1
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Bose M, Lampe M, Mahamid J, Ephrussi A. Liquid-to-solid phase transition of oskar ribonucleoprotein granules is essential for their function in Drosophila embryonic development. Cell 2022; 185:1308-1324.e23. [PMID: 35325593 PMCID: PMC9042795 DOI: 10.1016/j.cell.2022.02.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/24/2021] [Accepted: 02/18/2022] [Indexed: 01/05/2023]
Abstract
Asymmetric localization of oskar ribonucleoprotein (RNP) granules to the oocyte posterior is crucial for abdominal patterning and germline formation in the Drosophila embryo. We show that oskar RNP granules in the oocyte are condensates with solid-like physical properties. Using purified oskar RNA and scaffold proteins Bruno and Hrp48, we confirm in vitro that oskar granules undergo a liquid-to-solid phase transition. Whereas the liquid phase allows RNA incorporation, the solid phase precludes incorporation of additional RNA while allowing RNA-dependent partitioning of client proteins. Genetic modification of scaffold granule proteins or tethering the intrinsically disordered region of human fused in sarcoma (FUS) to oskar mRNA allowed modulation of granule material properties in vivo. The resulting liquid-like properties impaired oskar localization and translation with severe consequences on embryonic development. Our study reflects how physiological phase transitions shape RNA-protein condensates to regulate the localization and expression of a maternal RNA that instructs germline formation.
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Affiliation(s)
- Mainak Bose
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marko Lampe
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
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2
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Wickhorst PJ, Druzhinin SI, Ihmels H, Müller M, Sutera Sardo M, Schönherr H, Viola G. A Dimethylaminophenyl‐Substituted Naphtho[1,2‐
b
]quinolizinium as a Multicolor NIR Probe for the Fluorimetric Detection of Intracellular Nucleic Acids and Proteins. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Peter Jonas Wickhorst
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Sergey I. Druzhinin
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Heiko Ihmels
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Mareike Müller
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | | | - Holger Schönherr
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Giampietro Viola
- Department of Women's and Child's health Oncohematology laboratory University of Padova Via Giustiniani 2 I-35128 Padova Italy
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3
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Suss O, Motiei L, Margulies D. Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions. Molecules 2021; 26:2828. [PMID: 34068759 PMCID: PMC8126248 DOI: 10.3390/molecules26092828] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
Fluorescent sensing of biomolecules has served as a revolutionary tool for studying and better understanding various biological systems. Therefore, it has become increasingly important to identify fluorescent building blocks that can be easily converted into sensing probes, which can detect specific targets with increasing sensitivity and accuracy. Over the past 30 years, thiazole orange (TO) has garnered great attention due to its low fluorescence background signal and remarkable 'turn-on' fluorescence response, being controlled only by its intramolecular torsional movement. These features have led to the development of numerous molecular probes that apply TO in order to sense a variety of biomolecules and metal ions. Here, we highlight the tremendous progress made in the field of TO-based sensors and demonstrate the different strategies that have enabled TO to evolve into a versatile dye for monitoring a collection of biomolecules.
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Affiliation(s)
| | | | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (O.S.); (L.M.)
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4
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Baladi T, Nilsson JR, Gallud A, Celauro E, Gasse C, Levi-Acobas F, Sarac I, Hollenstein MR, Dahlén A, Esbjörner EK, Wilhelmsson LM. Stealth Fluorescence Labeling for Live Microscopy Imaging of mRNA Delivery. J Am Chem Soc 2021; 143:5413-5424. [PMID: 33797236 PMCID: PMC8154517 DOI: 10.1021/jacs.1c00014] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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Methods for tracking
RNA inside living cells without perturbing
their natural interactions and functions are critical within biology
and, in particular, to facilitate studies of therapeutic RNA delivery.
We present a stealth labeling approach that can efficiently, and with
high fidelity, generate RNA transcripts, through enzymatic incorporation
of the triphosphate of tCO, a fluorescent tricyclic cytosine
analogue. We demonstrate this by incorporation of tCO in
up to 100% of the natural cytosine positions of a 1.2 kb mRNA encoding
for the histone H2B fused to GFP (H2B:GFP). Spectroscopic characterization
of this mRNA shows that the incorporation rate of tCO is
similar to cytosine, which allows for efficient labeling and controlled
tuning of labeling ratios for different applications. Using live cell
confocal microscopy and flow cytometry, we show that the tCO-labeled mRNA is efficiently translated into H2B:GFP inside human
cells. Hence, we not only develop the use of fluorescent base analogue
labeling of nucleic acids in live-cell microscopy but also, importantly,
show that the resulting transcript is translated into the correct
protein. Moreover, the spectral properties of our transcripts and
their translation product allow for their straightforward, simultaneous
visualization in live cells. Finally, we find that chemically transfected
tCO-labeled RNA, unlike a state-of-the-art fluorescently
labeled RNA, gives rise to expression of a similar amount of protein
as its natural counterpart, hence representing a methodology for studying
natural, unperturbed processing of mRNA used in RNA therapeutics and
in vaccines, like the ones developed against SARS-CoV-2.
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Affiliation(s)
- Tom Baladi
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Audrey Gallud
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Emanuele Celauro
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Cécile Gasse
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Fabienne Levi-Acobas
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Ivo Sarac
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Marcel R Hollenstein
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Anders Dahlén
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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5
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Loibl N, Arenz C, Seitz O. Monitoring Dicer-Mediated miRNA-21 Maturation and Ago2 Loading by a Dual-Colour FIT PNA Probe Set. Chembiochem 2020; 21:2527-2532. [PMID: 32270536 PMCID: PMC7496889 DOI: 10.1002/cbic.202000173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/06/2020] [Indexed: 12/14/2022]
Abstract
The inhibition of micro RNA (miRNA) maturation by Dicer and loading matured miRNAs into the RNA-induced silencing complex (RISC) is envisioned as a modality for treatment of cancer. Existing methods for evaluating maturation either focus on the conversion of modified precursors or detect mature miRNA. Whereas the former is not applicable to native pre-miRNA, the latter approach underestimates maturation when both nonmatured and matured miRNA molecules are subject to cleavage. We present a set of two orthogonally labelled FIT PNA probes that distinguish between cleaved pre-miRNA and the mature miRNA duplex. The probes allow Dicer-mediated miR21 maturation to be monitored and Ago2-mediated unwinding of the miR21 duplex to be assayed. A two-channel fluorescence readout enables measurement in real-time without the need for specialized instrumentation or further enzyme mediated amplification.
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Affiliation(s)
- Natalia Loibl
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
| | - Christoph Arenz
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
| | - Oliver Seitz
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
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6
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Knoll A, Kankowski S, Schöllkopf S, Meier JC, Seitz O. Chemo-biological mRNA imaging with single nucleotide specificity. Chem Commun (Camb) 2020; 55:14817-14820. [PMID: 31763632 DOI: 10.1039/c9cc06989e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Unambiguous imaging of C → U edited mRNA calls for a method that distinguishes a locally high concentration of unbound probe or single nucleotide mismatched target from a locally low concentration of matched mRNA target. To address this issue, we combine FIT probes as a "chemical" detection system with the "biological" MS2 technique. Ratio measurements provide a convenient parameter to discriminate the edited from the unedited state of mRNA encoding for GlyR α2 in HEK cells.
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Affiliation(s)
- Andrea Knoll
- Humboldt University Berlin, Department of Chemistry, Brook-Taylor-Str. 2, D-12489 Berlin, Germany.
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7
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Kitamura Y, Azuma Y, Katsuda Y, Ihara T. Catalytic formation of luminescent lanthanide complexes using an entropy-driven DNA circuit. Chem Commun (Camb) 2020; 56:3863-3866. [DOI: 10.1039/d0cc00602e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Luminescent lanthanide complexes were catalytically formed through an entropy-driven DNA circuit triggered by a target nucleic acid.
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Affiliation(s)
- Yusuke Kitamura
- Division of Materials Science and Chemistry
- Faculty of Advanced Science and Technology
- Kumamoto University
- Kumamoto 860-8555
- Japan
| | - Yukina Azuma
- Division of Materials Science and Chemistry
- Faculty of Advanced Science and Technology
- Kumamoto University
- Kumamoto 860-8555
- Japan
| | - Yousuke Katsuda
- Division of Materials Science and Chemistry
- Faculty of Advanced Science and Technology
- Kumamoto University
- Kumamoto 860-8555
- Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry
- Faculty of Advanced Science and Technology
- Kumamoto University
- Kumamoto 860-8555
- Japan
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8
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Klimkowski P, De Ornellas S, Singleton D, El-Sagheer AH, Brown T. Design of thiazole orange oligonucleotide probes for detection of DNA and RNA by fluorescence and duplex melting. Org Biomol Chem 2019; 17:5943-5950. [PMID: 31157811 PMCID: PMC6686645 DOI: 10.1039/c9ob00885c] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have synthesised a range of thiazole orange (TO) functionalised oligonucleotides for nucleic acid detection in which TO is attached to the nucleobase or sugar of thymidine. The properties of duplexes between TO-probes and their DNA and RNA targets strongly depend on the length of the linker between TO and the oligonucleotide, the position of attachment of TO to the nucleotide (major or minor groove) and the mode of attachment of thiazole orange (via benzothiazole or quinoline moiety). This information can be used to design probes for detection of target nucleic acids by fluorescence or duplex melting. With cellular imaging in mind we show that 2'-OMe RNA probes with TO at the 5-position of uracil or the 2'-position of the ribose sugar are particularly effective, exhibiting up to 44-fold fluorescence enhancement against DNA and RNA, and high duplex stability. Excellent mismatch discrimination is achieved when the mispaired base is located adjacent to the TO-modified nucleotide rather than opposite to it. The simple design, ease of synthesis and favourable properties of these TO probes suggest applications in fluorescent imaging of DNA and RNA in a cellular context.
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Affiliation(s)
- Piotr Klimkowski
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Sara De Ornellas
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DS, UK
| | - Daniel Singleton
- ATDBio, School of Chemistry University of Southampton, SO17 1BJ, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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9
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Kitamura Y, Nozaki A, Ozaki R, Katsuda Y, Ihara T. Catalytic Formation of Luminescent Complex Clusters Based on Autonomous Strand Exchange Reaction of DNA. ACS APPLIED BIO MATERIALS 2019; 2:2988-2993. [DOI: 10.1021/acsabm.9b00326] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Akihiro Nozaki
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Rie Ozaki
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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10
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Schultz C. The Life Science Toolbox Provided by Chemical Biology. Isr J Chem 2019. [DOI: 10.1002/ijch.201900020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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Chamiolo J, Fang GM, Hövelmann F, Friedrich D, Knoll A, Loewer A, Seitz O. Comparing Agent-Based Delivery of DNA and PNA Forced Intercalation (FIT) Probes for Multicolor mRNA Imaging. Chembiochem 2018; 20:595-604. [PMID: 30326174 PMCID: PMC6470956 DOI: 10.1002/cbic.201800526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 12/19/2022]
Abstract
Fluorogenic oligonucleotide probes allow mRNA imaging in living cells. A key challenge is the cellular delivery of probes. Most delivery agents, such as cell‐penetrating peptides (CPPs) and pore‐forming proteins, require interactions with the membrane. Charges play an important role. To explore the influence of charge on fluorogenic properties and delivery efficiency, we compared peptide nucleic acid (PNA)‐ with DNA‐based forced intercalation (FIT) probes. Perhaps counterintuitively, fluorescence signaling by charged DNA FIT probes proved tolerant to CPP conjugation, whereas CPP–FIT PNA conjugates were affected. Live‐cell imaging was performed with a genetically engineered HEK293 cell line to allow the inducible expression of a specific mRNA target. Blob‐like features and high background were recurring nuisances of the tested CPP and lipid conjugates. By contrast, delivery by streptolysin‐O provided high enhancements of the fluorescence of the FIT probe upon target induction. Notably, DNA‐based FIT probes were brighter and more responsive than PNA‐based FIT probes. Optimized conditions enabled live‐cell multicolor imaging of three different mRNA target sequences.
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Affiliation(s)
- Jasmine Chamiolo
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Ge-Min Fang
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany.,Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, P.R. China
| | - Felix Hövelmann
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Dhana Friedrich
- Max Delbrück Centrum für Molekulare Medizin, Robert Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 13, 64287, Darmstadt, Germany
| | - Andrea Knoll
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Alexander Loewer
- Max Delbrück Centrum für Molekulare Medizin, Robert Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 13, 64287, Darmstadt, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
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12
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Pasnuri N, Khuntia P, Mazumder A. Single transcript imaging to assay gene expression in wholemount Drosophila melanogaster tissues. Mech Dev 2018; 153:10-16. [PMID: 30118816 DOI: 10.1016/j.mod.2018.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 10/28/2022]
Abstract
Single molecule Fluorescence in situ Hybridization (smFISH) for mRNA provides a powerful quantitative handle on expression from endogenous gene loci. While the method has been widely applied in cells in culture, applications to primary tissue samples remain fewer, and often use involved cryosectioning. Even apart from quantitative access to absolute transcript counts in specific tissue volumes, many other advantages of smFISH can be envisaged in tissue samples. Primary among these are the ability to report on subtle differences in expression among different cell types within a tissue, and the ability to correlate the expression from different target genes. Here, we present a modified method of smFISH applicable on various primary wholemount tissues from the fruit fly Drosophila melanogaster, and show the efficacy of the method in a variety of larval and adult tissue, and embryos. We also combine smFISH in tissue with immunofluorescence to demonstrate the possibility of capturing transcriptional and translational aspects of gene expression in the same tissue. Given the widespread use of Drosophila melanogaster as a model system in Developmental Biology and Genetics, such methods are likely to be of wide interest and could yield rich information about gene expression in tissues from this organism.
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Affiliation(s)
- Nikhita Pasnuri
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500107, Telangana, India
| | - Purnati Khuntia
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500107, Telangana, India
| | - Aprotim Mazumder
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500107, Telangana, India.
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