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Liu W, Chen D, Pian H, Su F, Wang H, Zhang P, Li Z. One-by-one single-molecule counting method for digital quantification of SARS-CoV-2 RNA. NANO TODAY 2022; 47:101664. [PMID: 36340244 PMCID: PMC9618441 DOI: 10.1016/j.nantod.2022.101664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/11/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Digital counting individual nucleic acid molecule is of great significance for fundamental biological research and accurate diagnosis of genetic diseases, which is hard to achieve with existing single-molecule detection technologies. Herein, we report a novel one-by-one single-molecule counting method for digital quantification of SARS-Cov-2 RNA. This method uses one fluorescent micromotor functionalized with peptide nucleic acids (PNAs) to specially capture one target RNA molecule. The RNA-micromotors can be propelled by the electric field to target district and accurately counted. Moreover, the method can also clearly discriminate one-base mutation in the target RNAs, indicating the great potential for clinical diagnostics and virus traceability survey.
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Affiliation(s)
- Weiliang Liu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Desheng Chen
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Hongru Pian
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Fengxia Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Pengbo Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
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2
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St-Pierre B, Mahroug S, Guirimand G, Courdavault V, Burlat V. RNA In Situ Hybridization of Paraffin Sections to Characterize the Multicellular Compartmentation of Plant Secondary Metabolisms. Methods Mol Biol 2022; 2505:1-32. [PMID: 35732933 DOI: 10.1007/978-1-0716-2349-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As a mean to cope with their potential cytotoxicity for the host plant, secondary metabolisms are often sequestered within specific cell types. This spatial organization may reach complex sequential multicellular compartmentation. The most complex example so far characterized is the sequential multicellular biosynthesis of the anticancer monoterpene indole alkaloids in Catharanthus roseus. RNA in situ hybridization has proven a key technological approach to unravel this complex spatial organization. Pioneer work in 1999 discovered the involvement of epidermis and laticifer/idioblasts in the intermediate and late steps of the pathway, respectively. The localization of the early steps of the pathway to the internal phloem-associated parenchyma later came to complete the three-tissular block organization of the pathway. Since then, RNA in situ hybridization was routinely used to map the gene expression profile of most of the nearly 30 genes involved in this pathway. We introduce here a comparison of advantages and drawbacks of in situ hybridization and more popular promoter: GUS strategies. Two main advantages of in situ hybridization are the suitability to any plant species and the direct localization of transcripts rather than the localization of a promoter activity. We provide a step-by-step protocol describing every details allowing to reach a medium throughput including riboprobe synthesis, paraffin-embedded plant tissue array preparation, prehybridization, in situ hybridization, stringent washing and immunodetection of hybridized probes, and imaging steps. This should be helpful for new comers willing to domesticate the technique. This protocol has no species limitation and is particularly adapted to the increasingly studied model, nonmodel species, nonamenable to promoter::GUS transformation, such as C. roseus.
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Affiliation(s)
- Benoit St-Pierre
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Samira Mahroug
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Gregory Guirimand
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France.
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3
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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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4
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Tian T, Shu B, Jiang Y, Ye M, Liu L, Guo Z, Han Z, Wang Z, Zhou X. An Ultralocalized Cas13a Assay Enables Universal and Nucleic Acid Amplification-Free Single-Molecule RNA Diagnostics. ACS NANO 2021; 15:1167-1178. [PMID: 33498106 DOI: 10.1021/acsnano.0c08165] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Existing methods for RNA diagnostics, such as reverse transcription PCR (RT-PCR), mainly rely on nucleic acid amplification (NAA) and RT processes, which are known to introduce substantial issues, including amplification bias, cross-contamination, and sample loss. To address these problems, we introduce a confinement effect-inspired Cas13a assay for single-molecule RNA diagnostics, eliminating the need for NAA and RT. This assay involves confining the RNA-triggered Cas13a catalysis system in cell-like-sized reactors to enhance local concentrations of target and reporter simultaneously, via droplet microfluidics. It achieves >10 000-fold enhancement in sensitivity when compared to the bulk Cas13a assay and enables absolute digital single-molecule RNA quantitation. We experimentally demonstrate its broad applicability for precisely counting microRNAs, 16S rRNAs, and SARS-CoV-2 RNA from synthetic sequences to clinical samples with excellent accuracy. Notably, this direct RNA diagnostic technology enables detecting a wide range of RNA molecules at the single-molecule level. Moreover, its simplicity, universality, and excellent quantification capability might render it to be a dominant rival to RT-qPCR.
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Affiliation(s)
- Tian Tian
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Bowen Shu
- Department of Laboratory Medicine, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Yongzhong Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Miaomiao Ye
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Lei Liu
- Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, Center for Studies of Psychological Application, South China Normal University, Guangzhou 510631, China
| | - Zhonghui Guo
- Department of Clinical Laboratory Medicine, Central Hospital of Panyu District, Guangzhou 511400, China
| | - Zeping Han
- Department of Clinical Laboratory Medicine, Central Hospital of Panyu District, Guangzhou 511400, China
| | - Zhang Wang
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou 510180, China
| | - Xiaoming Zhou
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
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5
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Young AP, Jackson DJ, Wyeth RC. A technical review and guide to RNA fluorescence in situ hybridization. PeerJ 2020; 8:e8806. [PMID: 32219032 PMCID: PMC7085896 DOI: 10.7717/peerj.8806] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
RNA-fluorescence in situ hybridization (FISH) is a powerful tool to visualize target messenger RNA transcripts in cultured cells, tissue sections or whole-mount preparations. As the technique has been developed over time, an ever-increasing number of divergent protocols have been published. There is now a broad selection of options available to facilitate proper tissue preparation, hybridization, and post-hybridization background removal to achieve optimal results. Here we review the technical aspects of RNA-FISH, examining the most common methods associated with different sample types including cytological preparations and whole-mounts. We discuss the application of commonly used reagents for tissue preparation, hybridization, and post-hybridization washing and provide explanations of the functional roles for each reagent. We also discuss the available probe types and necessary controls to accurately visualize gene expression. Finally, we review the most recent advances in FISH technology that facilitate both highly multiplexed experiments and signal amplification for individual targets. Taken together, this information will guide the methods development process for investigators that seek to perform FISH in organisms that lack documented or optimized protocols.
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Affiliation(s)
- Alexander P Young
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
| | - Daniel J Jackson
- Department of Geobiology, Georg-August Universität Göttingen, Göttingen, Germany
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
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6
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Medium-Throughput RNA In Situ Hybridization of Serial Sections from Paraffin-Embedded Tissue Microarrays. Methods Mol Biol 2019. [PMID: 30945181 DOI: 10.1007/978-1-4939-9045-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
(m)RNA spatiotemporal pattern of distribution is of key importance to decipher gene function. In this post-genomic era, numerous transcriptomic studies are made publicly available, sometimes reaching a tissular resolution and even more rarely the cellular level. This "one tissue-numerous genes" information can be completed by the reverse "one gene-numerous tissues" picture through traditional RNA in situ hybridization (ISH). Here, we present a method including (1) principles of transcriptomic data mining to be performed prior and following ISH and (2) a detailed step-by-step medium-throughput ISH protocol performed on serial sections from tissue microarrays. In a recent work, we implemented this method for 39 selected genes studied by medium-throughput ISH complementing an existing tissue-specific transcriptomic dataset focused on the model plant Arabidopsis seed development kinetics (Francoz et al., Scientific Reports 6:24644, 2016). This full integration of ISH and transcriptomics demonstrated the complementarity of both techniques in terms of tissue/cell specificity, signal sensitivity, gene specificity, and spatiotemporal resolution.
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7
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Ying ZM, Yuan YY, Tu B, Tang LJ, Yu RQ, Jiang JH. A single promoter system co-expressing RNA sensor with fluorescent proteins for quantitative mRNA imaging in living tumor cells. Chem Sci 2019; 10:4828-4833. [PMID: 31160957 PMCID: PMC6509996 DOI: 10.1039/c9sc00458k] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/27/2019] [Indexed: 12/14/2022] Open
Abstract
Genetically encoded light-up RNA aptamers afford a valuable platform for developing RNA sensors toward live cell imaging. However, quantitative imaging of intracellular RNAs remains a grand challenge. Here we reported a novel genetically encoded RNA sensor strategy using a plasmid that expresses a splittable fusion of the RNA sensor and the GFP mRNA in an individual transcript using a single promoter system. This splittable fusion design enables synchronous co-expression of the RNA sensor with GFP mRNA while alleviates the interference with correct folding of RNA aptamers due to intramolecular hybridization. This single-promoter system is applied to ratiometric imaging of survivin mRNA in tumor cells. The results reveal that the ratiometric images dynamically correlated with survivin mRNA concentrations and allow quantitative imaging of survivin mRNA in different tumor cells. The RNA sensor strategy may provide a new paradigm for developing a robust imaging platform for quantitative mRNA studies in living cells.
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Affiliation(s)
- Zhan-Ming Ying
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Yue-Yan Yuan
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Bin Tu
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Li-Juan Tang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Ru-Qin Yu
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Jian-Hui Jiang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
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8
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Abstract
Optical microscopy has served biomedical research for decades due to its high temporal and spatial resolutions. Among various optical imaging techniques, fluorescence imaging offers superb sensitivity down to single molecule level but its multiplexing capacity is limited by intrinsically broad bandwidth. To simultaneously capture a vast number of targets, the newly emerging vibrational microscopy technique draws increasing attention as vibration spectroscopy features narrow transition linewidth. Nonetheless, unlike fluorophores that have been studied for centuries, a systematic investigation on vibrational probes is underemphasized. Herein, we reviewed some of the recent developments of vibrational probes for multiplex imaging applications, particularly those serving stimulated Raman scattering (SRS) microscopy, which is one of the most promising vibrational imaging techniques. We wish to summarize the general guidelines for developing bioorthogonal vibrational probes with high sensitivity, chemical specificity and most importantly, tunability to fulfill super-multiplexed optical imaging. Future directions to significantly improve the performance are also discussed.
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Affiliation(s)
- Yupeng Miao
- Department of Chemistry, Columbia University, New York, NY 10027, United States of America
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9
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Reynolds CJ, Koszewski NJ, Horst RL, Beitz DC, Goff JP. Localization of the 1,25-dihydroxyvitamin d-mediated response in the intestines of mice. J Steroid Biochem Mol Biol 2019; 186:56-60. [PMID: 30236486 PMCID: PMC6342631 DOI: 10.1016/j.jsbmb.2018.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/10/2018] [Accepted: 09/12/2018] [Indexed: 01/09/2023]
Abstract
1,25-Dihydroxyvitamin D3 (1,25(OH)2D) elicits a transcriptional response in the intestines. Assessments of this response are often derived from crude tissue homogenates and eliminate the ability to discriminate among different cell types. Here, we used an RNA in situ hybridization assay, RNAScope (Advanced Cell Diagnostics, Newark, CA), to identify the cells in the intestine that respond to 1,25(OH)2D with expression of cytochrome P450 family 24 subfamily A member 1 (Cyp24a1) mRNA. Mice were gavaged with a single bolus dose of 1,25(OH)2D to target the duodenum or a glucuronic acid conjugate of 1,25(OH)2D, β-G-1,25(OH)2D, to target the colon. QRT-PCR analysis of Cyp24a1 mRNA verified that the 1,25(OH)2D-induced responses were present. RNAScope revealed that the mRNA response present after six hours is limited to mature enterocytes exposed to the intestinal lumen in both the duodenum and colon. No detectable expression was observed in goblet cells, lamina propria, muscularis mucosa muscle, submucosa and submucosal lymphoid follicles, or tunica muscularis. Our findings have identified epithelial enterocytes to be the intestinal targets for 1,25(OH)2D in both the duodenum and colon.
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Affiliation(s)
- Carmen J Reynolds
- Department of Animal Science, Iowa State University, 806 Stange Road, Ames, Iowa 50011, USA.
| | - Nicholas J Koszewski
- Department of Biomedical Sciences, Iowa State University, 1800 Christensen Drive, Ames, Iowa, 50011, USA.
| | - Ronald L Horst
- Heartland Assays, 2711 South Loop Drive, Ames, Iowa, 50010, USA.
| | - Donald C Beitz
- Department of Animal Science, Iowa State University, 806 Stange Road, Ames, Iowa 50011, USA.
| | - Jesse P Goff
- Department of Biomedical Sciences, Iowa State University, 1800 Christensen Drive, Ames, Iowa, 50011, USA.
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10
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Identification of Insulin Receptor Splice Variant B in Neurons by in situ Detection in Human Brain Samples. Sci Rep 2018; 8:4070. [PMID: 29511314 PMCID: PMC5840297 DOI: 10.1038/s41598-018-22434-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/22/2018] [Indexed: 12/28/2022] Open
Abstract
Insulin and its receptor are widely expressed in a variety of tissues throughout the body including liver, adipose tissue, liver and brain. The insulin receptor is expressed as two functionally distinct isoforms, differentiated by a single 12 amino acid exon. The two receptor isoforms, designated IR/A and IR/B, are expressed in a highly tissue and cell specific manner and relative proportions of the different isoforms vary during development, aging and disease states. The high degree of similarity between the two isoforms has prevented detailed studies as differentiation of the two isoforms by traditional immunological methods cannot be achieved. We describe here a new in situ RT-PCR/ FISH assay that allows for the visualization of IR/A and IR/B in tissue along with tissue specific markers. We used this new method to show for the first time that IR/A and IR/B are both expressed in neurons in the adult human brain. Thus, we present a method that enables the investigation of IR/A and IR/B insulin receptor isoform expression in situ in various tissues.
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11
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Kim SC, Clark IC, Shahi P, Abate AR. Single-Cell RT-PCR in Microfluidic Droplets with Integrated Chemical Lysis. Anal Chem 2018; 90:1273-1279. [PMID: 29256243 PMCID: PMC5991602 DOI: 10.1021/acs.analchem.7b04050] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Droplet microfluidics can identify and sort cells using digital reverse transcription polymerase chain reaction (RT-PCR) signals from individual cells. However, current methods require multiple microfabricated devices for enzymatic cell lysis and PCR reagent addition, making the process complex and prone to failure. Here, we describe a new approach that integrates all components into a single device. The method enables controlled exposure of isolated single cells to a high pH buffer, which lyses cells and inactivates reaction inhibitors but can be instantly neutralized with RT-PCR buffer. Using our chemical lysis approach, we distinguish individual cells' gene expression with data quality equivalent to more complex two-step workflows. Our system accepts cells and produces droplets ready for amplification, making single-cell droplet RT-PCR faster and more reliable.
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Affiliation(s)
- Samuel C. Kim
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Iain C. Clark
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Payam Shahi
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, University of California, San Francisco, San Francisco, California, USA
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12
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Spear A, Wang FX, Kappes MA, Das PB, Faaberg KS. Progress toward an enhanced vaccine: Eight marked attenuated viruses to porcine reproductive and respiratory disease virus. Virology 2018; 516:30-37. [PMID: 29324359 DOI: 10.1016/j.virol.2017.12.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/21/2017] [Accepted: 12/25/2017] [Indexed: 01/31/2023]
Abstract
Recombinant viruses of strain Ingelvac® PRRS porcine reproductive and respiratory syndrome virus (PRRSV) modified live virus vaccine were produced with two individual small in-frame deletions in nonstructural protein 2 (nsp2; Δ23 and Δ87) and also the same deletions supplanted with foreign tags (Δ23-V5, Δ23-FLAG, Δ23-S, Δ87-V5, Δ87-FLAG, Δ87-S). The viruses, but one (Δ87-FLAG), were stable for 10 passages and showed minimal effects on in vitro growth. Northern hybridization showed that the Δ23-tagged probe detected intracellular viral genome RNA as well as shorter RNAs that may represent heteroclite species, while the Δ87-tagged probe detected predominantly only genome length RNAs. When the tagged viruses were used to probe nsp2 protein in infected cells, perinuclear localization similar to native nsp2 was seen. Dual infection of Δ23-S and Δ87-S viruses allowed some discrimination of individual tagged nsp2 protein, facilitating future research. The mutants could potentially also be used to differentiate infected from vaccinated animals.
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Affiliation(s)
- Allyn Spear
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, USA.
| | - Feng-Xue Wang
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, USA.
| | - Matthew A Kappes
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, USA.
| | - Phani B Das
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, USA.
| | - Kay S Faaberg
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, USA.
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13
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Beckman W, Vuist IM, Kempe H, Verschure PJ. Cell-to-Cell Transcription Variability as Measured by Single-Molecule RNA FISH to Detect Epigenetic State Switching. Methods Mol Biol 2018. [PMID: 29524147 DOI: 10.1007/978-1-4939-7774-1_21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Single-molecule RNA fluorescent in situ hybridization (smRNA FISH) allows for the visualization, localization, and quantification of RNA transcripts within individual cells and tissues using custom-designed fluorescently labeled oligonucleotide probes. Here we describe a protocol for the preparation, imaging, and analysis of a smRNA FISH experiment that can be applied to any RNA of choice. We also provide insights as to how this powerful tool can be used to study epigenetic regulation, for example, following the epigenetic editing of genes.
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Affiliation(s)
- William Beckman
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Ilona M Vuist
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Hermannus Kempe
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Pernette J Verschure
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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14
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George JT, Srivatsan SG. Vinyluridine as a Versatile Chemoselective Handle for the Post-transcriptional Chemical Functionalization of RNA. Bioconjug Chem 2017; 28:1529-1536. [PMID: 28406614 DOI: 10.1021/acs.bioconjchem.7b00169] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development of modular and efficient methods to functionalize RNA with biophysical probes is very important in advancing the understanding of the structural and functional relevance of RNA in various cellular events. Herein, we demonstrate a two-step bioorthogonal chemical functionalization approach for the conjugation of multiple probes onto RNA transcripts using a 5-vinyl-modified uridine nucleotide analog (VUTP). VUTP, containing a structurally noninvasive and versatile chemoselective handle, was efficiently incorporated into RNA transcripts by in vitro transcription reactions. Furthermore, we show for the first time the use of a palladium-mediated oxidative Heck reaction in functionalizing RNA with fluorogenic probes by reacting vinyl-labeled RNA transcripts with appropriate boronic acid substrates. The vinyl label also permitted the post-transcriptional functionalization of RNA by a reagent-free inverse electron demand Diels-Alder (IEDDA) reaction in the presence of tetrazine substrates. Collectively, our results demonstrate that the incorporation of VUTP provides newer possibilities for the modular functionalization of RNA with variety of reporters.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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15
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Precise small-molecule recognition of a toxic CUG RNA repeat expansion. Nat Chem Biol 2016; 13:188-193. [PMID: 27941760 DOI: 10.1038/nchembio.2251] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 10/03/2016] [Indexed: 01/10/2023]
Abstract
Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG)exp) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG)exp. In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG)exp and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG)exp in its natural context.
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16
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Liu J, Irudayaraj JMK. Non-fluorescent quantification of single mRNA with transient absorption microscopy. NANOSCALE 2016; 8:19242-19248. [PMID: 27883134 DOI: 10.1039/c6nr04433f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single molecule detection is confounded by the background signals from the biological environment, such as autofluorescence, Rayleigh scattering, or turbidity in cells and tissues. In this article, we report on the utilization of gold nanoparticles (AuNPs) as an orthogonal probe for non-fluorescence detection of single molecules with a transient absorption microscopy (TAM). The developed system and concepts were validated by quantitative evaluation of human epidermal receptor 2 (Her2) mRNA in cancer cells and tissues at single copy sensitivity. Results from TAM suggest that the average number of Her2 copies in SK-BR-3 and MCF-7 breast cancer cells is 203.19 ± 80.48, and 11.29 ± 4.47, respectively. Furthermore, TAM offers excellent signal-to-noise ratio in detecting mRNA in clinical tissues, indicating a significantly higher expression of Her2 genes in breast cancer tissues than that of normal tissues. Our single cell quantification TAM strategy was validated with a fluorescence in situ hybridization approach. Our demonstration shows that TAM has the potential to provide a new dimension in biomarker quantification at single molecule sensitivity in turbid biological environments providing a strong basis for clinical monitoring.
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Affiliation(s)
- Jing Liu
- Bindley Bioscience Center and Birck Nanotechnology Center, Agriculture & Biological Engineering, Purdue University, West Lafayette, IN 47907, USA. and Nanoscience and Nanoengineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA. and Biochemical Spatio-Temporal NetWork Resource (BioSNTR), State of South Dakota, USA
| | - Joseph M K Irudayaraj
- Bindley Bioscience Center and Birck Nanotechnology Center, Agriculture & Biological Engineering, Purdue University, West Lafayette, IN 47907, USA.
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17
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Complementarity of medium-throughput in situ RNA hybridization and tissue-specific transcriptomics: case study of Arabidopsis seed development kinetics. Sci Rep 2016; 6:24644. [PMID: 27095274 PMCID: PMC4837347 DOI: 10.1038/srep24644] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/29/2016] [Indexed: 12/28/2022] Open
Abstract
The rationale of this study is to compare and integrate two heterologous datasets intended to unravel the spatiotemporal specificities of gene expression in a rapidly growing and complex organ. We implemented medium-throughput RNA in situ hybridization (ISH) for 39 genes mainly corresponding to cell wall proteins for which we have particular interest, selected (i) on their sequence identity (24 class III peroxidase multigenic family members and 15 additional genes used as positive controls) and (ii) on their expression levels in a publicly available Arabidopsis thaliana seed tissue-specific transcriptomics study. The specificity of the hybridization signals was carefully studied, and ISH results obtained for the 39 selected genes were systematically compared with tissue-specific transcriptomics for 5 seed developmental stages. Integration of results illustrates the complementarity of both datasets. The tissue-specific transcriptomics provides high-throughput possibilities whereas ISH provides high spatial resolution. Moreover, depending on the tissues and the developmental stages considered, one or the other technique appears more sensitive than the other. For each tissue/developmental stage, we finally determined tissue-specific transcriptomic threshold values compatible with the spatiotemporally-specific detection limits of ISH for lists of hundreds to tens-of-thousands of genes.
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18
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Abstract
Over the last decade, the long accepted dogma that heterochromatin is silent has been challenged by increasing evidence of active transcription in these apocryphally annotated quiescent regions of the genome. The recent discovery of noncoding RNAs (ncRNAs) originating from, or localizing to, centromeres, pericentromeres, and telomeres (ie, constitutive heterochromatin) suggest a potential role for ncRNAs in genome integrity. This new paradigm suggests that ncRNAs may recruit chromatin-binding factors, stabilize the higher order folded state of the chromatin fiber, and participate in regulation of processes such as transcription-mediated nucleosome assembly. Thus, identifying, purifying, and elucidating the function of ncRNAs has the potential to provide key insights into genome organization and is currently a topic of intense experimental investigation.
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Affiliation(s)
- D Quénet
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
| | - D Sturgill
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Y Dalal
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
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19
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Liu Y, Sousa R, Wang YX. Specific labeling: An effective tool to explore the RNA world. Bioessays 2015; 38:192-200. [DOI: 10.1002/bies.201500119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
| | - Rui Sousa
- Department of Biochemistry; University of Texas Health Science Center; San Antonio TX USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
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20
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Sawant AA, Tanpure AA, Mukherjee PP, Athavale S, Kelkar A, Galande S, Srivatsan SG. A versatile toolbox for posttranscriptional chemical labeling and imaging of RNA. Nucleic Acids Res 2015; 44:e16. [PMID: 26384420 PMCID: PMC4737177 DOI: 10.1093/nar/gkv903] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 08/31/2015] [Indexed: 12/21/2022] Open
Abstract
Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple and modular posttranscriptional chemical labeling and imaging technique for RNA by using a novel toolbox comprised of azide-modified UTP analogs. These analogs facilitate the enzymatic incorporation of azide groups into RNA, which can be posttranscriptionally labeled with a variety of probes by click and Staudinger reactions. Importantly, we show for the first time the specific incorporation of azide groups into cellular RNA by endogenous RNA polymerases, which enabled the imaging of newly transcribing RNA in fixed and in live cells by click reactions. This labeling method is practical and provides a new platform to study RNA in vitro and in cells.
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Affiliation(s)
- Anupam A Sawant
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Progya P Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Soumitra Athavale
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Ashwin Kelkar
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sanjeev Galande
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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21
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Liu J, Cho IH, Cui Y, Irudayaraj J. Second harmonic super-resolution microscopy for quantification of mRNA at single copy sensitivity. ACS NANO 2014; 8:12418-27. [PMID: 25494326 PMCID: PMC4334232 DOI: 10.1021/nn505096t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cell-specific information on the quantity and localization of key mRNAs at single copy sensitivity in single cells is critical for evaluating basic cellular process, disease risk, and efficacy of therapy. Quantification of overexpressed mRNAs beyond the diffraction limit is constrained by the optical property of the probes and microscopy techniques. In this report, nanosized barium titanium oxide (BaTiO3, BTO) crystals were utilized as probes for mRNA quantification by a second harmonic super-resolution microscopy (SHaSM). The SHaSM was able to detect a single copy of the human epidermal growth factor receptor 2 (Her2) mRNA at a resolution of 55.6 nm with the ability to resolve multiple mRNA copies in a diffraction-limited spot. Her2 mRNA per cell was counted in SK-BR-3, MCF-7, and HeLa cell lines as 595±79.1, 38.9±8.26, and 1.5±2.8, respectively. Our single-cell quantification results were validated with the fluorescence in situ hybridization studies and quantitative PCR, showing better specificity and selectivity over current single-molecule approaches for transcript detection. The SHaSM is expected to have an upper limit of resolving ∼10(4) transcripts in a single cell with the ability to monitor intracellular transcriptional dynamics at video rate. The developed approach has strong potential in clinical research and in the early diagnosis of life-threatening diseases such as cancer.
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22
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Tian L, Okita TW. mRNA-based protein targeting to the endoplasmic reticulum and chloroplasts in plant cells. CURRENT OPINION IN PLANT BIOLOGY 2014; 22:77-85. [PMID: 25282588 DOI: 10.1016/j.pbi.2014.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/06/2014] [Accepted: 09/15/2014] [Indexed: 05/12/2023]
Abstract
The targeting of proteins to subcellular organelles is specified by the presence of signal/leader peptide sequences normally located on the N-terminus. In the past two decades, messenger RNA (mRNA) localization, a pathway driven by cis-acting localization elements within the RNA sequence, has emerged as an alternative mechanism for protein targeting to specific locations in the cytoplasm, on the endoplasmic reticulum or to mitochondria and chloroplasts. In this review, we will summarize studies on mRNA-based protein targeting to the endoplasmic reticulum and chloroplast within plant cells.
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Affiliation(s)
- Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA.
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23
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McDonald RI, Guilinger JP, Mukherji S, Curtis EA, Lee WI, Liu DR. Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling. Nat Chem Biol 2014; 10:1049-54. [PMID: 25306441 PMCID: PMC4232462 DOI: 10.1038/nchembio.1655] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/21/2014] [Indexed: 02/08/2023]
Abstract
Probes that form covalent bonds with RNA molecules on the basis of their chemical reactivity would advance our ability to study the transcriptome. We developed a set of electrophilic activity-based RNA probes designed to react with unusually nucleophilic RNAs. We used these probes to identify reactive genome-encoded RNAs, resulting in the discovery of a 42-nt catalytic RNA from an archaebacterium that reacts with a 2,3-disubstituted epoxide at N7 of a specific guanosine. Detailed characterization of the catalytic RNA revealed the structural requirements for reactivity. We developed this catalytic RNA into a general tool to selectively conjugate a small molecule to an RNA of interest. This strategy enabled up to 500-fold enrichment of target RNA from total mammalian RNA or from cell lysate. We demonstrated the utility of this approach by selectively capturing proteins in yeast cell lysate that bind the ASH1 mRNA.
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Affiliation(s)
- Richard I. McDonald
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - John P. Guilinger
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - Shankar Mukherji
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA
| | - Edward A. Curtis
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - Won I. Lee
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - David R. Liu
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
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24
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Hövelmann F, Gaspar I, Loibl S, Ermilov EA, Röder B, Wengel J, Ephrussi A, Seitz O. Brightness through local constraint--LNA-enhanced FIT hybridization probes for in vivo ribonucleotide particle tracking. Angew Chem Int Ed Engl 2014; 53:11370-5. [PMID: 25167966 DOI: 10.1002/anie.201406022] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Indexed: 11/11/2022]
Abstract
Imaging the dynamics of RNA in living cells is usually performed by means of transgenic approaches that require modification of RNA targets and cells. Fluorogenic hybridization probes would also allow the analysis of wild-type organisms. We developed nuclease-resistant DNA forced intercalation (FIT) probes that combine the high enhancement of fluorescence upon hybridization with the high brightness required to allow tracking of individual ribonucleotide particles (RNPs). In our design, a single thiazole orange (TO) intercalator dye is linked as a nucleobase surrogate and an adjacent locked nucleic acid (LNA) unit serves to introduce a local constraint. This closes fluorescence decay channels and thereby increases the brightness of the probe-target duplexes. As few as two probes were sufficient to enable the tracking of oskar mRNPs in wild-type living Drosophila melanogaster oocytes.
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Affiliation(s)
- Felix Hövelmann
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin (Germany)
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25
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Hövelmann F, Gaspar I, Loibl S, Ermilov EA, Röder B, Wengel J, Ephrussi A, Seitz O. Helligkeit durch lokale Rigidifizierung - LNA-verstärkte FIT-Sonden zur bildgebenden Darstellung von Ribonukleotidpartikeln in vivo. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Sun S, Wang J, Mu D, Wang J, Bao Y, Qiao B, Peng X. A heterodinuclear RuIr metal complex for direct imaging of rRNA in living cells. Chem Commun (Camb) 2014; 50:9149-52. [DOI: 10.1039/c4cc04501g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A novel dual luminescence heterodinuclear RuIr complex for RNA detection was developed, which was successfully used to image rRNA in living cells.
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Affiliation(s)
- Shiguo Sun
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian, China
| | - Jitao Wang
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian, China
| | - Daozhou Mu
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian, China
| | - Jingyun Wang
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian, China
| | - Yongming Bao
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian, China
| | - Bo Qiao
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian, China
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27
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Holstein JM, Schulz D, Rentmeister A. Bioorthogonal site-specific labeling of the 5′-cap structure in eukaryotic mRNAs. Chem Commun (Camb) 2014; 50:4478-81. [DOI: 10.1039/c4cc01549e] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A chemo-enzymatic approach for site-specific labeling of 5′-capped RNAs based on strain-promoted azide–alkyne cycloaddition (SPAAC) was developed.
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Affiliation(s)
| | - Daniela Schulz
- Institute of Biochemistry
- University of Muenster
- D-48149 Münster, Germany
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28
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Baker M. Erratum: RNA imaging in situ. Nat Methods 2012. [DOI: 10.1038/nmeth1012-1031d] [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]
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