Seongnam, Republic of Korea
- Department of Bioconvergence Engineering, Research Institute of Advanced Omics, Dankook University, Yongin, Republic of Korea
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9
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Englert D, Burger EM, Grün F, Verma MS, Lackner J, Lampe M, Bühler B, Schokolowski J, Nienhaus GU, Jäschke A, Sunbul M. Fast-exchanging spirocyclic rhodamine probes for aptamer-based super-resolution RNA imaging. Nat Commun 2023; 14:3879. [PMID: 37391423 PMCID: PMC10313827 DOI: 10.1038/s41467-023-39611-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
Live-cell RNA imaging with high spatial and temporal resolution remains a major challenge. Here we report the development of RhoBAST:SpyRho, a fluorescent light-up aptamer (FLAP) system ideally suited for visualizing RNAs in live or fixed cells with various advanced fluorescence microscopy modalities. Overcoming problems associated with low cell permeability, brightness, fluorogenicity, and signal-to-background ratio of previous fluorophores, we design a novel probe, SpyRho (Spirocyclic Rhodamine), which tightly binds to the RhoBAST aptamer. High brightness and fluorogenicity is achieved by shifting the equilibrium between spirolactam and quinoid. With its high affinity and fast ligand exchange, RhoBAST:SpyRho is a superb system for both super-resolution SMLM and STED imaging. Its excellent performance in SMLM and the first reported super-resolved STED images of specifically labeled RNA in live mammalian cells represent significant advances over other FLAPs. The versatility of RhoBAST:SpyRho is further demonstrated by imaging endogenous chromosomal loci and proteins.
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Affiliation(s)
- Daniel Englert
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Eva-Maria Burger
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Franziska Grün
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Mrigank S Verma
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Jens Lackner
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Marko Lampe
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bastian Bühler
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Janin Schokolowski
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.
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10
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Lu S, Hou Y, Zhang XE, Gao Y. Live cell imaging of DNA and RNA with fluorescent signal amplification and background reduction techniques. Front Cell Dev Biol 2023; 11:1216232. [PMID: 37342234 PMCID: PMC10277805 DOI: 10.3389/fcell.2023.1216232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Illuminating DNA and RNA dynamics in live cell can elucidate their life cycle and related biochemical activities. Various protocols have been developed for labeling the regions of interest in DNA and RNA molecules with different types of fluorescent probes. For example, CRISPR-based techniques have been extensively used for imaging genomic loci. However, some DNA and RNA molecules can still be difficult to tag and observe dynamically, such as genomic loci in non-repetitive regions. In this review, we will discuss the toolbox of techniques and methodologies that have been developed for imaging DNA and RNA. We will also introduce optimized systems that provide enhanced signal intensity or low background fluorescence for those difficult-to-tag molecules. These strategies can provide new insights for researchers when designing and using techniques to visualize DNA or RNA molecules.
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Affiliation(s)
- Song Lu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yu Hou
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
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11
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Hu XL, Gan HQ, Qin ZY, Liu Q, Li M, Chen D, Sessler JL, Tian H, He XP. Phenotyping of Methicillin-Resistant Staphylococcus aureus Using a Ratiometric Sensor Array. J Am Chem Soc 2023; 145:8917-8926. [PMID: 37040584 DOI: 10.1021/jacs.2c12798] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Chemical tools capable of classifying multidrug-resistant bacteria (superbugs) can facilitate early-stage disease diagnosis and help guide precision therapy. Here, we report a sensor array that permits the facile phenotyping of methicillin-resistant Staphylococcus aureus (MRSA), a clinically common superbug. The array consists of a panel of eight separate ratiometric fluorescent probes that provide characteristic vibration-induced emission (VIE) profiles. These probes bear a pair of quaternary ammonium salts in different substitution positions around a known VIEgen core. The differences in the substituents result in varying interactions with the negatively charged cell walls of bacteria. This, in turn, dictates the molecular conformation of the probes and affects their blue-to-red fluorescence intensity ratios (ratiometric changes). Within the sensor array, the differences in the ratiometric changes for the probes result in "fingerprints" for MRSA of different genotypes. This allows them to be identified using principal component analysis (PCA) without the need for cell lysis and nucleic acid isolation. The results obtained with the present sensor array agree well with those obtained using polymerase chain reaction (PCR) analysis.
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Affiliation(s)
- Xi-Le Hu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai 200237, China
| | - Hui-Qi Gan
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai 200237, China
| | - Zhao-Yang Qin
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai 200237, China
| | - Qian Liu
- Department of Laboratory Medicine, Ren Ji Hospital (Eastern), 160 Pujian Rd, Shanghai 200127, China
| | - Min Li
- Department of Laboratory Medicine, Ren Ji Hospital (Eastern), 160 Pujian Rd, Shanghai 200127, China
| | - Daijie Chen
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Rd, Minhang District, Shanghai 200240, China
| | - Jonathan L Sessler
- Department of Chemistry, The University of Texas at Austin, 105 East 24th Street-A5300, Austin, Texas 78712-1224, United States
| | - He Tian
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai 200237, China
| | - Xiao-Peng He
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai 200237, China
- The International Cooperation Laboratory on Signal Transduction, National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
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12
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Bradbury JJ, Lovegrove HE, Giralt-Pujol M, Herbert SP. Analysis of mRNA Subcellular Distribution in Collective Cell Migration. Methods Mol Biol 2023; 2608:389-407. [PMID: 36653719 DOI: 10.1007/978-1-0716-2887-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The movement of groups of cells by collective cell migration requires division of labor between group members. Therefore, distinct cell identities, unique cell behaviors, and specific cellular roles are acquired by cells undergoing collective movement. A key driving force behind the acquisition of discrete cell states is the precise control of where, when, and how genes are expressed, both at the subcellular and supracellular level. Unraveling the mechanisms underpinning the spatiotemporal control of gene expression in collective cell migration requires not only suitable experimental models but also high-resolution imaging of messenger RNA and protein localization during this process. In recent times, the highly stereotyped growth of new blood vessels by sprouting angiogenesis has become a paradigm for understanding collective cell migration, and consequently this has led to the development of numerous user-friendly in vitro models of angiogenesis. In parallel, single-molecule fluorescent in situ hybridization (smFISH) has come to the fore as a powerful technique that allows quantification of both RNA number and RNA spatial distribution in cells and tissues. Moreover, smFISH can be combined with immunofluorescence to understand the precise interrelationship between RNA and protein distribution. Here, we describe methods for use of smFISH and immunofluorescence microscopy in in vitro angiogenesis models to enable the investigation of RNA and protein expression and localization during endothelial collective cell migration.
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Affiliation(s)
- Joshua J Bradbury
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Holly E Lovegrove
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Marta Giralt-Pujol
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shane P Herbert
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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13
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Fluorophore-Tagged Poly(ʟ-Lysine) Block copolymer Nano-assemblies for Real-time Visualization and Antimicrobial Activity. Eur Polym J 2022. [DOI: 10.1016/j.eurpolymj.2022.111754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Dou CX, Ying ZM, Tang LJ, Wang F, Jiang JH. Genetically Encoded Light-Up RNA Amplifier Dissecting MicroRNA Activity in Live Cells. Anal Chem 2022; 94:15481-15488. [DOI: 10.1021/acs.analchem.2c03643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cai-Xia Dou
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Zhan-Ming Ying
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Li-Juan Tang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
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15
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Fam KT, Pelletier R, Bouhedda F, Ryckelynck M, Collot M, Klymchenko AS. Rational Design of Self-Quenched Rhodamine Dimers as Fluorogenic Aptamer Probes for Live-Cell RNA Imaging. Anal Chem 2022; 94:6657-6664. [PMID: 35486532 DOI: 10.1021/acs.analchem.1c04556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the growing interest in the understanding of the importance of RNAs in health and disease, detection of RNAs in living cells is of high importance. Fluorogenic dyes that light up specifically selected RNA aptamers constitute an attractive direction in the design of RNA imaging probes. In this work, based on our recently proposed concept of a fluorogenic dimer, we aim to develop a robust molecular tool for intracellular RNA imaging. We rationally designed a fluorogenic self-quenched dimer (orange Gemini, o-Gemini) based on rhodamine and evaluated its capacity to light up its cognate aptamer o-Coral in solution and live cells. We found that the removal of biotin from the dimer slightly improved the fluorogenic response without losing the affinity to the cognate aptamer (o-Coral). On the other hand, replacing sulforhodamine with a carboxyrhodamine produced drastic improvement of the affinity and the turn-on response to o-Coral and, thus, a better limit of detection. In live cells expressing o-Coral-tagged RNAs, the carboxyrhodamine analogue of o-Gemini without a biotin unit displayed a higher signal as well as faster internalization into the cells. We suppose that less hydrophilic carboxyrhodamine compared to sulforhodamine can more readily penetrate through the cell plasma membrane and, together with its higher affinity to o-Coral, provide the observed improvement in the imaging experiments. The promiscuity of the o-Coral RNA aptamer to the fluorogenic dimer allowed us to tune a fluorogen chemical structure and thus drastically improve the fluorescence response of the probe to o-Coral-tagged RNAs.
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Affiliation(s)
- Kyong Tkhe Fam
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
| | - Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
| | - Farah Bouhedda
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, F-67000 Strasbourg, France
| | - Michael Ryckelynck
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, F-67000 Strasbourg, France
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
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16
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Aptamer-based Cas14a1 biosensor for amplification-free live pathogenic detection. Biosens Bioelectron 2022; 211:114282. [DOI: 10.1016/j.bios.2022.114282] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/22/2022] [Accepted: 04/10/2022] [Indexed: 01/04/2023]
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17
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18
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Huang K, Chen X, Li C, Song Q, Li H, Zhu L, Yang Y, Ren A. Structure-based investigation of fluorogenic Pepper aptamer. Nat Chem Biol 2021; 17:1289-1295. [PMID: 34725509 DOI: 10.1038/s41589-021-00884-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 08/20/2021] [Indexed: 11/09/2022]
Abstract
Pepper fluorescent RNAs are a recently reported bright, stable and multicolor fluorogenic aptamer tag that enable imaging of diverse RNAs in live cells. To investigate the molecular basis of the superior properties of Pepper, we determined the structures of complexes of Pepper aptamer bound with its cognate HBC or HBC-like fluorophores at high resolution by X-ray crystallography. The Pepper aptamer folds in a monomeric non-G-quadruplex tuning-fork-like architecture composed of a helix and one protruded junction region. The near-planar fluorophore molecule intercalates in the middle of the structure and is sandwiched between one non-G-quadruplex base quadruple and one noncanonical G·U wobble helical base pair. In addition, structure-based mutational analysis is evaluated by in vitro and live-cell fluorogenic detection. Taken together, our research provides a structural basis for demystifying the fluorescence activation mechanism of Pepper aptamer and for further improvement of its future application in RNA visualization.
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Affiliation(s)
- Kaiyi Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Chunyan Li
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qianqian Song
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Huiwen Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, China.
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19
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Zhang J, Wang L, Jäschke A, Sunbul M. A Color‐Shifting Near‐Infrared Fluorescent Aptamer–Fluorophore Module for Live‐Cell RNA Imaging. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jingye Zhang
- Institute of Pharmacy and Molecular Biotechnology (IPMB) Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Lu Wang
- Department of Chemical Biology Max Planck Institute for Medical Research Jahnstraße 29 69120 Heidelberg Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB) Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB) Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
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20
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Rombouts S, Nollmann M. RNA imaging in bacteria. FEMS Microbiol Rev 2021; 45:5917984. [PMID: 33016325 DOI: 10.1093/femsre/fuaa051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/01/2020] [Indexed: 12/25/2022] Open
Abstract
The spatiotemporal regulation of gene expression plays an essential role in many biological processes. Recently, several imaging-based RNA labeling and detection methods, both in fixed and live cells, were developed and now enable the study of transcript abundance, localization and dynamics. Here, we review the main single-cell techniques for RNA visualization with fluorescence microscopy and describe their applications in bacteria.
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Affiliation(s)
- Sara Rombouts
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 Rue de Navacelles, 34090, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 Rue de Navacelles, 34090, Montpellier, France
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21
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Zhang J, Wang L, Jäschke A, Sunbul M. A Color-Shifting Near-Infrared Fluorescent Aptamer-Fluorophore Module for Live-Cell RNA Imaging. Angew Chem Int Ed Engl 2021; 60:21441-21448. [PMID: 34309994 PMCID: PMC8518806 DOI: 10.1002/anie.202107250] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Indexed: 11/07/2022]
Abstract
Fluorescent light‐up RNA aptamers (FLAPs) have become promising tools for visualizing RNAs in living cells. Specific binding of FLAPs to their non‐fluorescent cognate ligands results in a dramatic fluorescence increase, thereby allowing RNA imaging. Here, we present a color‐shifting aptamer‐fluorophore system, where the free dye is cyan fluorescent and the aptamer‐dye complex is near‐infrared (NIR) fluorescent. Unlike other reported FLAPs, this system enables ratiometric RNA imaging. To design the color‐shifting system, we synthesized a series of environmentally sensitive benzopyrylium‐coumarin hybrid fluorophores which exist in equilibrium between a cyan fluorescent spirocyclic form and a NIR fluorescent zwitterionic form. As an RNA tag, we evolved a 38‐nucleotide aptamer that selectively binds the zwitterionic forms with nanomolar affinity. We used this system as a light‐up RNA marker to image mRNAs in the NIR region and demonstrated its utility in ratiometric analysis of target RNAs expressed at different levels in single cells.
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Affiliation(s)
- Jingye Zhang
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Lu Wang
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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22
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Huang Y, Chen W, Chung J, Yin J, Yoon J. Recent progress in fluorescent probes for bacteria. Chem Soc Rev 2021; 50:7725-7744. [PMID: 34013918 DOI: 10.1039/d0cs01340d] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Food fermentation, antibiotics, and pollutant degradation are closely related to bacteria. Bacteria play an irreplaceable role in life. However, some bacteria seriously threaten human health and cause large-scale infectious diseases. Therefore, there is a pressing need to develop strategies to accurately monitor bacteria. Technology based on molecular probes and fluorescence imaging is noninvasive, results in little damage, and has high specificity and sensitivity, so it has been widely applied in the detection of bacteria. In this review, we summarize the recent progress in bacterial detection using fluorescence. In particular, we generalize the mechanisms commonly used to design organic fluorescent probes for detecting and imaging bacteria. Moreover, a perspective regarding fluorescent probes for bacterial detection is discussed.
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Affiliation(s)
- Yurou Huang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Weijie Chen
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Jeewon Chung
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyon-Dong, Sodaemun-Ku, Seoul 120-750, Korea.
| | - Jun Yin
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Juyoung Yoon
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyon-Dong, Sodaemun-Ku, Seoul 120-750, Korea.
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23
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Litke JL, Jaffrey SR. Trans ligation of RNAs to generate hybrid circular RNAs using highly efficient autocatalytic transcripts. Methods 2021; 196:104-112. [PMID: 33992775 DOI: 10.1016/j.ymeth.2021.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs are useful entities for various biotechnology applications, such as templating translation and binding or sequestering miRNA and RNA binding proteins. Circular RNA as highly resistant to degradation in cells and are more long-lived than linear RNAs. Here, we describe a method for intracellular trans ligation of RNA transcripts that can generate hybrid circular RNAs. These hybrid circular RNAs comprise two separate RNA that are covalently linked by ligation to form a circular RNA. By incorporating self-cleaving ribozymes at each site of ligation, trans ligation of the transcripts occurs in mammalian cells with no additional material. We provide a protocol for designing and testing trans ligation of transcripts and demonstrate detection of hybrid circular RNAs using fluorescence microscopy.
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Affiliation(s)
- Jacob L Litke
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY 10065, USA.
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24
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Yu Q, Ren K, You M. Genetically encoded RNA nanodevices for cellular imaging and regulation. NANOSCALE 2021; 13:7988-8003. [PMID: 33885099 PMCID: PMC8122502 DOI: 10.1039/d0nr08301a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nucleic acid-based nanodevices have been widely used in the fields of biosensing and nanomedicine. Traditionally, the majority of these nanodevices were first constructed in vitro using synthetic DNA or RNA oligonucleotides and then delivered into cells. Nowadays, the emergence of genetically encoded RNA nanodevices has provided a promising alternative approach for intracellular analysis and regulation. These genetically encoded RNA-based nanodevices can be directly transcribed and continuously produced inside living cells. A variety of highly precise and programmable nanodevices have been constructed in this way during the last decade. In this review, we will summarize the recent advances in the design and function of these artificial genetically encoded RNA nanodevices. In particular, we will focus on their applications in regulating cellular gene expression, imaging, logic operation, structural biology, and optogenetics. We believe these versatile RNA-based nanodevices will be broadly used in the near future to probe and program cells and other biological systems.
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Affiliation(s)
- Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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25
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Cubi R, Bouhedda F, Collot M, Klymchenko AS, Ryckelynck M. µIVC-Useq: a microfluidic-assisted high-throughput functionnal screening in tandem with next generation sequencing and artificial neural network to rapidly characterize RNA molecules. RNA (NEW YORK, N.Y.) 2021; 27:rna.077586.120. [PMID: 33952671 PMCID: PMC8208054 DOI: 10.1261/rna.077586.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 05/01/2021] [Indexed: 05/10/2023]
Abstract
The function of an RNA is intimately linked to its three-dimensional structure. X-ray crystallography or NMR allow the fine structural characterization of small RNA (e.g., aptamers) with a precision down to atomic resolution. Yet, these technics are time consuming, laborious and do not inform on mutational robustness and the extent to which a sequence can be modified without altering RNA function, an important set of information to assist RNA engineering. On another hand, thought powerful, in silico predictions still lack the required accuracy. These limitations can be overcome by using high-throughput microfluidic-assisted functional screening technologies, as they allow exploring large mutant libraries in a rapid and cost-effective manner. Among them, we recently introduced the microfluidic-assisted In Vitro Compartmentalization (µIVC), an efficient screening strategy in which reactions are performed in picoliter droplets at rates of several thousand per second. We later improved µIVC efficiency by using in tandem with high throughput sequencing, thought a laborious bioinformatic step was still required at the end of the process. In the present work, we strongly increased the automation level of the pipeline by implementing an artificial neural network enabling unsupervised bioinformatic analysis. We demonstrate the efficiency of this "µIVC-Useq" technology by rapidly identifying a set of sequences readily accepted by a key domain of the light-up RNA aptamer SRB-2. This work not only shed some new light on the way this aptamer can be engineered, but it also allowed us to easily identify new variants with an up-to 10-fold improved performance.
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26
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Abstract
Technologies for RNA imaging in live cells play an important role in understanding the function and regulatory process of RNAs. One approach for genetically encoded fluorescent RNA imaging involves fluorescent light-up aptamers (FLAPs), which are short RNA sequences that can bind cognate fluorogens and activate their fluorescence greatly. Over the past few years, FLAPs have emerged as genetically encoded RNA-based fluorescent biosensors for the cellular imaging and detection of various targets of interest. In this review, we first give a brief overview of the development of the current FLAPs based on various fluorogens. Then we further discuss on the photocycles of the reversibly photoswitching properties in FLAPs and their photostability. Finally, we focus on the applications of FLAPs as genetically encoded RNA-based fluorescent biosensors in biosensing and bioimaging, including RNA, non-nucleic acid molecules, metal ions imaging and quantitative imaging. Their design strategies and recent cellular applications are emphasized and summarized in detail.
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Affiliation(s)
- Huangmei Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, China.,NYU-ECNU Institute of Physics at NYU Shanghai, Shanghai, China
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27
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Du X, Wang W, Wu C, Jia B, Li W, Qiu L, Jiang P, Wang J, Li YQ. Enzyme-responsive turn-on nanoprobes for in situ fluorescence imaging and localized photothermal treatment of multidrug-resistant bacterial infections. J Mater Chem B 2021; 8:7403-7412. [PMID: 32658955 DOI: 10.1039/d0tb00750a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sensitive diagnosis and elimination of multidrug-resistant bacterial infections at an early stage remain paramount challenges. Herein, we present a gelatinase-responsive turn-on nanoprobe for in situ near-infrared (NIR) fluorescence imaging and localized photothermal treatment (PTT) of in vivo methicillin-resistant Staphylococcus aureus (MRSA) infections. The designed nanoprobe (named AuNS-Apt-Cy) is based on gold nanostars functionalized with MRSA-identifiable aptamer and gelatinase-responsive heptapeptide linker (CPLGVRG)-cypate complexes. The AuNS-Apt-Cy nanoprobe is non-fluorescent in aqueous environments due to the fluorescence resonance energy transfer between the gold nanostar core and cypate dye. We demonstrate that the AuNS-Apt-Cy nanoprobe can achieve MRSA targeting and accumulation as well as gelatinase (overexpressed in MRSA environments)-responsive turn-on NIR fluorescence due to the cleavage of the CPLGVRG linker and localized in vitro PTT via a mechanism involving bacterial cell wall and membrane disruption. In vivo experiments show that the AuNS-Apt-Cy nanoprobe can enable rapid (1 h post-administration) and in situ turn-on NIR fluorescence imaging with high sensitivity (105 colony-forming units) in diabetic wound and implanted bone plate mouse models. Remarkably, the AuNS-Apt-Cy nanoprobe can afford efficient localized PTT of diabetic wound and implanted bone plate-associated MRSA infections under the guidance of turn-on NIR fluorescence imaging, showing robust capability for early diagnosis and treatment of in vivo MRSA infections. In addition, the nanoprobe exhibits negligible damage to surrounding healthy tissues during PTT due to its targeted accumulation in the MRSA-infected site, guaranteeing its excellent in vivo biocompatibility and solving the main bottlenecks that hinder the clinical application of PTT-based antibacterial strategies.
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Affiliation(s)
- Xuancheng Du
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou 213164, China.
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28
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Ryckelynck M. Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More. Methods Mol Biol 2021; 2166:73-102. [PMID: 32710404 DOI: 10.1007/978-1-0716-0712-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.
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Affiliation(s)
- Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
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29
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Swetha P, Fan Z, Wang F, Jiang JH. Genetically encoded light-up RNA aptamers and their applications for imaging and biosensing. J Mater Chem B 2021; 8:3382-3392. [PMID: 31984401 DOI: 10.1039/c9tb02668a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intracellular small ligands and biomacromolecules are playing crucial roles not only as executors but also as regulators. It is essential to develop tools to investigate their dynamics to interrogate their functions and reflect the cellular status. Light-up RNA aptamers are RNA sequences that can bind with their cognate nonfluorescent fluorogens and greatly activate their fluorescence. The emergence of genetically encoded light-up RNA aptamers has provided fascinating tools for studying intracellular small ligands and biomacromolecules owing to their high fluorescence activation degree and facile programmability. Here we review the burgeoning field of light-up RNA aptamers. We first briefly introduce light-up RNA aptamers with a focus on the photophysical properties of the fluorogens. Then design strategies of genetically encoded light-up RNA aptamer based sensors including turn-on, signal amplification and ratiometric rationales are emphasized.
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Affiliation(s)
- Puchakayala Swetha
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hu-nan University, Changsha, 410082, P. R. China.
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30
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Sunbul M, Lackner J, Martin A, Englert D, Hacene B, Grün F, Nienhaus K, Nienhaus GU, Jäschke A. Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics. Nat Biotechnol 2021; 39:686-690. [PMID: 33574610 DOI: 10.1038/s41587-020-00794-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 12/10/2020] [Indexed: 11/09/2022]
Abstract
Overcoming limitations of previous fluorescent light-up RNA aptamers for super-resolution imaging, we present RhoBAST, an aptamer that binds a fluorogenic rhodamine dye with fast association and dissociation kinetics. Its intermittent fluorescence emission enables single-molecule localization microscopy with a resolution not limited by photobleaching. We use RhoBAST to image subcellular structures of RNA in live and fixed cells with about 10-nm localization precision and a high signal-to-noise ratio.
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Affiliation(s)
- Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.
| | - Jens Lackner
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Annabell Martin
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Daniel Englert
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Benjamin Hacene
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Franziska Grün
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Karin Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany. .,Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.
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31
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Dou CX, Liu C, Ying ZM, Dong W, Wang F, Jiang JH. Genetically Encoded Dual-Color Light-Up RNA Sensor Enabled Ratiometric Imaging of MicroRNA. Anal Chem 2021; 93:2534-2540. [PMID: 33461295 DOI: 10.1021/acs.analchem.0c04588] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
MicroRNAs (miRNAs) play essential roles in regulating gene expression and cell fate. However, it remains a great challenge to image miRNAs with high accuracy in living cells. Here, we report a novel genetically encoded dual-color light-up RNA sensor for ratiometric imaging of miRNAs using Mango as an internal reference and SRB2 as the sensor module. This genetically encoded sensor is designed by expressing a splittable fusion of the internal reference and sensor module under a single promoter. This design strategy allows synchronous expression of the two modules with negligible interference. Live cell imaging studies reveal that the genetically encoded ratiometric RNA sensor responds specifically to mir-224. Moreover, the sensor-to-Mango fluorescence ratios are linearly correlated with the concentrations of mir-224, confirming their capability of determining mir-224 concentrations in living cells. Our genetically encoded light-up RNA sensor also enables ratiometric imaging of mir-224 in different cell lines. This strategy could provide a versatile approach for ratiometric imaging of intracellular RNAs, affording powerful tools for interrogating RNA functions and abundance in living cells.
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Affiliation(s)
- Cai-Xia Dou
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Chaoyang Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Zhan-Ming Ying
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Wanrong Dong
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
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32
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Ordoñez AA, Jain SK. Imaging of Bacterial Infections. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00089-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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33
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Al Mazid MF, Shkel O, Kharkivska Y, Lee JS. Application of fluorescent turn-on aptamers in RNA studies. Mol Omics 2021; 17:483-491. [PMID: 34137415 DOI: 10.1039/d1mo00085c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA is an intermediate player between DNA transcription and protein translation. RNAs also interact with other macromolecules and metabolites and regulate their fate. The emerging number of RNA identifications expanded new areas of study to determine their applicability and functional analysis. Recently, extensive research has been focused on visualizing RNA in living biological samples and a method has been developed by the evolution of specific fluorophore-binding aptamers through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method. Several promising fluorescent turn-on aptamers are currently available, and they can detect RNA-RNA, RNA-protein, ligand binding, small molecule, and metabolite interactions in vitro and under live-cell conditions. Here we review the currently available fluorescent turn-on aptamers and discuss their applicability for analyzing the fate of targeted RNAs in in vitro and in vivo systems.
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Affiliation(s)
| | - Olha Shkel
- Bio-Med Program KIST-School UST, Seoul, 02792, Republic of Korea
| | | | - Jun-Seok Lee
- Department of Pharmacology, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
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34
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Zhu X, Qu B, Ying ZM, Liu JW, Wu Z, Yu RQ, Jiang JH. Cascade Circuits on Self-Assembled DNA Polymers for Targeted RNA Imaging In Vivo. Anal Chem 2020; 92:15953-15958. [PMID: 33275414 DOI: 10.1021/acs.analchem.0c03400] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA molecular probes have emerged as a powerful tool for RNA imaging. Hurdles in cell-specific delivery and other issues such as insufficient stability, limited sensitivity, or slow reaction kinetics, however, hinder the further application of DNA molecular probes in vivo. Herein, we report an aptamer-tethered DNA polymer for cell-specific transportation and amplified imaging of RNA in vivo via a DNA cascade reaction. DNA polymers are constructed through an initiator-triggered hybridization chain reaction using two functional DNA monomers. The prepared DNA polymers show low cytotoxicity and good stability against nuclease degradation and enable cell-specific transportation of DNA circuits via aptamer-receptor binding. Moreover, assembling the reactants of hairpins C1 and C2 on the DNA polymers accelerates the response kinetics and improves the sensitivity of the cascade reaction. We also show that the DNA polymers enable efficient imaging of microRNA-21 in live cells and in vivo via intravenous injection. The DNA polymers provide a valuable platform for targeted and amplified RNA imaging in vivo, which holds great implications for early clinical diagnosis and therapy.
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Affiliation(s)
- Xueli Zhu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China.,Henan Province Function-Oriented Porous Materials Key Laboratory, College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471934, Henan, China
| | - Bin Qu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Zhan-Ming Ying
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Jin-Wen Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China.,The First Affiliated Hospital of Guangxi Medical University, School of Preclinical Medicine & Centre for Translational Medicine, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China
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35
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Ren K, Keshri P, Wu R, Sun Z, Yu Q, Tian Q, Zhao B, Bagheri Y, Xie Y, You M. A Genetically Encoded RNA Photosensitizer for Targeted Cell Regulation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kewei Ren
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Puspam Keshri
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Rigumula Wu
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Zhining Sun
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Qikun Yu
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Qian Tian
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Bin Zhao
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Yousef Bagheri
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Yiwen Xie
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Mingxu You
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
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36
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Ren K, Keshri P, Wu R, Sun Z, Yu Q, Tian Q, Zhao B, Bagheri Y, Xie Y, You M. A Genetically Encoded RNA Photosensitizer for Targeted Cell Regulation. Angew Chem Int Ed Engl 2020; 59:21986-21990. [PMID: 32797667 PMCID: PMC7747015 DOI: 10.1002/anie.202010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/13/2020] [Indexed: 12/12/2022]
Abstract
Genetically encoded RNA devices have emerged for various cellular applications in imaging and biosensing, but their functions as precise regulators in living systems are still limited. Inspired by protein photosensitizers, we propose here a genetically encoded RNA aptamer based photosensitizer (GRAP). Upon illumination, the RNA photosensitizer can controllably generate reactive oxygen species for targeted cell regulation. The GRAP system can be selectively activated by endogenous stimuli and light of different wavelengths. Compared with their protein analogues, GRAP is highly programmable and exhibits reduced off-target effects. These results indicate that GRAP enables efficient noninvasive target cell ablation with high temporal and spatial precision. This new RNA regulator system will be widely used for optogenetics, targeted cell ablation, subcellular manipulation, and imaging.
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Affiliation(s)
- Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Qian Tian
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Bin Zhao
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Yousef Bagheri
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Yiwen Xie
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
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37
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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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38
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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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39
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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40
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Braselmann E, Rathbun C, Richards EM, Palmer AE. Illuminating RNA Biology: Tools for Imaging RNA in Live Mammalian Cells. Cell Chem Biol 2020; 27:891-903. [PMID: 32640188 PMCID: PMC7595133 DOI: 10.1016/j.chembiol.2020.06.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/30/2020] [Accepted: 06/15/2020] [Indexed: 01/06/2023]
Abstract
The central dogma teaches us that DNA makes RNA, which in turn makes proteins, the main building blocks of the cell. But this over simplified linear transmission of information overlooks the vast majority of the genome produces RNAs that do not encode proteins and the myriad ways that RNA regulates cellular functions. Historically, one of the challenges in illuminating RNA biology has been the lack of tools for visualizing RNA in live cells. But clever approaches for exploiting RNA binding proteins, in vitro RNA evolution, and chemical biology have resulted in significant advances in RNA visualization tools in recent years. This review provides an overview of current tools for tagging RNA with fluorescent probes and tracking their dynamics, localization andfunction in live mammalian cells.
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Affiliation(s)
- Esther Braselmann
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Colin Rathbun
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Erin M Richards
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Amy E Palmer
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA.
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41
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Sending messages in moving cells: mRNA localization and the regulation of cell migration. Essays Biochem 2020; 63:595-606. [PMID: 31324705 DOI: 10.1042/ebc20190009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022]
Abstract
Cell migration is a fundamental biological process involved in tissue formation and homeostasis. The correct polarization of motile cells is critical to ensure directed movement, and is orchestrated by many intrinsic and extrinsic factors. Of these, the subcellular distribution of mRNAs and the consequent spatial control of translation are key modulators of cell polarity. mRNA transport is dependent on cis-regulatory elements within transcripts, which are recognized by trans-acting proteins that ensure the efficient delivery of certain messages to the leading edge of migrating cells. At their destination, translation of localized mRNAs then participates in regional cellular responses underlying cell motility. In this review, we summarize the key findings that established mRNA targetting as a critical driver of cell migration and how the characterization of polarized mRNAs in motile cells has been expanded from just a few species to hundreds of transcripts. We also describe the molecular control of mRNA trafficking, subsequent mechanisms of local protein synthesis and how these ultimately regulate cell polarity during migration.
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42
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Wirth R, Gao P, Nienhaus GU, Sunbul M, Jäschke A. Confocal and Super-resolution Imaging of RNA in Live Bacteria Using a Fluorogenic Silicon Rhodamine-binding Aptamer. Bio Protoc 2020; 10:e3603. [PMID: 33659569 DOI: 10.21769/bioprotoc.3603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/15/2020] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
Genetically encoded light-up RNA aptamers have been shown to be promising tools for the visualization of RNAs in living cells, helping us to advance our understanding of the broad and complex life of RNA. Although a handful of light-up aptamers spanning the visible wavelength region have been developed, none of them have yet been reported to be compatible with advanced super-resolution techniques, mainly due to poor photophysical properties of their small-molecule fluorogens. Here, we describe a detailed protocol for fluorescence microscopy of mRNA in live bacteria using the recently reported fluorogenic silicon rhodamine binding aptamer (SiRA) featuring excellent photophysical properties. Notably, with SiRA, we demonstrated the first aptamer-based RNA visualization using super-resolution (STED) microscopy. This imaging method can be especially valuable for visualization of RNA in prokaryotes since the size of a bacterium is only a few times greater than the optical resolution of a conventional microscope.
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Affiliation(s)
- Regina Wirth
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Peng Gao
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
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43
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Wu R, Karunanayake Mudiyanselage AP, Ren K, Sun Z, Tian Q, Zhao B, Bagheri Y, Lutati D, Keshri P, You M. Ratiometric Fluorogenic RNA-Based Sensors for Imaging Live-Cell Dynamics of Small Molecules. ACS APPLIED BIO MATERIALS 2020; 3:2633-2642. [DOI: 10.1021/acsabm.9b01237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | | | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Qian Tian
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Bin Zhao
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Yousef Bagheri
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - David Lutati
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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44
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RNA-based fluorescent biosensors for live cell imaging of small molecules and RNAs. Curr Opin Biotechnol 2020; 63:157-166. [PMID: 32086101 DOI: 10.1016/j.copbio.2020.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/23/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022]
Abstract
Genetically encodable fluorescent biosensors provide spatiotemporal information on their target analytes in a label-free manner, which has enabled the study of cell biology and signaling in living cells. Over the past three decades, fueled by the development of a wide palette of fluorescent proteins, protein-based fluorescent biosensors against a broad array of targets have been developed. Recently, with the development of fluorogenic RNA aptamer-dye pairs that function in live cells, RNA-based fluorescent (RBF) biosensors have emerged as a complementary class of biosensors. Here we review the current state-of-the-art for fluorogenic RNA aptamers and RBF biosensors for imaging small molecules and RNAs, and highlight some emerging opportunities.
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45
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Schmidt A, Gao G, Little SR, Jalihal AP, Walter NG. Following the messenger: Recent innovations in live cell single molecule fluorescence imaging. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1587. [PMID: 31990126 DOI: 10.1002/wrna.1587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/19/2019] [Accepted: 01/04/2020] [Indexed: 01/16/2023]
Abstract
Messenger RNAs (mRNAs) convey genetic information from the DNA genome to proteins and thus lie at the heart of gene expression and regulation of all cellular activities. Live cell single molecule tracking tools enable the investigation of mRNA trafficking, translation and degradation within the complex environment of the cell and in real time. Over the last 5 years, nearly all tools within the mRNA tracking toolbox have been improved to achieve high-quality multi-color tracking in live cells. For example, the bacteriophage-derived MS2-MCP system has been improved to facilitate cloning and achieve better signal-to-noise ratio, while the newer PP7-PCP system now allows for orthogonal tracking of a second mRNA or mRNA region. The coming of age of epitope-tagging technologies, such as the SunTag, MoonTag and Frankenbody, enables monitoring the translation of single mRNA molecules. Furthermore, the portfolio of fluorogenic RNA aptamers has been expanded to improve cellular stability and achieve a higher fluorescence "turn-on" signal upon fluorogen binding. Finally, microinjection-based tools have been shown to be able to track multiple RNAs with only small fluorescent appendages and to track mRNAs together with their interacting partners. We systematically review and compare the advantages, disadvantages and demonstrated applications in discovering new RNA biology of this refined, expanding toolbox. Finally, we discuss developments expected in the near future based on the limitations of the current methods. This article is categorized under: RNA Export and Localization > RNA Localization RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Andreas Schmidt
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Guoming Gao
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan.,Biophysics Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Saffron R Little
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan
| | - Ameya P Jalihal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan.,Cell and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan
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46
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Anhäuser L, Hüwel S, Zobel T, Rentmeister A. Multiple covalent fluorescence labeling of eukaryotic mRNA at the poly(A) tail enhances translation and can be performed in living cells. Nucleic Acids Res 2019; 47:e42. [PMID: 30726958 PMCID: PMC6468298 DOI: 10.1093/nar/gkz084] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
Post-transcriptional regulation of gene expression occurs by multiple mechanisms, including subcellular localization of mRNA and alteration of the poly(A) tail length. These mechanisms play crucial roles in the dynamics of cell polarization and embryonic development. Furthermore, mRNAs are emerging therapeutics and chemical alterations to increase their translational efficiency are highly sought after. We show that yeast poly(A) polymerase can be used to install multiple azido-modified adenosine nucleotides to luciferase and eGFP-mRNAs. These mRNAs can be efficiently reacted in a bioorthogonal click reaction with fluorescent reporters without degradation and without sequence alterations in their coding or untranslated regions. Importantly, the modifications in the poly(A) tail impact positively on the translational efficiency of reporter-mRNAs in vitro and in cells. Therefore, covalent fluorescent labeling at the poly(A) tail presents a new way to increase the amount of reporter protein from exogenous mRNA and to label genetically unaltered and translationally active mRNAs.
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Affiliation(s)
- Lea Anhäuser
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Thomas Zobel
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
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47
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Xiao M, Zou K, Li L, Wang L, Tian Y, Fan C, Pei H. Stochastic DNA Walkers in Droplets for Super‐Multiplexed Bacterial Phenotype Detection. Angew Chem Int Ed Engl 2019; 58:15448-15454. [DOI: 10.1002/anie.201906438] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/12/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Kui Zou
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Lihua Wang
- Department School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 200240 China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Chunhai Fan
- Department School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 200240 China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
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48
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A dimerization-based fluorogenic dye-aptamer module for RNA imaging in live cells. Nat Chem Biol 2019; 16:69-76. [PMID: 31636432 PMCID: PMC6920041 DOI: 10.1038/s41589-019-0381-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 08/22/2019] [Indexed: 01/19/2023]
Abstract
Live-cell imaging of RNA has remained a challenge because of the lack of naturally fluorescent RNAs. Recently developed RNA aptamers that can light-up small fluorogenic dyes could overcome this limitation, but they still suffer from poor brightness and photostability. Here, we propose a concept of cell-permeable fluorogenic dimer of sulforhodamine B dyes (Gemini-561) and corresponding dimerized aptamer (o-Coral) that can drastically enhance performance of the current RNA imaging method. The unprecedented brightness and photostability together with high affinity of this complex allowed, for the first time, direct fluorescence imaging in live mammalian cells of RNA polymerase-III transcription products as well as messenger RNAs labelled with a single copy of the aptamer, i.e. without tag multimerization. The developed fluorogenic module enables fast and sensitive detection of RNA inside live cells, while the proposed design concept opens the route to new generation of ultrabright RNA probes.
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49
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Chen X, Zhang D, Su N, Bao B, Xie X, Zuo F, Yang L, Wang H, Jiang L, Lin Q, Fang M, Li N, Hua X, Chen Z, Bao C, Xu J, Du W, Zhang L, Zhao Y, Zhu L, Loscalzo J, Yang Y. Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs. Nat Biotechnol 2019; 37:1287-1293. [PMID: 31548726 DOI: 10.1038/s41587-019-0249-1] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 08/02/2019] [Indexed: 12/15/2022]
Abstract
Fluorescent RNAs (FRs), aptamers that bind and activate fluorescent dyes, have been used to image abundant cellular RNA species. However, limitations such as low brightness and limited availability of dye/aptamer combinations with different spectral characteristics have limited use of these tools in live mammalian cells and in vivo. Here, we develop Peppers, a series of monomeric, bright and stable FRs with a broad range of emission maxima spanning from cyan to red. Peppers allow simple and robust imaging of diverse RNA species in live cells with minimal perturbation of the target RNA's transcription, localization and translation. Quantification of the levels of proteins and their messenger RNAs in single cells suggests that translation is governed by normal enzyme kinetics but with marked heterogeneity. We further show that Peppers can be used for imaging genomic loci with CRISPR display, for real-time tracking of protein-RNA tethering, and for super-resolution imaging. We believe these FRs will be useful tools for live imaging of cellular RNAs.
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Affiliation(s)
- Xianjun Chen
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Dasheng Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Ni Su
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Xin Xie
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Fangting Zuo
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Lipeng Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Hui Wang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Jiang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Mengyue Fang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ningfeng Li
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Xin Hua
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhengda Chen
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Chunyan Bao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Jinjin Xu
- Key Laboratory of Advanced Control and Optimization for Chemical Processed of Ministry of Education, School of information Science and Engineering, East China University of Science and Technology, Shanghai, China
| | - Wenli Du
- Key Laboratory of Advanced Control and Optimization for Chemical Processed of Ministry of Education, School of information Science and Engineering, East China University of Science and Technology, Shanghai, China
| | - Lixin Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Linyong Zhu
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China. .,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China. .,School of Pharmacy, East China University of Science and Technology, Shanghai, China.
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50
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Xiao M, Zou K, Li L, Wang L, Tian Y, Fan C, Pei H. Stochastic DNA Walkers in Droplets for Super‐Multiplexed Bacterial Phenotype Detection. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906438] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Kui Zou
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Lihua Wang
- Department School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Chunhai Fan
- Department School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
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