51
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2019; 58:1266-1279. [PMID: 30102012 PMCID: PMC6391945 DOI: 10.1002/anie.201806482] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 12/16/2022]
Abstract
The cellular functions of RNA are not limited to their role as blueprints for protein synthesis. In particular, noncoding RNA, such as, snRNAs, lncRNAs, miRNAs, play important roles. With increasing numbers of RNAs being identified, it is well known that the transcriptome outnumbers the proteome by far. This emphasizes the great importance of functional RNA characterization and the need to further develop tools for these investigations, many of which are still in their infancy. Fluorescent light-up aptamers (FLAPs) are RNA sequences that can bind nontoxic, cell-permeable small-molecule fluorogens and enhance their fluorescence over many orders of magnitude upon binding. FLAPs can be encoded on the DNA level using standard molecular biology tools and are subsequently transcribed into RNA by the cellular machinery, so that they can be used as fluorescent RNA tags (FLAP-tags). In this Minireview, we give a brief overview of the fluorogens that have been developed and their binding RNA aptamers, with a special focus on published crystal structures. A summary of current and future cellular FLAP applications with an emphasis on the study of RNA-RNA and RNA-protein interactions using split-FLAP and Förster resonance energy transfer (FRET) systems is given.
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Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
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52
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
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53
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Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nat Commun 2018; 9:4542. [PMID: 30382099 PMCID: PMC6208384 DOI: 10.1038/s41467-018-06942-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/26/2018] [Indexed: 12/24/2022] Open
Abstract
The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO3 bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure. The DIR2s RNA aptamer activates the fluorescence of cyanine dyes allowing detection of two well-resolved emission colors. Here authors solve the crystal structures of the apo and OTB-SO3 fluorophore-bound DIR2s and show how the fluorophore ligand is bound.
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Affiliation(s)
- Sandip A Shelke
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Artur Laski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Deepak Koirala
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | | | - James R Fuller
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaohong Tan
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Tudor P Constantin
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Alan S Waggoner
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Marcel P Bruchez
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Bruce A Armitage
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA. .,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
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54
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Zaitseva SO, Golodukhina SV, Baleeva NS, Levina EA, Smirnov AY, Zagudaylova MB, Baranov MS. Azidoacetic Acid Amides in the Synthesis of Substituted Arylidene‐1‐
H
‐imidazol‐5‐(4
H
)‐ones. ChemistrySelect 2018. [DOI: 10.1002/slct.201801349] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Snizhana O. Zaitseva
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Svetlana V. Golodukhina
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S. Baleeva
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Evgenia A. Levina
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu. Smirnov
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Marina B. Zagudaylova
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1 117997 Moscow Russia
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55
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Tang X, Deng R, Sun Y, Ren X, Zhou M, Li J. Amplified Tandem Spinach-Based Aptamer Transcription Enables Low Background miRNA Detection. Anal Chem 2018; 90:10001-10008. [PMID: 30016869 DOI: 10.1021/acs.analchem.8b02471] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs) play key roles in regulating gene expression and cell functions, which are recognized as potential biomarkers for many human diseases. Sensitive, specific, and reliable detection of miRNA is highly demanded for clinical diagnosis and therapy. Herein, we describe a label-free and low-background fluorescent assay, termed amplified tandem Spinach-based aptamer transcription assay (AmptSpi assay) for highly sensitive miRNA detection by polymeric rolling circle amplicon mediated multiple transcription. Target miRNA is recognized by padlock probe to form polymeric rolling circle amplicon. Then the following transcription process rapidly produces large amounts of repeats of RNA Spinach aptamers, lightened up by the addition of fluorescent dye DFHBI for miRNA quantitative analysis, achieving label-free and nearly zero-background. Besides, the assay could also confer high selectivity to distinguish miRNA among the miRNA family members with 1- or 2-nucleotide (nt) difference. This method was capable of completing detection in human serum sample or cell extracts in hours, indicating great potential in the early diagnosis of diseases.
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Affiliation(s)
- Xin Tang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Yupeng Sun
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Xiaojun Ren
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Mengxi Zhou
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
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56
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A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells. Nat Chem Biol 2018; 14:964-971. [PMID: 30061719 PMCID: PMC6143402 DOI: 10.1038/s41589-018-0103-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/13/2018] [Indexed: 11/29/2022]
Abstract
RNAs directly regulate a vast array of cellular processes, emphasizing the need for robust approaches to fluorescently label and track RNAs in living cells. Here, we develop an RNA imaging platform using the cobalamin riboswitch as an RNA tag and a series of probes containing cobalamin as a fluorescence quencher. This highly modular ‘Riboglow’ platform leverages different colored fluorescent dyes, linkers and riboswitch RNA tags to elicit fluorescent turn-on upon binding RNA. We demonstrate the ability of two different Riboglow probes to track mRNA and small non-coding RNA in live mammalian cells. A side-by-side comparison revealed that Riboglow outperformed the dye binding aptamer Broccoli and performed on par with the gold standard RNA imaging system, the MS2-fluorescent protein system, while featuring a much smaller RNA tag. Together, the versatility of the Riboglow platform and ability to track diverse RNAs suggest broad applicability for a variety of imaging approaches.
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57
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Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines. Nat Commun 2018; 9:2283. [PMID: 29891903 PMCID: PMC5995956 DOI: 10.1038/s41467-018-04691-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/09/2018] [Indexed: 02/07/2023] Open
Abstract
Large RNAs and ribonucleoprotein complexes have powerful therapeutic potential, but effective cell-targeted delivery tools are limited. Aptamers that internalize into target cells can deliver siRNAs (<15 kDa, 19–21 nt/strand). We demonstrate a modular nanostructure for cellular delivery of large, functional RNA payloads (50–80 kDa, 175–250 nt) by aptamers that recognize multiple human B cell cancer lines and transferrin receptor-expressing cells. Fluorogenic RNA reporter payloads enable accelerated testing of platform designs and rapid evaluation of assembly and internalization. Modularity is demonstrated by swapping in different targeting and payload aptamers. Both modules internalize into leukemic B cell lines and remained colocalized within endosomes. Fluorescence from internalized RNA persists for ≥2 h, suggesting a sizable window for aptamer payloads to exert influence upon targeted cells. This demonstration of aptamer-mediated, cell-internalizing delivery of large RNAs with retention of functional structure raises the possibility of manipulating endosomes and cells by delivering large aptamers and regulatory RNAs. Large RNAs and ribonucleoprotein complexes have shown potential as novel therapeutic agents, but their targeted delivery to cells is still challenging. Here the authors present a modular aptamer nanostructure for intracellular delivery of RNAs up to 250 nucleotides to cancer cells.
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58
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Kikuchi N, Kolpashchikov DM. A universal split spinach aptamer (USSA) for nucleic acid analysis and DNA computation. Chem Commun (Camb) 2018; 53:4977-4980. [PMID: 28425510 DOI: 10.1039/c7cc01540b] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We demonstrate how a single universal spinach aptamer (USSA) probe can be used to detect multiple (potentially any) nucleic acid sequences. USSA can be used for cost-efficient and highly selective analysis of even folded DNA and RNA analytes, as well as for the readout of outputs of DNA logic circuits.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA
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59
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Li C, Plamont MA, Aujard I, Le Saux T, Jullien L, Gautier A. Design and characterization of red fluorogenic push-pull chromophores holding great potential for bioimaging and biosensing. Org Biomol Chem 2018; 14:9253-9261. [PMID: 27714200 DOI: 10.1039/c6ob01612j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorogenic chromophores have been used recently for fluorescence reporting and biosensing. Their ability to turn on upon specific interaction with a given target has been exploited in particular for the design of fluorogen-based reporters enabling biomolecule labeling and imaging. In this paper, we report the development and exhaustive characterization of a new family of red fluorogenic push-pull chromophores, holding great potential for the development of fluorogen-based reporters or intracellular fluorogenic markers. The proposed methodology is generic and should find general applicability in the discovery of new fluorogenic dyes suitable for the design of fluorogen-based reporters and biosensors.
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Affiliation(s)
- Chenge Li
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Marie-Aude Plamont
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Isabelle Aujard
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Le Saux
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Ludovic Jullien
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Arnaud Gautier
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
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60
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Ying ZM, Tu B, Liu L, Tang H, Tang LJ, Jiang JH. Spinach-based fluorescent light-up biosensors for multiplexed and label-free detection of microRNAs. Chem Commun (Camb) 2018; 54:3010-3013. [PMID: 29511749 DOI: 10.1039/c8cc00123e] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel Spinach-based fluorescent light-up biosensor utilizing the T7 in vitro transcription process to generate unmodified Spinach sequences for multiplexed microRNA detection has been developed.
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Affiliation(s)
- Zhan-Ming Ying
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Bin Tu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Lan Liu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Hao Tang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Li-Juan Tang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Jian-Hui Jiang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
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61
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Autour A, C Y Jeng S, D Cawte A, Abdolahzadeh A, Galli A, Panchapakesan SSS, Rueda D, Ryckelynck M, Unrau PJ. Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells. Nat Commun 2018; 9:656. [PMID: 29440634 PMCID: PMC5811451 DOI: 10.1038/s41467-018-02993-8] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/11/2018] [Indexed: 12/26/2022] Open
Abstract
Despite having many key roles in cellular biology, directly imaging biologically important RNAs has been hindered by a lack of fluorescent tools equivalent to the fluorescent proteins available to study cellular proteins. Ideal RNA labelling systems must preserve biological function, have photophysical properties similar to existing fluorescent proteins, and be compatible with established live and fixed cell protein labelling strategies. Here, we report a microfluidics-based selection of three new high-affinity RNA Mango fluorogenic aptamers. Two of these are as bright or brighter than enhanced GFP when bound to TO1-Biotin. Furthermore, we show that the new Mangos can accurately image the subcellular localization of three small non-coding RNAs (5S, U6, and a box C/D scaRNA) in fixed and live mammalian cells. These new aptamers have many potential applications to study RNA function and dynamics both in vitro and in mammalian cells.
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Affiliation(s)
- Alexis Autour
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000, Strasbourg, France
| | - Sunny C Y Jeng
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Adam D Cawte
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.,Department of Medicine, Molecular Virology, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Amir Abdolahzadeh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Angela Galli
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Shanker S S Panchapakesan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - David Rueda
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK. .,Department of Medicine, Molecular Virology, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000, Strasbourg, France.
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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62
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Bouhedda F, Autour A, Ryckelynck M. Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications. Int J Mol Sci 2017; 19:ijms19010044. [PMID: 29295531 PMCID: PMC5795994 DOI: 10.3390/ijms19010044] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 12/31/2022] Open
Abstract
An RNA-based fluorogenic module consists of a light-up RNA aptamer able to specifically interact with a fluorogen to form a fluorescent complex. Over the past decade, significant efforts have been devoted to the development of such modules, which now cover the whole visible spectrum, as well as to their engineering to serve in a wide range of applications. In this review, we summarize the different strategies used to develop each partner (the fluorogen and the light-up RNA aptamer) prior to giving an overview of their applications that range from live-cell RNA imaging to the set-up of high-throughput drug screening pipelines. We then conclude with a critical discussion on the current limitations of these modules and how combining in vitro selection with screening approaches may help develop even better molecules.
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Affiliation(s)
- Farah Bouhedda
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
| | - Alexis Autour
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
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63
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Wang Z, Luo Y, Xie X, Hu X, Song H, Zhao Y, Shi J, Wang L, Glinsky G, Chen N, Lal R, Fan C. In Situ Spatial Complementation of Aptamer-Mediated Recognition Enables Live-Cell Imaging of Native RNA Transcripts in Real Time. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707795] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Zejun Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
| | - Yao Luo
- School of Life Sciences; Sichuan University; Chengdu 610064 China
| | - Xiaodong Xie
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
| | - Xingjie Hu
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
| | - Haiyun Song
- Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai 200031 China
| | - Yun Zhao
- School of Life Sciences; Sichuan University; Chengdu 610064 China
| | - Jiye Shi
- UCB Pharma; 208 Bath Road Slough SL1 3WE UK
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
| | - Gennadi Glinsky
- University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Nan Chen
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
| | - Ratnesh Lal
- University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
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64
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Wang Z, Luo Y, Xie X, Hu X, Song H, Zhao Y, Shi J, Wang L, Glinsky G, Chen N, Lal R, Fan C. In Situ Spatial Complementation of Aptamer-Mediated Recognition Enables Live-Cell Imaging of Native RNA Transcripts in Real Time. Angew Chem Int Ed Engl 2017; 57:972-976. [PMID: 28991414 DOI: 10.1002/anie.201707795] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/18/2017] [Indexed: 12/18/2022]
Abstract
Direct cellular imaging of the localization and dynamics of biomolecules helps to understand their function and reveals novel mechanisms at the single-cell resolution. In contrast to routine fluorescent-protein-based protein imaging, technology for RNA imaging remains less well explored because of the lack of enabling technology. Herein, we report the development of an aptamer-initiated fluorescence complementation (AiFC) method for RNA imaging by engineering a green fluorescence protein (GFP)-mimicking turn-on RNA aptamer, Broccoli, into two split fragments that could tandemly bind to target mRNA. When genetically encoded in cells, endogenous mRNA molecules recruited Split-Broccoli and brought the two fragments into spatial proximity, which formed a fluorophore-binding site in situ and turned on fluorescence. Significantly, we demonstrated the use of AiFC for high-contrast and real-time imaging of endogenous RNA molecules in living mammalian cells. We envision wide application and practical utility of this enabling technology to in vivo single-cell visualization and mechanistic analysis of macromolecular interactions.
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Affiliation(s)
- Zejun Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yao Luo
- School of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Xiaodong Xie
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Xingjie Hu
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Haiyun Song
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yun Zhao
- School of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Jiye Shi
- UCB Pharma, 208 Bath Road, Slough, SL1 3WE, UK
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Gennadi Glinsky
- University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nan Chen
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Ratnesh Lal
- University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
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65
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Fernandez-Millan P, Autour A, Ennifar E, Westhof E, Ryckelynck M. Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI. RNA (NEW YORK, N.Y.) 2017; 23:1788-1795. [PMID: 28939697 PMCID: PMC5689000 DOI: 10.1261/rna.063008.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 09/05/2017] [Indexed: 05/05/2023]
Abstract
Fluorogenic RNA aptamers are short nucleic acids able to specifically interact with small molecules and strongly enhance their fluorescence upon complex formation. Among the different systems recently introduced, Spinach, an aptamer forming a fluorescent complex with the 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), is one of the most promising. Using random mutagenesis and ultrahigh-throughput screening, we recently developed iSpinach, an improved version of the aptamer, endowed with an increased folding efficiency and thermal stability. iSpinach is a shorter version of Spinach, comprising five mutations for which the exact role has not yet been deciphered. In this work, we cocrystallized a reengineered version of iSpinach in complex with the DFHBI and solved the X-ray structure of the complex at 2 Å resolution. Only a few mutations were required to optimize iSpinach production and crystallization, underlying the good folding capacity of the molecule. The measured fluorescence half-lives in the crystal were 60% higher than in solution. Comparisons with structures previously reported for Spinach sheds some light on the possible function of the different beneficial mutations carried by iSpinach.
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Affiliation(s)
- Pablo Fernandez-Millan
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Alexis Autour
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Eric Ennifar
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Eric Westhof
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
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66
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Song W, Filonov GS, Kim H, Hirsch M, Li X, Moon JD, Jaffrey SR. Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex. Nat Chem Biol 2017; 13:1187-1194. [PMID: 28945233 PMCID: PMC5679246 DOI: 10.1038/nchembio.2477] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 08/09/2017] [Indexed: 11/09/2022]
Abstract
Quantitative measurement of transcription rates in live cells is important for revealing mechanisms of transcriptional regulation. This is particularly challenging when measuring the activity of RNA polymerase III (Pol III), which transcribes growth-promoting small RNAs. To address this issue, we developed Corn, a genetically encoded fluorescent RNA reporter suitable for quantifying RNA transcription in cells. Corn binds and induces fluorescence of 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime, which resembles the fluorophore found in red fluorescent protein (RFP). Notably, Corn shows high photostability, enabling quantitative fluorescence imaging of mTOR-dependent Pol III transcription. We found that, unlike actinomycin D, mTOR inhibitors resulted in heterogeneous transcription suppression in individual cells. Quantitative imaging of Corn-tagged Pol III transcript levels revealed distinct Pol III transcription 'trajectories' elicited by mTOR inhibition. Together, these studies provide an approach for quantitative measurement of Pol III transcription by direct imaging of Pol III transcripts containing a photostable RNA-fluorophore complex.
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Affiliation(s)
- Wenjiao Song
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Grigory S. Filonov
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Hyaeyeong Kim
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Markus Hirsch
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Xing Li
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Jared D. Moon
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
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67
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Warner KD, Sjekloća L, Song W, Filonov GS, Jaffrey SR, Ferré-D’Amaré AR. A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nat Chem Biol 2017; 13:1195-1201. [PMID: 28945234 PMCID: PMC5663454 DOI: 10.1038/nchembio.2475] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 08/03/2017] [Indexed: 11/09/2022]
Abstract
Corn, a 28-nucleotide RNA, increases yellow fluorescence of its cognate ligand 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO) by >400-fold. Corn was selected in vitro to overcome limitations of other fluorogenic RNAs, particularly rapid photobleaching. We now report the Corn-DFHO co-crystal structure, discovering that the functional species is a quasisymmetric homodimer. Unusually, the dimer interface, in which six unpaired adenosines break overall two-fold symmetry, lacks any intermolecular base pairs. The homodimer encapsulates one DFHO at its interprotomer interface, sandwiching it with a G-quadruplex from each protomer. Corn and the green-fluorescent Spinach RNA are structurally unrelated. Their convergent use of G-quadruplexes underscores the usefulness of this motif for RNA-induced small-molecule fluorescence. The asymmetric dimer interface of Corn could provide a basis for the development of mutants that only fluoresce as heterodimers. Such variants would be analogous to Split GFP, and may be useful for analyzing RNA co-expression or association, or for designing self-assembling RNA nanostructures.
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Affiliation(s)
- Katherine Deigan Warner
- Biochemistry and Biophysics Center, National Heart, Lung and Blood
Institute, Bethesda, Maryland, USA
| | - Ljiljana Sjekloća
- Biochemistry and Biophysics Center, National Heart, Lung and Blood
Institute, Bethesda, Maryland, USA
| | - Wenjiao Song
- Department of Pharmacology, Weill-Cornell Medical College, Cornell
University, New York, New York, USA
| | - Grigory S. Filonov
- Department of Pharmacology, Weill-Cornell Medical College, Cornell
University, New York, New York, USA
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell
University, New York, New York, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood
Institute, Bethesda, Maryland, USA
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68
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Okuda M, Fourmy D, Yoshizawa S. Use of Baby Spinach and Broccoli for imaging of structured cellular RNAs. Nucleic Acids Res 2017; 45:1404-1415. [PMID: 28180326 PMCID: PMC5388419 DOI: 10.1093/nar/gkw794] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 08/23/2016] [Accepted: 08/27/2016] [Indexed: 11/16/2022] Open
Abstract
Fluorogenic RNA aptamers provide a powerful tool for study of RNA analogous to green fluorescent protein for the study of proteins. Spinach and Broccoli are RNAs selected in vitro or in vivo respectively to bind to an exogenous chromophore. They can be genetically inserted into an RNA of interest for live-cell imaging. Spinach aptamer has been altered to increase thermal stability and stabilize the desired folding. How well these fluorogenic RNA aptamers behave when inserted into structured cellular RNAs and how aptamer properties might be affected remains poorly characterized. Here, we report a study of the performance of distinct RNA Spinach and Broccoli aptamer sequences in isolation or inserted into the small subunit of the bacterial ribosome. We found that the ribosomal context helped maintaining the yield of the folded Baby Spinach aptamer; other versions of Spinach did not perform well in the context of ribosomes. In vivo, two aptamers clearly stood out. Baby Spinach and Broccoli aptamers yielded fluorescence levels markedly superior to all previous Spinach sequences including the super-folder tRNA scaffolded tSpinach2. Overall, the results suggest the use of Broccoli and Baby Spinach aptamers for live cell imaging of structured RNAs.
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Affiliation(s)
- Maho Okuda
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Dominique Fourmy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Satoko Yoshizawa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
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69
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Huang K, Doyle F, Wurz ZE, Tenenbaum SA, Hammond RK, Caplan JL, Meyers BC. FASTmiR: an RNA-based sensor for in vitro quantification and live-cell localization of small RNAs. Nucleic Acids Res 2017; 45:e130. [PMID: 28586459 PMCID: PMC5737440 DOI: 10.1093/nar/gkx504] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 05/27/2017] [Indexed: 01/19/2023] Open
Abstract
Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play a variety of important regulatory roles in many eukaryotes. Their small size has made it challenging to study them directly in live cells. Here we describe an RNA-based fluorescent sensor for small RNA detection both in vitro and in vivo, adaptable for any small RNA. It utilizes an sxRNA switch for detection of miRNA–mRNA interactions combined with a fluorophore-binding sequence ‘Spinach’, a GFP-like RNA aptamer for which the RNA–fluorophore complex exhibits strong and consistent fluorescence under an excitation wavelength. Two example sensors, FASTmiR171 and FASTmiR122, can rapidly detect and quantify the levels of miR171 and miR122 in vitro. The sensors can determine relative levels of miRNAs in total RNA extracts with sensitivity similar to small RNA sequencing and northern blots. FASTmiR sensors were also used to estimate the copy number range of miRNAs in total RNA extracts. To localize and analyze the spatial distribution of small RNAs in live, single cells, tandem copies of FASTmiR122 were expressed in different cell lines. FASTmiR122 was able to quantitatively detect the differences in miR122 levels in Huh7 and HEK293T cells demonstrating its potential for tracking miRNA expression and localization in vivo.
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Affiliation(s)
- Kun Huang
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.,Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Francis Doyle
- Nanobioscience Constellation, State University of New York- Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - Zachary E Wurz
- Nanobioscience Constellation, State University of New York- Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - Scott A Tenenbaum
- Nanobioscience Constellation, State University of New York- Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - Reza K Hammond
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Jeffrey L Caplan
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.,Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA.,Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA.,University of Missouri-Columbia, Division of Plant Sciences, 52 Agriculture Lab, Columbia, MO 65211, USA
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70
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Feng G, Luo C, Yi H, Yuan L, Lin B, Luo X, Hu X, Wang H, Lei C, Nie Z, Yao S. DNA mimics of red fluorescent proteins (RFP) based on G-quadruplex-confined synthetic RFP chromophores. Nucleic Acids Res 2017; 45:10380-10392. [PMID: 28981852 PMCID: PMC5737560 DOI: 10.1093/nar/gkx803] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/26/2017] [Accepted: 08/31/2017] [Indexed: 12/29/2022] Open
Abstract
Red fluorescent proteins (RFPs) have emerged as valuable biological markers for biomolecule imaging in living systems. Developing artificial fluorogenic systems that mimic RFPs remains an unmet challenge. Here, we describe the design and synthesis of six new chromophores analogous to the chromophores in RFPs. We demonstrate, for the first time, that encapsulating RFP chromophore analogues in canonical DNA G-quadruplexes (G4) can activate bright fluorescence spanning red and far-red spectral regions (Em = 583-668 nm) that nearly match the entire RFP palette. Theoretical calculations and molecular dynamics simulations reveal that DNA G4 greatly restricts radiationless deactivation of chromophores induced by a twisted intramolecular charge transfer (TICT). These DNA mimics of RFP exhibit attractive photophysical properties comparable or superior to natural RFPs, including high quantum yield, large Stokes shifts, excellent anti-photobleaching properties, and two-photon fluorescence. Moreover, these RFP chromophore analogues are a novel and distinctive type of topology-selective G4 probe specific to parallel G4 conformation. The DNA mimics of RFP have been further exploited for imaging of target proteins. Using cancer-specific cell membrane biomarkers as targets, long-term real-time monitoring in single live cell and two-photon fluorescence imaging in tissue sections have been achieved without the need for genetic coding.
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Affiliation(s)
- Guangfu Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Chao Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Haibo Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaoxiao Hu
- Molecular Science and Biomedicine laboratory, Hunan University, Changsha 410082, PR China
| | - Honghui Wang
- College of Biology, Hunan University, Changsha 410082, PR China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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71
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Trachman RJ, Truong L, Ferré-D'Amaré AR. Structural Principles of Fluorescent RNA Aptamers. Trends Pharmacol Sci 2017; 38:928-939. [PMID: 28728963 DOI: 10.1016/j.tips.2017.06.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/21/2017] [Accepted: 06/21/2017] [Indexed: 11/26/2022]
Abstract
Several aptamer RNAs have been selected in vitro that bind to otherwise weakly fluorescent small molecules and enhance their fluorescence several thousand-fold. By genetically tagging cellular RNAs of interest with these aptamers and soaking cells in their cell-permeable cognate small-molecule fluorophores, it is possible to use them to study RNA localization and trafficking. These aptamers have also been fused to metabolite-binding RNAs to generate fluorescent biosensors. The 3D structures of three unrelated fluorogenic RNAs have been determined, and reveal a shared reliance on base quadruples (tetrads) to constrain the photo-excited chromophore. The structural diversity of fluorogenic RNAs and the chemical diversity of potential fluorophores to be activated are likely to yield a variety of future fluorogenic RNA tags that are optimized for different applications in RNA imaging and in the design of fluorescent RNA biosensors.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Lynda Truong
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA.
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72
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Yeung E, Dy AJ, Martin KB, Ng AH, Del Vecchio D, Beck JL, Collins JJ, Murray RM. Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks. Cell Syst 2017; 5:11-24.e12. [DOI: 10.1016/j.cels.2017.06.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/08/2017] [Accepted: 06/05/2017] [Indexed: 01/25/2023]
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73
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van Gijtenbeek LA, Kok J. Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol 2017; 8:1161. [PMID: 28690601 PMCID: PMC5479882 DOI: 10.3389/fmicb.2017.01161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
To be able to visualize the abundance and spatiotemporal features of RNAs in bacterial cells would permit obtaining a pivotal understanding of many mechanisms underlying bacterial cell biology. The first methods that allowed observing single mRNA molecules in individual cells were introduced by Bertrand et al. (1998) and Femino et al. (1998). Since then, a plethora of techniques to image RNA molecules with the aid of fluorescence microscopy has emerged. Many of these approaches are useful for the large eukaryotic cells but their adaptation to study RNA, specifically mRNA molecules, in bacterial cells progressed relatively slow. Here, an overview will be given of fluorescent techniques that can be used to reveal specific RNA molecules inside fixed and living single bacterial cells. It includes a critical evaluation of their caveats as well as potential solutions.
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Affiliation(s)
- Lieke A van Gijtenbeek
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
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74
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Nilaratanakul V, Hauer DA, Griffin DE. Development and characterization of Sindbis virus with encoded fluorescent RNA aptamer Spinach2 for imaging of replication and immune-mediated changes in intracellular viral RNA. J Gen Virol 2017; 98:992-1003. [PMID: 28555544 DOI: 10.1099/jgv.0.000755] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viral RNA studies often rely on in situ hybridization and reverse transcriptase-PCR to provide snapshots of RNA dynamics in infected cells. To facilitate analysis of cellular RNAs, aptamers Spinach and Spinach2 that bind and activate the conditional fluorophore 3, 5-difluoro-4-hydroxybenzylidene imidazolinon have been developed. To determine the feasibility of applying this technology to viral RNA, we have used cDNA clones of the TE strain of Sindbis virus (SINV) to construct multiple viruses containing one or two copies of tRNA-scaffolded Spinach2 after a second subgenomic promoter, TEds-1Sp and TEds-2Sp within the 3'UTR, TE-1UTRSp, or after a second subgenomic promoter and in the 3'UTR, TEds-1Sp+1 UTRSp. TEds-1Sp+1 UTRSp gave the brightest signal and replicated well in cell culture, while TEds-2Sp was the dimmest and replicated poorly. Selection of baby hamster kidney cells infected with TEds-1Sp+1 UTRSp for improved signal intensity identified a virus with a stronger signal and point mutations in the tRNA scaffold. Imaging of SINV in BHK cells showed RNA to be concentrated in filopodia that contacted and transferred RNA to adjacent cells. The effect of treatment with anti-E2 antibody, which effects non-cytolytic clearance of SINV from neurons, on viral RNA was cell-type-dependent. In antibody-treated BHK cells, intracellular viral RNA increased and spread of infection continued. In undifferentiated and differentiated AP7 neuronal cells antibody treatment induced viral RNA clearance. Both viruses with two inserted aptamers were prone to deletion. These studies form the basis for further development of aptamer-labelled viral RNAs that will facilitate functional studies on the dynamics of infection and clearance.
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Affiliation(s)
- Voraphoj Nilaratanakul
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Debra A Hauer
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Diane E Griffin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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75
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Trachman RJ, Demeshkina NA, Lau MWL, Panchapakesan SSS, Jeng SCY, Unrau PJ, Ferré-D'Amaré AR. Structural basis for high-affinity fluorophore binding and activation by RNA Mango. Nat Chem Biol 2017; 13:807-813. [PMID: 28553947 PMCID: PMC5550021 DOI: 10.1038/nchembio.2392] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 03/22/2017] [Indexed: 02/08/2023]
Abstract
Genetically encoded fluorescent protein tags revolutionized proteome studies, while the lack of intrinsically fluorescent RNAs has hindered transcriptome exploration. Among several RNA-fluorophore complexes that potentially address this problem, RNA Mango has an exceptionally high affinity for its thiazole orange (TO)-derived fluorophore, TO1-Biotin (Kd ~3 nM), and in complex with related ligands, is one of the most red-shifted fluorescent macromolecular tags known. To elucidate how this small aptamer exhibits such properties, which make it well suited for studying low-copy cellular RNAs, we determined its 1.7 Å resolution co-crystal structure. Unexpectedly, the entire ligand, including TO, biotin, and the linker connecting them, abuts one of the near-planar faces of the three-tiered G-quadruplex. The two heterocycles of TO are held in place by two loop adenines and make a 45° angle with respect to each other. Minimizing this angle would increase quantum yield and further improve this tool for in vivo RNA visualization.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Natalia A Demeshkina
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Matthew W L Lau
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | | | - Sunny C Y Jeng
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
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76
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Bose S, Chakrabarty S, Ghosh D. Electrostatic Origin of the Red Solvatochromic Shift of DFHBDI in RNA Spinach. J Phys Chem B 2017; 121:4790-4798. [DOI: 10.1021/acs.jpcb.7b02445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samik Bose
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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77
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Sheet SK, Sen B, Thounaojam R, Aguan K, Khatua S. Ruthenium(II) Complex-Based Luminescent Bifunctional Probe for Ag+ and Phosphate Ions: Ag+-Assisted Detection and Imaging of rRNA. Inorg Chem 2017; 56:1249-1263. [DOI: 10.1021/acs.inorgchem.6b02343] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sanjoy Kumar Sheet
- Centre for Advanced
Studies, Department of Chemistry, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Bhaskar Sen
- Centre for Advanced
Studies, Department of Chemistry, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Romita Thounaojam
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Kripamoy Aguan
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Snehadrinarayan Khatua
- Centre for Advanced
Studies, Department of Chemistry, North Eastern Hill University, Shillong, Meghalaya 793022, India
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78
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Tsuji G, Sintim HO. Cyclic dinucleotide detection with riboswitch-G-quadruplex hybrid. MOLECULAR BIOSYSTEMS 2016; 12:773-7. [PMID: 26739090 DOI: 10.1039/c5mb00751h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A cyclic dinucleotide riboswitch has been fused with a G-quadruplex motif to produce a conditional riboswitch-peroxidase-mimicking sensor that oxidizes both colorimetric and fluorogenic substrates in the presence of c-di-GMP. We find that signal-to-noise ratio could be improved by using a two-, not three-, floor split G-quadruplex for this conditional peroxidase-mimicking riboswitch.
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Affiliation(s)
- Genichiro Tsuji
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA and Center for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA.
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79
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Jeng SCY, Chan HHY, Booy EP, McKenna SA, Unrau PJ. Fluorophore ligand binding and complex stabilization of the RNA Mango and RNA Spinach aptamers. RNA (NEW YORK, N.Y.) 2016; 22:1884-1892. [PMID: 27777365 PMCID: PMC5113208 DOI: 10.1261/rna.056226.116] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/23/2016] [Indexed: 05/29/2023]
Abstract
The effective tracking and purification of biological RNAs and RNA protein complexes is currently challenging. One promising strategy to simultaneously address both of these problems is to develop high-affinity RNA aptamers against taggable small molecule fluorophores. RNA Mango is a 39-nucleotide, parallel-stranded G-quadruplex RNA aptamer motif that binds with nanomolar affinity to a set of thiazole orange (TO1) derivatives while simultaneously inducing a 103-fold increase in fluorescence. We find that RNA Mango has a large increase in its thermal stability upon the addition of its TO1-Biotin ligand. Consistent with this thermal stabilization, RNA Mango can effectively discriminate TO1-Biotin from a broad range of small molecule fluorophores. In contrast, RNA Spinach, which is known to have a substantially more rigid G-quadruplex structure, was found to bind to this set of fluorophores, often with higher affinity than to its native ligand, 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), and did not exhibit thermal stabilization in the presence of the TO1-Biotin fluorophore. Our data suggest that RNA Mango is likely to use a concerted ligand-binding mechanism that allows it to simultaneously bind and recognize its TO1-Biotin ligand, whereas RNA Spinach appears to lack such a mechanism. The high binding affinity and fluorescent efficiency of RNA Mango provides a compelling alternative to RNA Spinach as an RNA reporter system and paves the way for the future development of small fluorophore RNA reporter systems.
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Affiliation(s)
- Sunny C Y Jeng
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Hedy H Y Chan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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80
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A specific and biocompatible fluorescent sensor based on the hybrid of GFP chromophore and peptide for HSA detection. Biosens Bioelectron 2016; 86:489-495. [DOI: 10.1016/j.bios.2016.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/01/2016] [Accepted: 07/02/2016] [Indexed: 11/23/2022]
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81
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Detection of human immunodeficiency virus RNAs in living cells using Spinach RNA aptamers. Virus Res 2016; 228:141-146. [PMID: 27914932 DOI: 10.1016/j.virusres.2016.11.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/28/2016] [Accepted: 11/23/2016] [Indexed: 12/22/2022]
Abstract
Many techniques currently used to measure HIV RNA production in cells suffer from limitations that include high background signal or the potential to destroy cellular context. Fluorophore-binding RNA aptamers offer the potential for visualizing RNAs directly in living cells with minimal cellular perturbation. We inserted a sequence encoding a fluorophore-binding RNA aptamer, known as Spinach, into the HIV genome such that predicted RNA secondary structures in both Spinach and HIV were preserved. Chimeric HIV-Spinach RNAs were functionally validated in vitro by testing their ability to enhance the fluorescence of a conditional fluorophore (DFHBI), which specifically binds Spinach. Fluorescence microscopy and PCR were used to verify expression of HIV-Spinach RNAs in human cells. HIV-1 gag RNA production and fluorescence were measured by qPCR and fluorometry, respectively. HIV-Spinach RNAs were fluorometrically detectable in vitro and were transcribed in human cell lines and primary cells, with both spliced and unspliced species detected by PCR. HIV-Spinach RNAs were visible by fluorescence microscopy in living cells, although signal was reproducibly weak. Cells expressing HIV-Spinach RNAs were capable of producing fluorometrically detectable virions, although detection of single viral particles was not possible. In summary, we have investigated a novel method for detecting HIV RNAs in living cells using the Spinach RNA aptamer. Despite the limitations of the present aptamer/fluorophore combination, this is the first application of this technology to an infectious disease and provides a foundation for future research into improved methods for studying HIV expression.
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82
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Li X, Chung LW, Li G. Multiscale Simulations on Spectral Tuning and the Photoisomerization Mechanism in Fluorescent RNA Spinach. J Chem Theory Comput 2016; 12:5453-5464. [PMID: 27685000 DOI: 10.1021/acs.jctc.6b00578] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Fluorescent RNA aptamer Spinach can bind and activate a green fluorescent protein (GFP)-like chromophore (an anionic DFHBDI chromophore) displaying green fluorescence. Spectroscopic properties, spectral tuning, and the photoisomerization mechanism in the Spinach-DFHBDI complex have been investigated by high-level QM and hybrid ONIOM(QM:AMBER) methods (QM method: (TD)DFT, SF-BHHLYP, SAC-CI, LT-DF-LCC2, CASSCF, or MS-CASPT2), as well as classical molecular dynamics (MD) simulations. First, our benchmark calculations have shown that TD-DFT and spin-flip (SF) TD-DFT (SF-BHHLYP) failed to give a satisfactory description of absorption and emission of the anionic DFHBDI chromophore. Comparatively, SAC-CI, LT-DF-LCC2, and MS-CASPT2 can give more reliable transition energies and are mainly used to further study the spectra of the anionic DFHBDI chromophore in Spinach. The RNA environmental effects on the spectral tuning and the photoisomerization mechanism have been elucidated. Our simulations show that interactions of the anionic cis-DFHBDI chromophore with two G-quadruplexes as well as a UAU base triple suppress photoisomerization of DFHBDI. In addition, strong hydrogen bonds between the anionic cis-DFHBDI chromophore and nearby nucleotides facilitate its binding to Spinach and further inhibit the cis-trans photoisomerization of DFHBDI. Solvent molecules, ions, and loss of key hydrogen bonds with nearby nucleotides could induce dissociation of the anionic trans-DFHBDI chromophore from the binding site. These results provide new insights into fluorescent RNA Spinach and may help rational design of other fluorescent RNAs.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Lung Wa Chung
- Department of Chemistry, South University of Science and Technology of China , Shenzhen 518055, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
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83
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Kikuchi N, Kolpashchikov DM. Split Spinach Aptamer for Highly Selective Recognition of DNA and RNA at Ambient Temperatures. Chembiochem 2016; 17:1589-92. [PMID: 27305425 DOI: 10.1002/cbic.201600323] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Indexed: 12/25/2022]
Abstract
Split spinach aptamer (SSA) probes for fluorescent analysis of nucleic acids were designed and tested. In SSA design, two RNA or RNA/DNA strands hybridized to a specific nucleic acid analyte and formed a binding site for low-fluorescent 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) dye, which resulted in up to a 270-fold increase in fluorescence. The major advantage of the SSA over state-of-the art fluorescent probes is high selectivity: it produces only background fluorescence in the presence of a single-base-mismatched analyte, even at room temperature. SSA is therefore a promising tool for label-free analysis of nucleic acids at ambient temperatures.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA.
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84
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Abstract
Seeing is not only believing; it also includes understanding. Cellular imaging with GFP in live cells has been transformative in many research fields. Modulation of cellular regulation is tightly regulated and innovative imaging technologies contribute to further understand cellular signaling and physiology. New types of genetically encoded biosensors have been developed over the last decade. They are RNA aptamers that bind with their cognate fluorogen ligands and activate their fluorescence. The emergence and the evolution of these RNA aptamers as well as their conversion into a wide spectrum of applications are examined in a global way.
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Affiliation(s)
- Jonathan Ouellet
- Department of Chemistry and Physics, Monmouth UniversityWest Long Branch, NJ, USA
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85
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Acousto-microfluidics for screening of ssDNA aptamer. Sci Rep 2016; 6:27121. [PMID: 27272884 PMCID: PMC4897735 DOI: 10.1038/srep27121] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/16/2016] [Indexed: 12/31/2022] Open
Abstract
We demonstrate a new screening method for obtaining a prostate-specific antigen (PSA) binding aptamer based on an acoustofluidic separation (acoustophoreis) technique. Since acoustophoresis provides simultaneous washing and separation in a continuous flow mode, we efficiently obtained a PSA binding aptamer that shows high affinity without any additional washing step, which is necessary in other screening methods. In addition, next-generation sequencing (NGS) was applied to accelerate the identification of the screened ssDNA pool, improving the selecting process of the aptamer candidate based on the frequency ranking of the sequences. After the 8th round of the acoustophoretic systematic evolution of ligands by exponential enrichment (SELEX) and following sequence analysis with NGS, 7 PSA binding ssDNA aptamer-candidates were obtained and characterized with surface plasmon resonance (SPR) for affinity and specificity. As a result of the new SELEX method with PSA as the model target protein, the best PSA binding aptamer showed specific binding to PSA with a dissociation constant (Kd) of 0.7 nM.
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86
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Bose S, Chakrabarty S, Ghosh D. Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant. J Phys Chem B 2016; 120:4410-20. [DOI: 10.1021/acs.jpcb.6b03723] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samik Bose
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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87
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Filonov GS, Jaffrey SR. RNA Imaging with Dimeric Broccoli in Live Bacterial and Mammalian Cells. ACTA ACUST UNITED AC 2016; 8:1-28. [PMID: 26995352 DOI: 10.1002/9780470559277.ch150174] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
RNA spatial dynamics play a crucial role in cell physiology, and thus the ability to monitor RNA localization in live cells can provide insight into important biological problems. This unit focuses on imaging RNAs using an RNA mimic of GFP. This approach relies on an RNA aptamer called dimeric Broccoli, which binds to and switches on the fluorescence of DFHBI, a small molecule mimicking the fluorophore in GFP. Dimeric Broccoli is tagged to heterologously expressed RNAs and, upon DFHBI binding, the fluorescent signal of dimeric Broccoli reports the transcript's localization in cells. This protocol describes the process of validating the fluorescence of dimeric Broccoli--labeled transcripts in vitro and in cells, flow cytometry analysis to determine overall fluorescence levels in cells, and fluorescence imaging in bacterial and mammalian cells. Overall, the protocol should be useful for researchers seeking to image high-abundance RNAs, such as those transcribed off the T7 promoter in bacteria or off Pol III--dependent promoters in mammalian cells.
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Affiliation(s)
- Grigory S Filonov
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York
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88
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Autour A, Westhof E, Ryckelynck M. iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications. Nucleic Acids Res 2016; 44:2491-500. [PMID: 26932363 PMCID: PMC4824111 DOI: 10.1093/nar/gkw083] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/01/2016] [Indexed: 01/03/2023] Open
Abstract
Using random mutagenesis and high throughput screening by microfluidic-assisted In Vitro Compartmentalization, we report the isolation of an order of magnitude times brighter mutants of the light-up RNA aptamers Spinach that are far less salt-sensitive and with a much higher thermal stability than the parent molecule. Further engineering gave iSpinach, a molecule with folding and fluorescence properties surpassing those of all currently known aptamer based on the fluorogenic co-factor 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI). We illustrate the potential of iSpinach in a new sensitive and high throughput-compatible fluorogenic assay that measures co-transcriptionally the catalytic constant (kcat) of a model ribozyme.
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Affiliation(s)
- Alexis Autour
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
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89
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Filonov GS, Kam CW, Song W, Jaffrey SR. In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies. ACTA ACUST UNITED AC 2016; 22:649-60. [PMID: 26000751 DOI: 10.1016/j.chembiol.2015.04.018] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 04/14/2015] [Accepted: 04/20/2015] [Indexed: 11/18/2022]
Abstract
RNA aptamers can be expressed in cells to influence and image cellular processes. Aptamer folding is maintained by inserting the aptamers into highly structured RNA scaffolds. Here, we show that commonly used RNA scaffolds exhibit unexpected instability and cleavage in bacterial and mammalian cells. Using an in-gel staining approach for rapid and simple detection of Spinach- or Broccoli-tagged RNAs in cells, we monitored the processing of RNAs tagged with scaffolded aptamers, revealing endonucleolytic cleavage, RNA instability, and poor expression. We reengineered a natural three-way junction structure to generate an alternative scaffold that enables stable aptamer expression in cells. This scaffold was used to create cassettes containing up to four Broccoli units, markedly enhancing the brightness of mammalian cells expressing cassette-tagged RNAs. These experiments describe methods for screening RNA cleavage events in cells and identify cell-compatible scaffolds that enable efficient tagging of RNAs with aptamers for cellular expression.
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Affiliation(s)
- Grigory S Filonov
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Christina W Kam
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Wenjiao Song
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA.
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90
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Abstract
RNAs have highly complex and dynamic cellular localization patterns. Technologies for imaging RNA in living cells are important for uncovering their function and regulatory pathways. One approach for imaging RNA involves genetically encoding fluorescent RNAs using RNA mimics of green fluorescent protein (GFP). These mimics are RNA aptamers that bind fluorophores resembling those naturally found in GFP and activate their fluorescence. These RNA-fluorophore complexes, including Spinach, Spinach2, and Broccoli, can be used to tag RNAs and to image their localization in living cells. In this article, we describe the generation and optimization of these aptamers, along with strategies for expanding the spectral properties of their associated RNA-fluorophore complexes. We also discuss the structural basis for the fluorescence and photophysical properties of Spinach, and we describe future prospects for designing enhanced RNA-fluorophore complexes with enhanced photostability and increased sensitivity.
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Affiliation(s)
- Mingxu You
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York 10065; ,
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91
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Zhang J, Fei J, Leslie BJ, Han KY, Kuhlman TE, Ha T. Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells. Sci Rep 2015; 5:17295. [PMID: 26612428 PMCID: PMC4661537 DOI: 10.1038/srep17295] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/15/2015] [Indexed: 12/24/2022] Open
Abstract
Live cell RNA imaging using genetically encoded fluorescent labels is an important tool for monitoring RNA activities. A recently reported RNA aptamer-fluorogen system, the Spinach, in which an RNA aptamer binds and induces the fluorescence of a GFP-like 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) ligand, can be readily tagged to the RNA of interest. Although the aptamer-fluorogen system is sufficient for imaging highly abundant non-coding RNAs (tRNAs, rRNAs, etc.), it performs poorly for mRNA imaging due to low brightness. In addition, whether the aptamer-fluorogen system may perturb the native RNA characteristics has not been systematically characterized at the levels of RNA transcription, translation and degradation. To increase the brightness of these aptamer-fluorogen systems, we constructed and tested tandem arrays containing multiple Spinach aptamers (8-64 aptamer repeats). Such arrays enhanced the brightness of the tagged mRNA molecules by up to ~17 fold in living cells. Strong laser excitation with pulsed illumination further increased the imaging sensitivity of Spinach array-tagged RNAs. Moreover, transcriptional fusion to the Spinach array did not affect mRNA transcription, translation or degradation, indicating that aptamer arrays might be a generalizable labeling method for high-performance and low-perturbation live cell RNA imaging.
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Affiliation(s)
- Jichuan Zhang
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jingyi Fei
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Benjamin J. Leslie
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
| | - Kyu Young Han
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
| | - Thomas E. Kuhlman
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Taekjip Ha
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
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92
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Ketterer S, Fuchs D, Weber W, Meier M. Systematic reconstruction of binding and stability landscapes of the fluorogenic aptamer spinach. Nucleic Acids Res 2015; 43:9564-72. [PMID: 26400180 PMCID: PMC4627091 DOI: 10.1093/nar/gkv944] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/10/2015] [Indexed: 01/08/2023] Open
Abstract
Fluorogenic RNAs that are based on the complex formed by 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) derivatives and the RNA aptamer named Spinach were used to engineer a new generation of in vitro and in vivo sensors for bioanalytics. With the resolved crystal structure of the RNA/small molecule complex, the engineering map becomes available, but comprehensive information regarding the thermodynamic profile of the molecule is missing. Here, we reconstructed the full thermodynamic binding and stability landscapes between DFHBI and a truncated sequence of first-generation Spinach. For this purpose, we established a systematic screening procedure for single- and double-point mutations on a microfluidic large-scale integrated chip platform for 87-nt long RNAs. The thermodynamic profile with single base resolution was used to engineer an improved fluorogenic spinach generation via a directed rather than evolutional approach.
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Affiliation(s)
- Simon Ketterer
- Microfluidic and Biological Engineering, Department of Microsystems Engineering - IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany Centre for Biological Signalling Studies - BIOSS, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - David Fuchs
- Microfluidic and Biological Engineering, Department of Microsystems Engineering - IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany Centre for Biological Signalling Studies - BIOSS, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Wilfried Weber
- Centre for Biological Signalling Studies - BIOSS, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Matthias Meier
- Microfluidic and Biological Engineering, Department of Microsystems Engineering - IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany Centre for Biological Signalling Studies - BIOSS, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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93
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Walker CL, Lukyanov KA, Yampolsky IV, Mishin AS, Bommarius AS, Duraj-Thatte AM, Azizi B, Tolbert LM, Solntsev KM. Fluorescence imaging using synthetic GFP chromophores. Curr Opin Chem Biol 2015; 27:64-74. [DOI: 10.1016/j.cbpa.2015.06.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/21/2015] [Accepted: 06/05/2015] [Indexed: 01/22/2023]
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94
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Li F, Dong J, Hu X, Gong W, Li J, Shen J, Tian H, Wang J. A Covalent Approach for Site-Specific RNA Labeling in Mammalian Cells. Angew Chem Int Ed Engl 2015; 54:4597-602. [DOI: 10.1002/anie.201410433] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/08/2014] [Indexed: 11/10/2022]
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95
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Li F, Dong J, Hu X, Gong W, Li J, Shen J, Tian H, Wang J. A Covalent Approach for Site-Specific RNA Labeling in Mammalian Cells. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410433] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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96
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Abstract
The ability to monitor RNAs of interest in living cells is crucial to understanding the function, dynamics, and regulation of this important class of molecules. In recent years, numerous strategies have been developed with the goal of imaging individual RNAs of interest in living cells, each with their own advantages and limitations. This chapter provides an overview of current methods of live-cell RNA imaging, including a detailed discussion of genetically encoded strategies for labeling RNAs in mammalian cells. This chapter then focuses on the development and use of "RNA mimics of GFP" or Spinach technology for tagging mammalian RNAs and includes a detailed protocol for imaging 5S and CGG60 RNA with the recently described Spinach2 tag.
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Affiliation(s)
- Rita L Strack
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA.
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97
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Perez-Gonzalez DC, Penedo JC. Single-Molecule Strategies for DNA and RNA Diagnostics. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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98
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An improved surface passivation method for single-molecule studies. Nat Methods 2014; 11:1233-6. [PMID: 25306544 PMCID: PMC4245390 DOI: 10.1038/nmeth.3143] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 08/24/2014] [Indexed: 11/08/2022]
Abstract
We report a surface passivation method based on dichlorodimethylsilane (DDS)-Tween-20 for in vitro single-molecule studies, which, under the conditions tested here, more efficiently prevented nonspecific binding of biomolecules than the standard poly(ethylene glycol) surface. The DDS-Tween-20 surface was simple and inexpensive to prepare and did not perturb the behavior and activities of tethered biomolecules. It can also be used for single-molecule imaging in the presence of high concentrations of labeled species in solution.
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99
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Toh SY, Citartan M, Gopinath SCB, Tang TH. Aptamers as a replacement for antibodies in enzyme-linked immunosorbent assay. Biosens Bioelectron 2014; 64:392-403. [PMID: 25278480 DOI: 10.1016/j.bios.2014.09.026] [Citation(s) in RCA: 368] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/05/2014] [Accepted: 09/11/2014] [Indexed: 01/08/2023]
Abstract
The application of antibodies in enzyme-linked immunosorbent assay (ELISA) is the basis of this diagnostic technique which is designed to detect a potpourri of complex target molecules such as cell surface antigens, allergens, and food contaminants. However, development of the systematic evolution of Ligands by Exponential Enrichment (SELEX) method, which can generate a nucleic acid-based probe (aptamer) that possess numerous advantages compared to antibodies, offers the possibility of using aptamers as an alternative molecular recognition element in ELISA. Compared to antibodies, aptamers are smaller in size, can be easily modified, are cheaper to produce, and can be generated against a wide array of target molecules. The application of aptamers in ELISA gives rise to an ELISA-derived assay called enzyme-linked apta-sorbent assay (ELASA). As with the ELISA method, ELASA can be used in several different configurations, including direct, indirect, and sandwich assays. This review provides an overview of the strategies involved in aptamer-based ELASA.
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Affiliation(s)
- Saw Yi Toh
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia
| | - Subash C B Gopinath
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia; Department of Oral Biology & Biomedical Sciences and OCRCC, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia.
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Advances in fluorescence labeling strategies for dynamic cellular imaging. Nat Chem Biol 2014; 10:512-23. [PMID: 24937069 DOI: 10.1038/nchembio.1556] [Citation(s) in RCA: 323] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/16/2014] [Indexed: 12/23/2022]
Abstract
Synergistic advances in optical physics, probe design, molecular biology, labeling techniques and computational analysis have propelled fluorescence imaging into new realms of spatiotemporal resolution and sensitivity. This review aims to discuss advances in fluorescent probes and live-cell labeling strategies, two areas that remain pivotal for future advances in imaging technology. Fluorescent protein- and bio-orthogonal-based methods for protein and RNA imaging are discussed as well as emerging bioengineering techniques that enable their expression at specific genomic loci (for example, CRISPR and TALENs). Important attributes that contribute to the success of each technique are emphasized, providing a guideline for future advances in dynamic live-cell imaging.
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