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Peng Y, Shu L, Deng X, Huang X, Mo X, Du F, Tang Z. Live-Cell Imaging of Endogenous RNA with a Genetically Encoded Fluorogenic Allosteric Aptamer. Anal Chem 2023; 95:13762-13768. [PMID: 37661353 DOI: 10.1021/acs.analchem.2c05724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Imaging and tracking tools for natural cellular RNA with improved biocompatibility, specificity, and sensitivity are critical to understanding RNA function and providing insights into disease therapeutics. We developed a new genetically encoded sensor using fluorogenic allosteric aptamer (FaApt) for the sensitive imaging of the localization and dynamics of RNA targets in live cells. Target RNAs can be specifically recognized with our sensor by forming perfectly complementary duplexes, which in turn can induce allosteric structural changes of the sensor to refold the native conformation of fluorogenic RNA aptamers. We demonstrated the ability of the sensor to monitor the effect of tumor necrosis factor and small-molecule inhibitor on the expression abundance of CXCL1 and survivin mRNA in human cancer cells, respectively. The asymmetrical distribution of endogenous Squint mRNA was confirmed in developing zebrafish embryos through microinjection of FaApt probes. This study provides an effective molecular tool for sensitive imaging and tracking endogenous RNA in living cells. Due to the high specificity and small size of our sensor system, it is expected to be applied to early diagnosis of RNA marker-related diseases and real-time evaluation of the treatment process.
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Affiliation(s)
- Yan Peng
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Linjuan Shu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 6100141, P. R. China
| | - Xiongfei Deng
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Xianming Mo
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 6100141, P. R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
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2
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Chen M, Sui T, Yang L, Qian Y, Liu Z, Liu Y, Wang G, Lai L, Li Z. Live imaging of RNA and RNA splicing in mammalian cells via the dcas13a-SunTag-BiFC system. Biosens Bioelectron 2022; 204:114074. [PMID: 35149451 DOI: 10.1016/j.bios.2022.114074] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 01/19/2022] [Accepted: 02/02/2022] [Indexed: 12/26/2022]
Abstract
Dynamic tracking of the localization of RNA molecules (nucleus and/or cytoplasm) and RNA splicing in living cells plays an important role in understanding their functions. However, a lack of dynamic imaging and high background fluorescence have been reported in the fluorescence in situ hybridization (FISH). Here, we developed a new tool, the dcas13a-SunTag-BiFC system, which fused the dLwacas13a and SunTag systems. dLwacas13a is used as a tracker to target specific RNAs, while SunTag recruits split Venus fluorescent proteins to label targeted RNAs. Our results showed that 4 × NLS-dCas13a-24 × SunTag-BiFC and 2 × NLS- dCas13a-24 × SunTag-BiFC systems can be used for imaging of endogenous RNA foci in the nucleus (Xist) and cytoplasm (Ppib and stress granules) in living cells, respectively. Compared to 12x MS2-MCP system, the dcas13a-SunTag-BiFC system showed a better performance of mRNA foci tracking in live cells. Furthermore, we confirmed the premature termination codon (PTC)-induced exon skipping of Oxt RNA using the dcas13a-SunTag-BiFC and MS2-MCP systems in the nucleus. Thus, the dcas13a-SunTag-BiFC system will facilitate the study of RNA localization in living cells and provide new insights into RNA translocation and splicing.
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Affiliation(s)
- Mao Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Tingting Sui
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Li Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Yuqiang Qian
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Zhiquan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Yongsai Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Gerong Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China.
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Depaix A, Mlynarska-Cieslak A, Warminski M, Sikorski PJ, Jemielity J, Kowalska J. RNA Ligation for Mono and Dually Labeled RNAs. Chemistry 2021; 27:12190-12197. [PMID: 34114681 DOI: 10.1002/chem.202101909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 12/27/2022]
Abstract
Labeled RNAs are invaluable probes for investigation of RNA function and localization. However, mRNA labeling remains challenging. Here, we developed an improved method for 3'-end labeling of in vitro transcribed RNAs. We synthesized novel adenosine 3',5'-bisphosphate analogues modified at the N6 or C2 position of adenosine with an azide-containing linker, fluorescent label, or biotin and assessed these constructs as substrates for RNA labeling directly by T4 ligase or via postenzymatic strain-promoted alkyne-azide cycloaddition (SPAAC). All analogues were substrates for T4 RNA ligase. Analogues containing bulky fluorescent labels or biotin showed better overall labeling yields than postenzymatic SPAAC. We successfully labeled uncapped RNAs, NAD-capped RNAs, and 5'-fluorescently labeled m7 Gp3 Am -capped mRNAs. The obtained highly homogenous dually labeled mRNA was translationally active and enabled fluorescence-based monitoring of decapping. This method will facilitate the use of various functionalized mRNA-based probes.
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Affiliation(s)
- Anaïs Depaix
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Agnieszka Mlynarska-Cieslak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
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Fang C, Li Y, Hu S, Wang H, Chen X, Zhu X. Self-Assembled Growing DNA Tree Mediated by Exosomes for Amplified Imaging of Messenger RNA in Living Cells. Anal Chem 2021; 93:8414-8422. [PMID: 34114453 DOI: 10.1021/acs.analchem.1c00211] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sensitive, accurate, and nondestructive probing of endogenous messenger RNA (mRNA) in living cells places extremely high demands on nanocarriers and probes and is still a challenge. In the present study, we describe a target-triggered self-assembled DNA tree for amplified analysis of mRNA in intact living cells. The probes assembled into a DNA tree are transported into cells by exosomes, which is beneficial for reducing cell damage and realizing nondestructive analysis. The probes are l-configured single-stranded DNAs (LDNAs) that can resist the degradation of exonuclease and endonuclease, thus laying the foundation for accurate analysis. Under the induction of the target mRNA, the probes in the cells assemble into a small plantlet and eventually grow into a tree after a few rounds of self-cycling, achieving the exponential amplification of fluorescence signals. Compared with the signal amplification based on one-dimensional DNA trunk self-assembly, the three-dimensional DNA tree shows an excellent sensitivity both ex situ and in situ. In this way, favorable sensitivity, accuracy, and nondestructive analysis are integrated into one system. This DNA tree expands the analysis platform for analyzing more biomarkers on a genetic level in an intracellular, nondestructive, and hypersensitive manner and holds great potential in clinical diagnostic and research applications.
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Affiliation(s)
- Cheng Fang
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Yuming Li
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Song Hu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Hao Wang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Xiaoxia Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.,School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China.,Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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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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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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Liu X, Yu S, Feng C, Mao D, Li J, Zhu X. In situ Analysis of Cancer Cells Based on DNA Signal Amplification and DNA Nanodevices. Crit Rev Anal Chem 2019; 51:8-19. [PMID: 31613139 DOI: 10.1080/10408347.2019.1674631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cancer is a global disease which has been disturbing researchers in medicine and seriously threatens patients' health and lifetime around the world in the past several decades. Due to the characteristics of cancer cells, such as uncontrollable cell proliferation, cell invasion and metastasis to surrounding tissues, lower grade of differentiation, higher telomerase activity and others, it has been one of the most usual lethal factors, next to heart disease in incidence. Cancer mortality can be decreased by early diagnosis, and the people who with treatment at an early stage have an obvious improved survival rate. Consequently, early detection is significant for better understanding the pathogenesis of cancer and improving the prognosis of patients. In situ detection technique is a vital tool for imaging and cellular pathology research, which can provide effective information about tumor markers in the early cancer detection. In view of low expression of most tumor markers in the early stage of cancers, detection techniques based on DNA signal amplification and DNA nanodevices can provide a strong support for the diagnosis and detection of cancers. In this review, we summarize the research progress of different analytical techniques for detecting various tumor markers that have been reported in recent years. We compare different DNA amplification and nanodevices, then provide guidance and suggestions for better understanding in situ analysis of cancer cells.
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Affiliation(s)
- Xiaohao Liu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Sinuo Yu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Dongsheng Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Jinlong Li
- Department of Laboratory Medicine, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, P. R. China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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Ryckelynck M. Development and engineering of artificial RNAs. Methods 2019; 161:1-2. [DOI: 10.1016/j.ymeth.2019.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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