151
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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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152
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Abstract
Localization of mRNA plays a crucial role in a variety of neuronal processes including synaptogenesis, axonal guidance, and long-term plasticity. Recent advances in fluorescence imaging and RNA labeling techniques allow us to visualize how individual mRNA molecules are dynamically regulated inside live neurons and brain tissues. Here, we describe key methods in imaging mRNA dynamics, including preparation of neuron culture and brain slices from transgenic mice expressing GFP-labeled mRNA, high-resolution detection of single molecules, live tissue imaging, and analysis of mRNA transport.
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Affiliation(s)
- Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, University 1 Gwanak-ro, Gwanak-gu, Seoul, 151-747, South Korea.
| | - Minho Song
- Department of Physics and Astronomy, Seoul National University, University 1 Gwanak-ro, Gwanak-gu, Seoul, 151-747, South Korea
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153
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Radford F, Tyagi S, Gennaro ML, Pine R, Bushkin Y. Flow Cytometric Characterization of Antigen-Specific T Cells Based on RNA and Its Advantages in Detecting Infections and Immunological Disorders. Crit Rev Immunol 2016; 36:359-378. [PMID: 28605344 PMCID: PMC5548664 DOI: 10.1615/critrevimmunol.2017018316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fluorescence in situ hybridization coupled with flow cytometry (FISH-Flow) is a highly quantitative, high-throughput platform allowing precise quantification of total mRNA transcripts in single cells. In undiagnosed infections posing a significant health burden worldwide, such as latent tuberculosis or asymptomatic recurrent malaria, an important challenge is to develop accurate diagnostic tools. Antigen-specific T cells create a persistent memory to pathogens, making them useful for diagnosis of infection. Stimulation of memory response initiates T-cell transitions between functional states. Numerous studies have shown that changes in protein levels lag real-time T-cell transitions. However, analysis at the single-cell transcriptional level can determine the differences. FISH-Flow is a powerful tool with which to study the functional states of T-cell subsets and to identify the gene expression profiles of antigen-specific T cells during disease progression. Advances in instrumentation, fluorophores, and FISH methodologies will broaden and deepen the use of FISH-Flow, changing the immunological field by allowing determination of functional immune signatures at the mRNA level and the development of new diagnostic tools.
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Affiliation(s)
- Felix Radford
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Richard Pine
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
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154
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Abstract
The field of fluorescent proteins (FPs) is constantly developing. The use of FPs changed the field of life sciences completely, starting a new era of direct observation and quantification of cellular processes. The broad spectrum of FPs (see Fig. 1) with a wide range of characteristics allows their use in many different experiments. This review discusses the use of FPs for imaging in budding yeast (Saccharomyces cerevisiae) and fission yeast Schizosaccharomyces pombe). The information included in this review is relevant for both species unless stated otherwise.
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Affiliation(s)
- Maja Bialecka-Fornal
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94158, USA
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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155
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Yoshimura H, Ozawa T. Monitoring of RNA Dynamics in Living Cells Using PUM-HD and Fluorescent Protein Reconstitution Technique. Methods Enzymol 2016; 572:65-85. [DOI: 10.1016/bs.mie.2016.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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156
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Rombouts K, Braeckmans K, Remaut K. Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies. Bioconjug Chem 2015; 27:280-97. [PMID: 26670733 DOI: 10.1021/acs.bioconjchem.5b00579] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.
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Affiliation(s)
- K Rombouts
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Braeckmans
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Remaut
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
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157
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Liu Y, Sousa R, Wang YX. Specific labeling: An effective tool to explore the RNA world. Bioessays 2015; 38:192-200. [DOI: 10.1002/bies.201500119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
| | - Rui Sousa
- Department of Biochemistry; University of Texas Health Science Center; San Antonio TX USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
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158
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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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159
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Guet D, Burns LT, Maji S, Boulanger J, Hersen P, Wente SR, Salamero J, Dargemont C. Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast. Nat Commun 2015; 6:8882. [PMID: 26582123 PMCID: PMC4673486 DOI: 10.1038/ncomms9882] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/13/2015] [Indexed: 11/14/2022] Open
Abstract
Although many factors required for the formation of export-competent mRNPs have been described, an integrative view of the spatiotemporal coordinated cascade leading mRNPs from their site of transcription to their site of nuclear exit, at a single cell level, is still partially missing due to technological limitations. Here we report that the RNA Spinach aptamer is a powerful tool for mRNA imaging in live S. cerevisiae with high spatial-temporal resolution and no perturbation of the mRNA biogenesis properties. Dedicated image processing workflows are developed to allow detection of very low abundance of transcripts, accurate quantitative dynamic studies, as well as to provide a localization precision close to 100 nm at consistent time scales. Combining these approaches has provided a state-of-the-art analysis of the osmotic shock response in live yeast by localizing induced transcription factors, target gene loci and corresponding transcripts. Measuring single-cell mRNA dynamics is critical to understand gene expression. Here, using RNA Spinach technique to detect very low abundant mRNAs, Guet et al. report an analysis of the osmotic shock response in live yeast by localizing induced transcription factors, target gene loci and corresponding transcripts.
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Affiliation(s)
- David Guet
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
| | - Laura T Burns
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 205 Kirkland Hall, Nashville, Tennessee 37232-8240, USA
| | - Suman Maji
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
| | - Jérôme Boulanger
- Team-Space Time Imaging of Endomembranes and Organelles Dynamics, UMR144 CNRS, Univ Pierre et Marie Curie, Institut Curie, 12 rue Lhomond, Paris 75005, France
| | - Pascal Hersen
- Univ Paris Diderot, Sorbonne Paris Cité, CNRS UMR7057, Laboratoire Matière et Systèmes Complexes, 10 rue Alice Domon et Léonie Duquet, Paris 75013, France
| | - Susan R Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 205 Kirkland Hall, Nashville, Tennessee 37232-8240, USA
| | - Jean Salamero
- Team-Space Time Imaging of Endomembranes and Organelles Dynamics, UMR144 CNRS, Univ Pierre et Marie Curie, Institut Curie, 12 rue Lhomond, Paris 75005, France.,PICT-IBiSA Imaging Core Facility, Institut Curie, 12 rue Lhomond, Paris 75005, France
| | - Catherine Dargemont
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
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160
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Jullien L, Gautier A. Fluorogen-based reporters for fluorescence imaging: a review. Methods Appl Fluoresc 2015; 3:042007. [PMID: 29148509 DOI: 10.1088/2050-6120/3/4/042007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fluorescence bioimaging has recently jumped into a new area of spatiotemporal resolution and sensitivity thanks to synergistic advances in both optical physics and probe/biosensor design. This review focuses on the recent development of genetically encodable fluorescent reporters that bind endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activate their fluorescence. We highlight the innovative engineering and design that gave rise to these new natural and synthetic fluorescent reporters, and describe some of the emerging applications in imaging and biosensing.
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Affiliation(s)
- Ludovic Jullien
- École Normale Supérieure-PSL Research University, Department of Chemistry, 24 rue Lhomond, F-75005 Paris, France. Sorbonne Universités, UPMC Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France. CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
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161
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Rowland CE, Brown CW, Medintz IL, Delehanty JB. Intracellular FRET-based probes: a review. Methods Appl Fluoresc 2015; 3:042006. [PMID: 29148511 DOI: 10.1088/2050-6120/3/4/042006] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Probes that exploit Förster resonance energy transfer (FRET) in their feedback mechanism are touted for their sensitivity, robustness, and low background, and thanks to the exceptional distance dependence of the energy transfer process, they provide a means of probing lengthscales well below the resolution of light. These attributes make FRET-based probes superbly suited to an intracellular environment, and recent developments in biofunctionalization and expansion of imaging capabilities have put them at the forefront of intracellular studies. Here, we present an overview of the engineering and execution of a variety of recent intracellular FRET probes, highlighting the diversity of this class of materials and the breadth of application they have found in the intracellular environment.
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Affiliation(s)
- Clare E Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA. National Research Council, Washington, DC 20036, USA
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162
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Wang S, Riahi R, Li N, Zhang DD, Wong PK. Single cell nanobiosensors for dynamic gene expression profiling in native tissue microenvironments. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:6034-6038. [PMID: 26314800 DOI: 10.1002/adma.201502814] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/09/2015] [Indexed: 06/04/2023]
Abstract
A gold nanorod-locked nucleic acid nano-biosensor for dynamic single-cell gene expression analysis in living cells and tissues is developed. The nanoparticle facilitates endocytic delivery and dynamic monitoring of the gene expression in human umbilical cord endothelial cells, mouse skin tissues, mouse retina tissues, and mouse cornea tissues at the single-cell level.
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Affiliation(s)
- Shue Wang
- Department of Aerospace and Mechanical Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | - Reza Riahi
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA, 02139, USA
| | - Na Li
- Department of Mechanical and Aerospace Engineering, University of Miami, Coral Gables, FL, 33146, USA
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, 85724, USA
| | - Pak Kin Wong
- Department of Aerospace and Mechanical Engineering, The University of Arizona, Tucson, AZ, 85721, USA
- Department of Biomedical Engineering and Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
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163
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Ameta S, Becker J, Jäschke A. RNA-peptide conjugate synthesis by inverse-electron demand Diels-Alder reaction. Org Biomol Chem 2015; 12:4701-7. [PMID: 24871687 DOI: 10.1039/c4ob00076e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Here we report an efficient method for the synthesis of RNA-peptide conjugates by inverse-electron demand Diels-Alder reaction. Various dienophiles were enzymatically incorporated into RNA and reacted with a chemically synthesized diene-modified peptide. The Diels-Alder reaction proceeds with near-quantitative yields in aqueous solution with stoichiometric amounts of reactants, even at low micromolar concentrations.
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Affiliation(s)
- Sandeep Ameta
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany.
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164
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Alexander SC, Busby KN, Cole CM, Zhou CY, Devaraj NK. Site-Specific Covalent Labeling of RNA by Enzymatic Transglycosylation. J Am Chem Soc 2015; 137:12756-9. [DOI: 10.1021/jacs.5b07286] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Seth C. Alexander
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Kayla N. Busby
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Christian M. Cole
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Cun Yu Zhou
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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165
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Smith CS, Stallinga S, Lidke KA, Rieger B, Grunwald D. Probability-based particle detection that enables threshold-free and robust in vivo single-molecule tracking. Mol Biol Cell 2015; 26:4057-62. [PMID: 26424801 PMCID: PMC4710236 DOI: 10.1091/mbc.e15-06-0448] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/17/2015] [Indexed: 01/11/2023] Open
Abstract
Any single-molecule study starts with finding those single-molecule signals in recorded images. Currently, parameters such as filter and thresholds are user set, and errors are unknown and not observed or controlled. A framework is presented in which expert knowledge and parameter tweaking are replaced with a probability-based hypothesis test. Single-molecule detection in fluorescence nanoscopy has become a powerful tool in cell biology but can present vexing issues in image analysis, such as limited signal, unspecific background, empirically set thresholds, image filtering, and false-positive detection limiting overall detection efficiency. Here we present a framework in which expert knowledge and parameter tweaking are replaced with a probability-based hypothesis test. Our method delivers robust and threshold-free signal detection with a defined error estimate and improved detection of weaker signals. The probability value has consequences for downstream data analysis, such as weighing a series of detections and corresponding probabilities, Bayesian propagation of probability, or defining metrics in tracking applications. We show that the method outperforms all current approaches, yielding a detection efficiency of >70% and a false-positive detection rate of <5% under conditions down to 17 photons/pixel background and 180 photons/molecule signal, which is beneficial for any kind of photon-limited application. Examples include limited brightness and photostability, phototoxicity in live-cell single-molecule imaging, and use of new labels for nanoscopy. We present simulations, experimental data, and tracking of low-signal mRNAs in yeast cells.
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Affiliation(s)
- Carlas S Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Sjoerd Stallinga
- Quantitative Imaging Group, Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - Bernd Rieger
- Quantitative Imaging Group, Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
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166
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Sawant AA, Tanpure AA, Mukherjee PP, Athavale S, Kelkar A, Galande S, Srivatsan SG. A versatile toolbox for posttranscriptional chemical labeling and imaging of RNA. Nucleic Acids Res 2015; 44:e16. [PMID: 26384420 PMCID: PMC4737177 DOI: 10.1093/nar/gkv903] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 08/31/2015] [Indexed: 12/21/2022] Open
Abstract
Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple and modular posttranscriptional chemical labeling and imaging technique for RNA by using a novel toolbox comprised of azide-modified UTP analogs. These analogs facilitate the enzymatic incorporation of azide groups into RNA, which can be posttranscriptionally labeled with a variety of probes by click and Staudinger reactions. Importantly, we show for the first time the specific incorporation of azide groups into cellular RNA by endogenous RNA polymerases, which enabled the imaging of newly transcribing RNA in fixed and in live cells by click reactions. This labeling method is practical and provides a new platform to study RNA in vitro and in cells.
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Affiliation(s)
- Anupam A Sawant
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Progya P Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Soumitra Athavale
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Ashwin Kelkar
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sanjeev Galande
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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167
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Urbanek MO, Galka-Marciniak P, Olejniczak M, Krzyzosiak WJ. RNA imaging in living cells - methods and applications. RNA Biol 2015; 11:1083-95. [PMID: 25483044 PMCID: PMC4615301 DOI: 10.4161/rna.35506] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Numerous types of transcripts perform multiple functions in cells, and these functions are mainly facilitated by the interactions of the RNA with various proteins and other RNAs. Insight into the dynamics of RNA biosynthesis, processing and cellular activities is highly desirable because this knowledge will deepen our understanding of cell physiology and help explain the mechanisms of RNA-mediated pathologies. In this review, we discuss the live RNA imaging systems that have been developed to date. We highlight information on the design of these systems, briefly discuss their advantages and limitations and provide examples of their numerous applications in various organisms and cell types. We present a detailed examination of one application of RNA imaging systems: this application aims to explain the role of mutant transcripts in human disease pathogenesis caused by triplet repeat expansions. Thus, this review introduces live RNA imaging systems and provides a glimpse into their various applications.
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Affiliation(s)
- Martyna O Urbanek
- a Department of Molecular Biomedicine; Institute of Bioorganic Chemistry; Polish Academy of Sciences ; Poznan , Poland
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168
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Asare-Okai PN, Agustin E, Fabris D, Royzen M. Site-specific fluorescence labelling of RNA using bio-orthogonal reaction of trans-cyclooctene and tetrazine. Chem Commun (Camb) 2015; 50:7844-7. [PMID: 24909672 DOI: 10.1039/c4cc02435d] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This communication describes a general approach for site-specific fluorescence labelling of RNA using a cytidine triphosphate (CTP) analogue derivatized with a trans-cyclooctene group. The analogue was efficiently incorporated into a model RNA strand using in vitro transcription. Bio-orthogonal reaction with fluorescein-labelled tetrazine was utilized to fluorescently tag the synthetic RNA strand.
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Affiliation(s)
- P N Asare-Okai
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA.
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169
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Ye S, Wu Y, Zhai X, Tang B. Asymmetric Signal Amplification for Simultaneous SERS Detection of Multiple Cancer Markers with Significantly Different Levels. Anal Chem 2015. [DOI: 10.1021/acs.analchem.5b01186] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Sujuan Ye
- College of Chemistry,
Chemical Engineering and Materials Science, Collaborative Innovation
Center of Functionalized Probes for Chemical Imaging in Universities
of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry
of Education, Shandong Provincial Key Laboratory of Clean Production
of Fine Chemicals, Shandong Normal University, Jinan 250014, P.R. China
- Key Laboratory
of Sensor Analysis of Tumor Marker Ministry of Education, College
of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Yanying Wu
- Key Laboratory
of Sensor Analysis of Tumor Marker Ministry of Education, College
of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Xiaomo Zhai
- Key Laboratory
of Sensor Analysis of Tumor Marker Ministry of Education, College
of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Bo Tang
- College of Chemistry,
Chemical Engineering and Materials Science, Collaborative Innovation
Center of Functionalized Probes for Chemical Imaging in Universities
of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry
of Education, Shandong Provincial Key Laboratory of Clean Production
of Fine Chemicals, Shandong Normal University, Jinan 250014, P.R. China
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170
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Arora A, Sunbul M, Jäschke A. Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers. Nucleic Acids Res 2015; 43:e144. [PMID: 26175046 PMCID: PMC4666381 DOI: 10.1093/nar/gkv718] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 07/02/2015] [Indexed: 01/12/2023] Open
Abstract
In order to gain deeper insight into the functions and dynamics of RNA in cells, the development of methods for imaging multiple RNAs simultaneously is of paramount importance. Here, we describe a modular approach to image RNA in living cells using an RNA aptamer that binds to dinitroaniline, an efficient general contact quencher. Dinitroaniline quenches the fluorescence of different fluorophores when directly conjugated to them via ethylene glycol linkers by forming a non-fluorescent intramolecular complex. Since the binding of the RNA aptamer to the quencher destroys the fluorophore-quencher complex, fluorescence increases dramatically upon binding. Using this principle, a series of fluorophores were turned into fluorescent turn-on probes by conjugating them to dinitroaniline. These probes ranged from fluorescein-dinitroaniline (green) to TexasRed-dinitroaniline (red) spanning across the visible spectrum. The dinitroaniline-binding aptamer (DNB) was generated by in vitro selection, and was found to bind all probes, leading to fluorescence increase in vitro and in living cells. When expressed in E. coli, the DNB aptamer could be labelled and visualized with different-coloured fluorophores and therefore it can be used as a genetically encoded tag to image target RNAs. Furthermore, combining contact-quenched fluorogenic probes with orthogonal DNB (the quencher-binding RNA aptamer) and SRB-2 aptamers (a fluorophore-binding RNA aptamer) allowed dual-colour imaging of two different fluorescence-enhancing RNA tags in living cells, opening new avenues for studying RNA co-localization and trafficking.
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Affiliation(s)
- Ankita Arora
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
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171
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Oomoto I, Suzuki-Hirano A, Umeshima H, Han YW, Yanagisawa H, Carlton P, Harada Y, Kengaku M, Okamoto A, Shimogori T, Wang DO. ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues. Nucleic Acids Res 2015; 43:e126. [PMID: 26101260 PMCID: PMC4627062 DOI: 10.1093/nar/gkv614] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/01/2015] [Indexed: 02/07/2023] Open
Abstract
Elucidating the dynamic organization of nuclear RNA foci is important for understanding and manipulating these functional sites of gene expression in both physiological and pathological states. However, such studies have been difficult to establish in vivo as a result of the absence of suitable RNA imaging methods. Here, we describe a high-resolution fluorescence RNA imaging method, ECHO-liveFISH, to label endogenous nuclear RNA in living mice and chicks. Upon in vivo electroporation, exciton-controlled sequence-specific oligonucleotide probes revealed focally concentrated endogenous 28S rRNA and U3 snoRNA at nucleoli and poly(A) RNA at nuclear speckles. Time-lapse imaging reveals steady-state stability of these RNA foci and dynamic dissipation of 28S rRNA concentrations upon polymerase I inhibition in native brain tissue. Confirming the validity of this technique in a physiological context, the in vivo RNA labeling did not interfere with the function of target RNA nor cause noticeable cytotoxicity or perturbation of cellular behavior.
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Affiliation(s)
- Ikumi Oomoto
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Asuka Suzuki-Hirano
- Brain Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan JSPS Research fellow, Japan Society of Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku,Tokyo 102-0083, Japan
| | - Hiroki Umeshima
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yong-Woon Han
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroyuki Yanagisawa
- Advanced Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Peter Carlton
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshie Harada
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mineko Kengaku
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Akimitsu Okamoto
- Advanced Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan Research Center for Advanced Science and Technology, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Tomomi Shimogori
- Brain Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Dan Ohtan Wang
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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172
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Choi CKK, Li J, Wei K, Xu YJ, Ho LWC, Zhu M, To KKW, Choi CHJ, Bian L. A gold@polydopamine core-shell nanoprobe for long-term intracellular detection of microRNAs in differentiating stem cells. J Am Chem Soc 2015; 137:7337-46. [PMID: 25996312 DOI: 10.1021/jacs.5b01457] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The capability of monitoring the differentiation process in living stem cells is crucial to the understanding of stem cell biology and the practical application of stem-cell-based therapies, yet conventional methods for the analysis of biomarkers related to differentiation require a large number of cells as well as cell lysis. Such requirements lead to the unavoidable loss of cell sources and preclude real-time monitoring of cellular events. In this work, we report the detection of microRNAs (miRNAs) in living human mesenchymal stem cells (hMSCs) by using polydopamine-coated gold nanoparticles (Au@PDA NPs). The PDA shell facilitates the immobilization of fluorescently labeled hairpin DNA strands (hpDNAs) that can recognize specific miRNA targets. The gold core and PDA shell quench the fluorescence of the immobilized hpDNAs, and subsequent binding of the hpDNAs to the target miRNAs leads to their dissociation from Au@PDA NPs and the recovery of fluorescence signals. Remarkably, these Au@PDA-hpDNA nanoprobes can naturally enter stem cells, which are known for their poor transfection efficiency, without the aid of transfection agents. Upon cellular uptake of these nanoprobes, we observe intense and time-dependent fluorescence responses from two important osteogenic marker miRNAs, namely, miR-29b and miR-31, only in hMSCs undergoing osteogenic differentiation and living primary osteoblasts but not in undifferentiated hMSCs and 3T3 fibroblasts. Strikingly, our nanoprobes can afford long-term tracking of miRNAs (5 days) in the differentiating hMSCs without the need of continuously replenishing cell culture medium with fresh nanoprobes. Our results demonstrate the capability of our Au@PDA-hpDNA nanoprobes for monitoring the differentiation status of hMSCs (i.e., differentiating versus undifferentiated) via the detection of specific miRNAs in living stem cells. Our nanoprobes show great promise in the investigation of the long-term dynamics of stem cell differentiation, identification and isolation of specific cell types, and high-throughput drug screening.
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Affiliation(s)
- Chun Kit K Choi
- †Department of Mechanical and Automation Engineering (Biomedical Engineering), ‡Department of Electronic Engineering (Biomedical Engineering), §School of Pharmacy, ∥Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jinming Li
- †Department of Mechanical and Automation Engineering (Biomedical Engineering), ‡Department of Electronic Engineering (Biomedical Engineering), §School of Pharmacy, ∥Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Kongchang Wei
- †Department of Mechanical and Automation Engineering (Biomedical Engineering), ‡Department of Electronic Engineering (Biomedical Engineering), §School of Pharmacy, ∥Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yang J Xu
- †Department of Mechanical and Automation Engineering (Biomedical Engineering), ‡Department of Electronic Engineering (Biomedical Engineering), §School of Pharmacy, ∥Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Lok Wai C Ho
- †Department of Mechanical and Automation Engineering (Biomedical Engineering), ‡Department of Electronic Engineering (Biomedical Engineering), §School of Pharmacy, ∥Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Meiling Zhu
- †Department of Mechanical and Automation Engineering (Biomedical Engineering), ‡Department of Electronic Engineering (Biomedical Engineering), §School of Pharmacy, ∥Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Kenneth K W To
- †Department of Mechanical and Automation Engineering (Biomedical Engineering), ‡Department of Electronic Engineering (Biomedical Engineering), §School of Pharmacy, ∥Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Chung Hang J Choi
- †Department of Mechanical and Automation Engineering (Biomedical Engineering), ‡Department of Electronic Engineering (Biomedical Engineering), §School of Pharmacy, ∥Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liming Bian
- †Department of Mechanical and Automation Engineering (Biomedical Engineering), ‡Department of Electronic Engineering (Biomedical Engineering), §School of Pharmacy, ∥Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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173
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Chang X, Yu C, Wang G, Fan J, Zhang J, Qi Y, Liu K, Fang Y. Constitutional Dynamic Chemistry-based New Concept of Molecular Beacons for High Efficient Development of Fluorescent Probes. J Phys Chem B 2015; 119:6721-9. [PMID: 25985384 DOI: 10.1021/acs.jpcb.5b02664] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Inspired by the concept of constitutional dynamic chemistry, we propose a new and well-adaptable strategy for developing molecular beacon (MB)-like fluorescent probes. To demonstrate the strategy, we synthesized and used an amino group containing pyrenyl derivative of cholesterol (CP) for the construction of new fluorescent probes with EDTA and sulfuric acid. The probes as created were successfully used for n-hexane purity checking and Ba(2+)and Pb(2+)sensing, respectively.
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Affiliation(s)
- Xingmao Chang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Chunmeng Yu
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Gang Wang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Jiayun Fan
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Jianyun Zhang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Yanyu Qi
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Kaiqiang Liu
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Yu Fang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
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174
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Guo L, Chan MS, Xu D, Tam DY, Bolze F, Lo PK, Wong MS. Indole-based cyanine as a nuclear RNA-selective two-photon fluorescent probe for live cell imaging. ACS Chem Biol 2015; 10:1171-5. [PMID: 25689264 DOI: 10.1021/cb500927r] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have demonstrated that the subcellular targeting properties of the indole-based cyanines can be tuned by the functional substituent attached onto the indole moiety in which the first example of a highly RNA-selective and two-photon active fluorescent light-up probe for high contrast and brightness TPEF images of rRNA in the nucleolus of live cells has been developed. It is important to find that this cyanine binds much stronger toward RNA than DNA in a buffer solution as well as selectively stains and targets to rRNA in the nucleolus. Remarkably, the TPEF brightness (Φσmax) is dramatically increased with 11-fold enhancement in the presence of rRNA, leading to the record high Φσmax of 228 GM for RNA. This probe not only shows good biocompatibility and superior photostability but also offers general applicability to various live cell lines including HeLa, HepG2, MCF-7, and KB cells and excellent counterstaining compatibility with commercially available DNA or protein trackers.
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Affiliation(s)
- Lei Guo
- Department
of Chemistry and Institute of Molecular Functional Materials, Hong Kong Baptist University, 224 Waterloo Road, Hong
Kong SAR, China
| | - Miu Shan Chan
- Department
of Biology and Chemistry, City University of Hong Kong, Tat Chee
Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Di Xu
- Department
of Chemistry and Institute of Molecular Functional Materials, Hong Kong Baptist University, 224 Waterloo Road, Hong
Kong SAR, China
| | - Dick Yan Tam
- Department
of Biology and Chemistry, City University of Hong Kong, Tat Chee
Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Frédéric Bolze
- Laboratoire
de Conception et Application des Molécules Bioactives, UMR University of Strasbourg-CNRS 7199, Faculté de Pharmacie, Université de Strasbourg, Strasbourg, France
| | - Pik Kwan Lo
- Department
of Biology and Chemistry, City University of Hong Kong, Tat Chee
Avenue, Kowloon Tong, Hong Kong SAR, China
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175
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Petty JT, Sergev OO, Kantor AG, Rankine IJ, Ganguly M, David FD, Wheeler SK, Wheeler JF. Ten-atom silver cluster signaling and tempering DNA hybridization. Anal Chem 2015; 87:5302-9. [PMID: 25923963 DOI: 10.1021/acs.analchem.5b01265] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Silver clusters with ∼10 atoms are molecules, and specific species develop within DNA strands. These molecular metals have sparsely organized electronic states with distinctive visible and near-infrared spectra that vary with cluster size, oxidation, and shape. These small molecules also act as DNA adducts and coordinate with their DNA hosts. We investigated these characteristics using a specific cluster-DNA conjugate with the goal of developing a sensitive and selective biosensor. The silver cluster has a single violet absorption band (λ(max) = 400 nm), and its single-stranded DNA host has two domains that stabilize this cluster and hybridize with target oligonucleotides. These target analytes transform the weakly emissive violet cluster to a new chromophore with blue-green absorption (λ(max) = 490 nm) and strong green emission (λ(max) = 550 nm). Our studies consider the synthesis, cluster size, and DNA structure of the precursor violet cluster-DNA complex. This species preferentially forms with relatively low amounts of Ag(+), high concentrations of the oxidizing agent O2, and DNA strands with ≳20 nucleotides. The resulting aqueous and gaseous forms of this chromophore have 10 silvers that coalesce into a single cluster. This molecule is not only a chromophore but also an adduct that coordinates multiple nucleobases. Large-scale DNA conformational changes are manifested in a 20% smaller hydrodynamic radius and disrupted nucleobase stacking. Multidentate coordination also stabilizes the single-stranded DNA and thereby inhibits hybridization with target complements. These observations suggest that the silver cluster-DNA conjugate acts like a molecular beacon but is distinguished because the cluster chromophore not only sensitively signals target analytes but also stringently discriminates against analogous competing analytes.
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Orlin O Sergev
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Andrew G Kantor
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Ian J Rankine
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Mainak Ganguly
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Frederic D David
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Sandra K Wheeler
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - John F Wheeler
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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176
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Wu C, Cansiz S, Zhang L, Teng IT, Qiu L, Li J, Liu Y, Zhou C, Hu R, Zhang T, Cui C, Cui L, Tan W. A Nonenzymatic Hairpin DNA Cascade Reaction Provides High Signal Gain of mRNA Imaging inside Live Cells. J Am Chem Soc 2015; 137:4900-3. [PMID: 25835750 PMCID: PMC4428327 DOI: 10.1021/jacs.5b00542] [Citation(s) in RCA: 253] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Enzyme-free signal
amplification has enabled sensitive in vitro detection
of biomolecules such as proteins and
nucleic acids. However, monitoring targets of interest in live cells
via enzyme-free amplification is still challenging, especially for
analytes with low concentrations. To the best of our knowledge, this
paper reports the first attempt to perform mRNA imaging inside live
cells, using a nonenzymatic hairpin DNA cascade reaction for high
signal gain, termed a hairpin DNA cascade amplifier (HDCA). In conventional
nucleic acid probes, such as linear hybridization probes, mRNA target
signaling occurs in an equivalent reaction ratio (1:1), whereas, in
HDCA, one mRNA target is able to yield multiple signal outputs (1:m),
thus achieving the goal of signal amplification for low-expression
mRNA targets. Moreover, the recycled mRNA target in the HDCA serves
as a catalyst for the assembly of multiple DNA duplexes, generating
the fluorescent signal of reduced MnSOD mRNA expression, thus indicating
amplified intracellular imaging. This programmable cascade reaction
presents a simple and modular amplification mechanism for intracellular
biomarkers of interest, providing a significant boost to the search
for clues leading to the accurate identification and effective treatment
of cancers.
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Affiliation(s)
- Cuichen Wu
- ‡Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.,†Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Sena Cansiz
- †Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liqin Zhang
- †Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - I-Ting Teng
- †Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liping Qiu
- ‡Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Juan Li
- †Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yuan Liu
- †Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Cuisong Zhou
- †Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Rong Hu
- ‡Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Tao Zhang
- †Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Cheng Cui
- †Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liang Cui
- ‡Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Weihong Tan
- ‡Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.,†Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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177
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Hayashi G, Yanase M, Takeda K, Sakakibara D, Sakamoto R, Wang DO, Okamoto A. Hybridization-sensitive fluorescent oligonucleotide probe conjugated with a bulky module for compartment-specific mRNA monitoring in a living cell. Bioconjug Chem 2015; 26:412-7. [PMID: 25710491 DOI: 10.1021/acs.bioconjchem.5b00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Live-cell RNA imaging at specific intracellular locations is technically limited because of the diffusive nature of small oligonucleotide probes. The bulky fluorescent light-up probes that possess streptavidin or gold nanoparticles at the end of oligonucleotides were designed and synthesized. The bulky probes allowed nucleus- and cytoplasm-selective monitoring of endogenous mRNAs through nuclear and cytoplasmic microinjection, respectively. Simultaneous use of bulky and unbulky probes conjugated with different fluorescent dyes enabled dual color imaging of mRNAs present in nucleus and cytoplasm. Furthermore, we observed that the fluorescence near the cell edge in a living HeLa cell traveled over time in coordination with the dynamic formation and deformation of the pseudopodial protrusions after lipofection of the bulky probes.
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Affiliation(s)
- Gosuke Hayashi
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masafumi Yanase
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Katsuya Takeda
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Daisuke Sakakibara
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryosuke Sakamoto
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Dan Ohtan Wang
- ‡Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Akimitsu Okamoto
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,§Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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178
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Fornasiero EF, Opazo F. Super-resolution imaging for cell biologists: concepts, applications, current challenges and developments. Bioessays 2015; 37:436-51. [PMID: 25581819 DOI: 10.1002/bies.201400170] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The recent 2014 Nobel Prize in chemistry honored an era of discoveries and technical advancements in the field of super-resolution microscopy. However, the applications of diffraction-unlimited imaging in biology have a long road ahead and persistently engage scientists with new challenges. Some of the bottlenecks that restrain the dissemination of super-resolution techniques are tangible, and include the limited performance of affinity probes and the yet not capillary diffusion of imaging setups. Likewise, super-resolution microscopy has introduced new paradigms in the design of projects that require imaging with nanometer-resolution and in the interpretation of biological images. Besides structural or morphological characterization, super-resolution imaging is quickly expanding towards interaction mapping, multiple target detection and live imaging. Here we review the recent progress of biologists employing super-resolution imaging, some pitfalls, implications and new trends, with the purpose of animating the field and spurring future developments.
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Affiliation(s)
- Eugenio F Fornasiero
- STED Microscopy Group, European Neuroscience Institute, Göttingen, Germany; Department of Neuro- and Sensory-physiology, University of Göttingen, Göttingen, Germany
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179
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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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180
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Abstract
Subcellular, sequence-specific detection of RNA in vivo is a powerful tool to study the macromolecular transport that occurs through plasmodesmata. The RNA-binding domain of Pumilio proteins can be engineered to bind RNA sequences of choice and fused to fluorescent proteins for RNA imaging. This chapter describes the construction of a Pumilio-based imaging system to track the RNA of Tobacco mosaic virus in vivo, and practical aspects of RNA live-cell imaging.
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Affiliation(s)
- Jens Tilsner
- Biomedical Sciences Research Complex, University of St Andrews, BMS Building, North Haugh, St Andrews, Fife, KY16 9ST, UK,
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181
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Abstract
The spectrum of RNA functions in the cell continues to widen and new types of RNA molecules continue to be discovered. However, methods to access and manipulate endogenous RNAs in live cells are limited. Here we describe a universal technique for labeling natural RNAs in live cells with the probes synthesized by the cell. The method is based on fluorescent protein complementation in combination with a split aptamer approach. Two RNA probes containing split aptamer sequences flanked with the antisense RNA target sequences are assembled on the target RNA to form a fluorescent ribonucleoprotein (RNP) complex. The mechanism of complex formation ensures highly sensitive RNA detection allowing visualization of endogenous bacterial mRNAs. We demonstrate the great potential of this method by detecting chromosomally low-level expressed unmodified bacterial mRNA in living bacterial cells. This method holds promise to become a broadly used tool in basic research, and eventually in diagnostics and therapeutics.
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Affiliation(s)
- Irina Smolina
- Department of Biomedical Engineering, Boston University, Boston, MA, 01225, USA,
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182
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Kim JS, Park YS, Nam HG, Park JW. Imaging a specific mRNA in pollen with atomic force microscopy. RSC Adv 2015. [DOI: 10.1039/c5ra00199d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Distribution of ammonium transporter mRNA in a sectioned pollen is studied at the higher resolution, and localization of the mRNA in the nucleus of the sperm cells is observed.
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Affiliation(s)
- Jung Sook Kim
- Department of Chemistry
- Pohang University of Science and Technology
- Pohang 790–784
- Republic of Korea
| | - Yu Shin Park
- Center for Core Research Facilities
- DGIST
- Daegu 711–873
- Republic of Korea
| | - Hong Gil Nam
- Center for Plant Aging Research
- Institute for Basic Science (IBS)
- Daegu 711–873
- Republic of Korea
- Department of New Biology
| | - Joon Won Park
- Department of Chemistry
- Pohang University of Science and Technology
- Pohang 790–784
- Republic of Korea
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183
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van Nies P, Canton AS, Nourian Z, Danelon C. Monitoring mRNA and Protein Levels in Bulk and in Model Vesicle-Based Artificial Cells. Methods Enzymol 2015; 550:187-214. [DOI: 10.1016/bs.mie.2014.10.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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184
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Spille JH, Kubitscheck U. Labelling and imaging of single endogenous messenger RNA particles in vivo. J Cell Sci 2015; 128:3695-706. [DOI: 10.1242/jcs.166728] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
ABSTRACT
RNA molecules carry out widely diverse functions in numerous different physiological processes in living cells. The RNA life cycle from transcription, through the processing of nascent RNA, to the regulatory function of non-coding RNA and cytoplasmic translation of messenger RNA has been studied extensively using biochemical and molecular biology techniques. In this Commentary, we highlight how single molecule imaging and particle tracking can yield further insight into the dynamics of RNA particles in living cells. In the past few years, a variety of bright and photo-stable labelling techniques have been developed to generate sufficient contrast for imaging of single endogenous RNAs in vivo. New imaging modalities allow determination of not only lateral but also axial positions with high precision within the cellular context, and across a wide range of specimen from yeast and bacteria to cultured cells, and even multicellular organisms or live animals. A whole range of methods to locate and track single particles, and to analyze trajectory data are available to yield detailed information about the kinetics of all parts of the RNA life cycle. Although the concepts presented are applicable to all types of RNA, we showcase here the wealth of information gained from in vivo imaging of single particles by discussing studies investigating dynamics of intranuclear trafficking, nuclear pore transport and cytoplasmic transport of endogenous messenger RNA.
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Affiliation(s)
- Jan-Hendrik Spille
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, Bonn 53115, Germany
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, Bonn 53115, Germany
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185
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Wang Z, Zhang R, Wang Z, Wang HF, Wang Y, Zhao J, Wang F, Li W, Niu G, Kiesewetter DO, Chen X. Bioinspired nanocomplex for spatiotemporal imaging of sequential mRNA expression in differentiating neural stem cells. ACS NANO 2014; 8:12386-96. [PMID: 25494492 PMCID: PMC4278684 DOI: 10.1021/nn505047n] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 12/10/2014] [Indexed: 05/19/2023]
Abstract
Messenger RNA plays a pivotal role in regulating cellular activities. The expression dynamics of specific mRNA contains substantial information on the intracellular milieu. Unlike the imaging of stationary mRNAs, real-time intracellular imaging of the dynamics of mRNA expression is of great value for investigating mRNA biology and exploring specific cellular cascades. In addition to advanced imaging methods, timely extracellular stimulation is another key factor in regulating the mRNA expression repertoire. The integration of effective stimulation and imaging into a single robust system would significantly improve stimulation efficiency and imaging accuracy, producing fewer unwanted artifacts. In this study, we developed a multifunctional nanocomplex to enable self-activating and spatiotemporal imaging of the dynamics of mRNA sequential expression during the neural stem cell differentiation process. This nanocomplex showed improved enzymatic stability, fast recognition kinetics, and high specificity. With a mechanism regulated by endogenous cell machinery, this nanocomplex realized the successive stimulating motif release and the dynamic imaging of chronological mRNA expression during neural stem cell differentiation without the use of transgenetic manipulation. The dynamic imaging montage of mRNA expression ultimately facilitated genetic heterogeneity analysis. In vivo lateral ventricle injection of this nanocomplex enabled endogenous neural stem cell activation and labeling at their specific differentiation stages. This nanocomplex is highly amenable as an alternative tool to explore the dynamics of intricate mRNA activities in various physiological and pathological conditions.
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Affiliation(s)
- Zhe Wang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ruili Zhang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, China
| | - Zhongliang Wang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, China
- Address correspondence to ,
| | - He-Fang Wang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yu Wang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jun Zhao
- Unit on Synapse Development and Plasticity, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Fu Wang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, China
| | - Weitao Li
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Gang Niu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dale O. Kiesewetter
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
- Address correspondence to ,
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186
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Sato SI, Watanabe M, Katsuda Y, Murata A, Wang DO, Uesugi M. Live-Cell Imaging of Endogenous mRNAs with a Small Molecule. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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187
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Sato SI, Watanabe M, Katsuda Y, Murata A, Wang DO, Uesugi M. Live-cell imaging of endogenous mRNAs with a small molecule. Angew Chem Int Ed Engl 2014; 54:1855-8. [PMID: 25537455 DOI: 10.1002/anie.201410339] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Indexed: 11/06/2022]
Abstract
Determination of subcellular localization and dynamics of mRNA is increasingly important to understanding gene expression. A new convenient and versatile method is reported that permits spatiotemporal imaging of specific non-engineered RNAs in living cells. The method uses transfection of a plasmid encoding a gene-specific RNA aptamer, combined with a cell-permeable synthetic small molecule, the fluorescence of which is restored only when the RNA aptamer hybridizes with its cognitive mRNA. The method was validated by live-cell imaging of the endogenous mRNA of β-actin. Application of the technology to mRNAs of a total of 84 human cytoskeletal genes allowed us to observe cellular dynamics of several endogenous mRNAs including arfaptin-2, cortactin, and cytoplasmic FMR1-interacting protein 2. The RNA-imaging technology and its further optimization might permit live-cell imaging of any RNA molecules.
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Affiliation(s)
- Shin-ichi Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS) and Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan).
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188
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Abstract
Analysis of the mechanisms underlying cell fates requires the molecular quantification of cellular features. Classical techniques use population average readouts at single time points. However, these approaches mask cellular heterogeneity and dynamics and are limited for studying rare and heterogeneous cell populations like stem cells. Techniques for single-cell analyses, ideally allowing non-invasive quantification of molecular dynamics and cellular behaviour over time, are required for studying stem cells. Here, we review the development and application of these techniques to stem cell research.
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189
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Filonov GS, Moon JD, Svensen N, Jaffrey SR. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J Am Chem Soc 2014; 136:16299-308. [PMID: 25337688 PMCID: PMC4244833 DOI: 10.1021/ja508478x] [Citation(s) in RCA: 479] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Genetically
encoded fluorescent ribonucleic acids (RNAs) have diverse
applications, including imaging RNA trafficking and as a component
of RNA-based sensors that exhibit fluorescence upon binding small
molecules in live cells. These RNAs include the Spinach and Spinach2
aptamers, which bind and activate the fluorescence of fluorophores
similar to that found in green fluorescent protein. Although additional
highly fluorescent RNA–fluorophore complexes would extend the
utility of this technology, the identification of novel RNA–fluorophore
complexes is difficult. Current approaches select aptamers on the
basis of their ability to bind fluorophores, even though fluorophore
binding alone is not sufficient to activate fluorescence. Additionally,
aptamers require extensive mutagenesis to efficiently fold and exhibit
fluorescence in living cells. Here we describe a platform for rapid
generation of highly fluorescent RNA–fluorophore complexes
that are optimized for function in cells. This procedure involves
selection of aptamers on the basis of their binding to fluorophores,
coupled with fluorescence-activated cell sorting (FACS) of millions
of aptamers expressed in Escherichia coli. Promising
aptamers are then further optimized using a FACS-based directed evolution
approach. Using this approach, we identified several novel aptamers,
including a 49-nt aptamer, Broccoli. Broccoli binds and activates
the fluorescence of (Z)-4-(3,5-difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one. Broccoli shows
robust folding and green fluorescence in cells, and increased fluorescence
relative to Spinach2. This reflects, in part, improved folding in
the presence of low cytosolic magnesium concentrations. Thus, this
novel fluorescence-based selection approach simplifies the generation
of aptamers that are optimized for expression and performance in living
cells.
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Affiliation(s)
- Grigory S Filonov
- Department of Pharmacology, Weill Cornell Medical College , New York, New York 10065, United States
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190
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Peterson AM, Heemstra JM. Controlling self‐assembly of
DNA
‐polymer conjugates for applications in imaging and drug delivery. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:282-97. [DOI: 10.1002/wnan.1309] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/18/2014] [Accepted: 09/16/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Amberlyn M. Peterson
- Department of Chemistry and the Center for Cell and Genome ScienceUniversity of UtahSalt Lake CityUTUSA
| | - Jennifer M. Heemstra
- Department of Chemistry and the Center for Cell and Genome ScienceUniversity of UtahSalt Lake CityUTUSA
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191
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Dolgosheina EV, Jeng SCY, Panchapakesan SSS, Cojocaru R, Chen PSK, Wilson PD, Hawkins N, Wiggins PA, Unrau PJ. RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking. ACS Chem Biol 2014; 9:2412-20. [PMID: 25101481 DOI: 10.1021/cb500499x] [Citation(s) in RCA: 296] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Because RNA lacks strong intrinsic fluorescence, it has proven challenging to track RNA molecules in real time. To address this problem and to allow the purification of fluorescently tagged RNA complexes, we have selected a high affinity RNA aptamer called RNA Mango. This aptamer binds a series of thiazole orange (fluorophore) derivatives with nanomolar affinity, while increasing fluorophore fluorescence by up to 1,100-fold. Visualization of RNA Mango by single-molecule fluorescence microscopy, together with injection and imaging of RNA Mango/fluorophore complex in C. elegans gonads demonstrates the potential for live-cell RNA imaging with this system. By inserting RNA Mango into a stem loop of the bacterial 6S RNA and biotinylating the fluorophore, we demonstrate that the aptamer can be used to simultaneously fluorescently label and purify biologically important RNAs. The high affinity and fluorescent properties of RNA Mango are therefore expected to simplify the study of RNA complexes.
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Affiliation(s)
- Elena V Dolgosheina
- Department of Molecular Biology and Biochemistry and ‡Department of Chemistry, Simon Fraser University , 8888 University Road, Burnaby, British Columbia V5A 1S6, Canada
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192
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Wile BM, Ban K, Yoon YS, Bao G. Molecular beacon-enabled purification of living cells by targeting cell type-specific mRNAs. Nat Protoc 2014; 9:2411-24. [PMID: 25232937 PMCID: PMC4326061 DOI: 10.1038/nprot.2014.154] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular beacons (MBs) are dual-labeled oligonucleotides that fluoresce only in the presence of complementary mRNA. The use of MBs to target specific mRNAs allows sorting of specific cells from a mixed cell population. In contrast to existing approaches that are limited by available surface markers or selectable metabolic characteristics, the MB-based method enables the isolation of a wide variety of cells. For example, the ability to purify specific cell types derived from pluripotent stem cells (PSCs) is important for basic research and therapeutics. In addition to providing a general protocol for MB design, validation and nucleofection into cells, we describe how to isolate a specific cell population from differentiating PSCs. By using this protocol, we have successfully isolated cardiomyocytes differentiated from mouse or human PSCs (hPSCs) with ∼ 97% purity, as confirmed by electrophysiology and immunocytochemistry. After designing MBs, their ordering and validation requires 2 weeks, and the isolation process requires 3 h.
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Affiliation(s)
- Brian M. Wile
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Kiwon Ban
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Young-Sup Yoon
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
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193
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Blackstock D, Sun Q, Chen W. Fluorescent protein-based molecular beacons by zinc finger protein-guided assembly. Biotechnol Bioeng 2014; 112:236-41. [DOI: 10.1002/bit.25441] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/30/2014] [Accepted: 08/18/2014] [Indexed: 01/20/2023]
Affiliation(s)
- Daniel Blackstock
- Department of Chemical and Biomolecular Engineering; University of Delaware; Newark Delaware 19716
| | - Qing Sun
- Department of Chemical and Biomolecular Engineering; University of Delaware; Newark Delaware 19716
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering; University of Delaware; Newark Delaware 19716
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194
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Qiu L, Zhang T, Jiang J, Wu C, Zhu G, You M, Chen X, Zhang L, Cui C, Yu R, Tan W. Cell membrane-anchored biosensors for real-time monitoring of the cellular microenvironment. J Am Chem Soc 2014; 136:13090-3. [PMID: 25188419 PMCID: PMC4183634 DOI: 10.1021/ja5047389] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Indexed: 01/01/2023]
Abstract
Cell membrane-anchored biochemical sensors that allow real-time monitoring of the interactions of cells with their microenvironment would be powerful tools for studying the mechanisms underlying various biological processes, such as cell metabolism and signaling. Despite the significance of these techniques, unfortunately, their development has lagged far behind due to the lack of a desirable membrane engineering method. Here, we propose a simple, efficient, biocompatible, and universal strategy for one-step self-construction of cell-surface sensors using diacyllipid-DNA conjugates as the building and sensing elements. The sensors exploit the high membrane-insertion capacity of a diacyllipid tail and good sensing performance of the DNA probes. Based on this strategy, we have engineered specific DNAzymes on the cell membrane for metal ion assay in the extracellular microspace. The immobilized DNAzyme showed excellent performance for reporting and semiquantifying both exogenous and cell-extruded target metal ions in real time. This membrane-anchored sensor could also be used for multiple target detection by having different DNA probes inserted, providing potentially useful tools for versatile applications in cell biology, biomedical research, drug discovery, and tissue engineering.
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Affiliation(s)
- Liping Qiu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha, 410082, China
- Center
for Research at Bio/Nano Interface, Department of Chemistry and Department
of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute,
University of Florida, Gainesville, Florida 32611-7200, United States
| | - Tao Zhang
- Center
for Research at Bio/Nano Interface, Department of Chemistry and Department
of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute,
University of Florida, Gainesville, Florida 32611-7200, United States
| | - Jianhui Jiang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha, 410082, China
| | - Cuichen Wu
- Center
for Research at Bio/Nano Interface, Department of Chemistry and Department
of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute,
University of Florida, Gainesville, Florida 32611-7200, United States
| | - Guizhi Zhu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha, 410082, China
- Center
for Research at Bio/Nano Interface, Department of Chemistry and Department
of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute,
University of Florida, Gainesville, Florida 32611-7200, United States
| | - Mingxu You
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha, 410082, China
- Center
for Research at Bio/Nano Interface, Department of Chemistry and Department
of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute,
University of Florida, Gainesville, Florida 32611-7200, United States
| | - Xigao Chen
- Center
for Research at Bio/Nano Interface, Department of Chemistry and Department
of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute,
University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liqin Zhang
- Center
for Research at Bio/Nano Interface, Department of Chemistry and Department
of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute,
University of Florida, Gainesville, Florida 32611-7200, United States
| | - Cheng Cui
- Center
for Research at Bio/Nano Interface, Department of Chemistry and Department
of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute,
University of Florida, Gainesville, Florida 32611-7200, United States
| | - Ruqin Yu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha, 410082, China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha, 410082, China
- Center
for Research at Bio/Nano Interface, Department of Chemistry and Department
of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute,
University of Florida, Gainesville, Florida 32611-7200, United States
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195
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Hövelmann F, Gaspar I, Loibl S, Ermilov EA, Röder B, Wengel J, Ephrussi A, Seitz O. Brightness through local constraint--LNA-enhanced FIT hybridization probes for in vivo ribonucleotide particle tracking. Angew Chem Int Ed Engl 2014; 53:11370-5. [PMID: 25167966 DOI: 10.1002/anie.201406022] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Indexed: 11/11/2022]
Abstract
Imaging the dynamics of RNA in living cells is usually performed by means of transgenic approaches that require modification of RNA targets and cells. Fluorogenic hybridization probes would also allow the analysis of wild-type organisms. We developed nuclease-resistant DNA forced intercalation (FIT) probes that combine the high enhancement of fluorescence upon hybridization with the high brightness required to allow tracking of individual ribonucleotide particles (RNPs). In our design, a single thiazole orange (TO) intercalator dye is linked as a nucleobase surrogate and an adjacent locked nucleic acid (LNA) unit serves to introduce a local constraint. This closes fluorescence decay channels and thereby increases the brightness of the probe-target duplexes. As few as two probes were sufficient to enable the tracking of oskar mRNPs in wild-type living Drosophila melanogaster oocytes.
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Affiliation(s)
- Felix Hövelmann
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin (Germany)
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196
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Hövelmann F, Gaspar I, Loibl S, Ermilov EA, Röder B, Wengel J, Ephrussi A, Seitz O. Helligkeit durch lokale Rigidifizierung - LNA-verstärkte FIT-Sonden zur bildgebenden Darstellung von Ribonukleotidpartikeln in vivo. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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197
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Song Y, Zhang X, Huang L, Behlke MA, Tsourkas A. Real-time imaging of single engineered RNA transcripts in living cells using ratiometric bimolecular beacons. J Vis Exp 2014:e51544. [PMID: 25146531 DOI: 10.3791/51544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the development of diverse techniques to visualize individual RNA transcripts in single living cells. One promising technique that has recently been described utilizes an oligonucleotide-based optical probe, ratiometric bimolecular beacon (RBMB), to detect RNA transcripts that were engineered to contain at least four tandem repeats of the RBMB target sequence in the 3'-untranslated region. RBMBs are specifically designed to emit a bright fluorescent signal upon hybridization to complementary RNA, but otherwise remain quenched. The use of a synthetic probe in this approach allows photostable, red-shifted, and highly emissive organic dyes to be used for imaging. Binding of multiple RBMBs to the engineered RNA transcripts results in discrete fluorescence spots when viewed under a wide-field fluorescent microscope. Consequently, the movement of individual RNA transcripts can be readily visualized in real-time by taking a time series of fluorescent images. Here we describe the preparation and purification of RBMBs, delivery into cells by microporation and live-cell imaging of single RNA transcripts.
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Affiliation(s)
- Yang Song
- Department of Bioengineering, University of Pennsylvania
| | - Xuemei Zhang
- Department of Bioengineering, University of Pennsylvania
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198
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Lin X, Ishihara K. Water-soluble polymers bearing phosphorylcholine group and other zwitterionic groups for carrying DNA derivatives. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2014; 25:1461-78. [DOI: 10.1080/09205063.2014.934319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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199
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Yoshimura H, Ozawa T. Methods of Split Reporter Reconstitution for the Analysis of Biomolecules. CHEM REC 2014; 14:492-501. [DOI: 10.1002/tcr.201402001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Takeaki Ozawa
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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Wu Y, Zhang DY, Yin P, Vollmer F. Ultraspecific and highly sensitive nucleic acid detection by integrating a DNA catalytic network with a label-free microcavity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:2067-76. [PMID: 24585636 PMCID: PMC4096343 DOI: 10.1002/smll.201303558] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/15/2014] [Indexed: 05/22/2023]
Abstract
Nucleic acid detection with label-free biosensors circumvents costly fluorophore functionalization steps associated with conventional assays by utilizing transducers of impressive ultimate detection limits. Despite this technological prowess, molecular recognition at a surface limits the biosensors' sensitivity, specificity, and reusability. It is therefore imperative to integrate novel molecular approaches with existing label-free transducers to overcome those limitations. Here, we demonstrate this concept by integrating a DNA strand displacement circuit with a micron-scale whispering gallery mode (WGM) microsphere biosensor. The integrated biosensor exhibits at least 25-fold improved nucleic acid sensitivity, and sets a new record for label-free microcavity biosensors by detecting 80 pM (32 fmol) of a 22nt oligomer; this improvement results from the catalytic behavior of the circuit. Furthermore, the integrated sensor exhibits extremely high specificity; single nucleotide variants yield 40- to 100-fold lower signal. Finally, the same physical sensor was demonstrated to alternatingly detect 2 different nucleic acid sequences through 5 cycles of detection, showcasing both its reusability and its versatility.
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Affiliation(s)
- Yuqiang Wu
- Laboratory of Nanophotonics and Biosensing, Max Planck Insitute for the Science of Light, Erlangen 91058, Germany
| | - David Yu Zhang
- Department of Bioengineering Rice, University Houston, USA
| | - Peng Yin
- The Wyss Institute for Biologically Inspired Engineering and Department of Systems Biology, Harvard Medical School, Boston, USA
| | - Frank Vollmer
- Laboratory of Nanophotonics and Biosensing, Max Planck Insitute for the Science of Light, Erlangen 91058, Germany. Division of Biomedical Engineering, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA
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