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Kozarski M, Drazkowska K, Bednarczyk M, Warminski M, Jemielity J, Kowalska J. Towards superior mRNA caps accessible by click chemistry: synthesis and translational properties of triazole-bearing oligonucleotide cap analogs. RSC Adv 2023; 13:12809-12824. [PMID: 37114020 PMCID: PMC10126820 DOI: 10.1039/d3ra00026e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
Messenger RNA (mRNA)-based gene delivery is a powerful strategy for the development of vaccines and therapeutics. Consequently, approaches that enable efficient synthesis of mRNAs with high purity and biological activity are in demand. Chemically modified 7-methylguanosine (m7G) 5' caps can augment the translational properties of mRNA; however, efficient synthesis of structurally complex caps, especially on a large scale, is challenging. Previously, we proposed a new strategy to assemble dinucleotide mRNA caps by replacing the traditional pyrophosphate bond formation by copper-catalyzed azide-alkyne cycloaddition (CuAAC). Here, we used CuAAC to synthesize 12 novel triazole-containing tri- and tetranucleotide cap analogs with the aim of exploring the chemical space around the first transcribed nucleotide in mRNA and overcoming some of the limitations previously reported for the triazole-containing dinucleotide analogs. We evaluated the efficiency of incorporation into RNA for these analogs and their influence on the translational properties of in vitro transcribed (IVT) mRNAs in rabbit reticulocyte lysate and JAWS II cultured cells. The incorporation of the triazole moiety within the 5',5'-oligophosphate of trinucleotide cap produced compounds that were well incorporated into RNA by T7 polymerase while replacing the 5',3'-phosphodiester bond with triazole impaired incorporation and translation efficiency, despite a neutral effect on the interaction with the translation initiation factor eIF4E. One of the compounds (m7Gppp-tr-C2H4pAmpG), had translational activity and other biochemical properties comparable to natural cap 1 structure, thus being a promising mRNA capping reagent for potential in cellulo and in vivo applications in the field of mRNA-based therapeutics.
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Affiliation(s)
- Mateusz Kozarski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw Pasteura 5 02-093 Warsaw Poland
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Karolina Drazkowska
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Marcelina Bednarczyk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw Pasteura 5 02-093 Warsaw Poland
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw Pasteura 5 02-093 Warsaw Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw Pasteura 5 02-093 Warsaw Poland
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Wanat P, Kasprzyk R, Kopcial M, Sikorski PJ, Strzelecka D, Jemielity J, Kowalska J. ExciTides: NTP-derived probes for monitoring pyrophosphatase activity based on excimer-to-monomer transitions. Chem Commun (Camb) 2018; 54:9773-9776. [PMID: 30105342 DOI: 10.1039/c8cc04968h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a new type of nucleotide-derived fluorescent probe designed for monitoring pyrophosphatase activity based on excimer-to-monomer transitions, called ExciTide. The nucleotides were designed with two self-interacting dye moieties and synthesised using copper-catalysed azide-alkyne cycloaddition click chemistry. We applied these probes for enzyme activity monitoring and inhibitor evaluation. Some of the probes permeated into living cells, yielding interesting prospects for future applications.
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Affiliation(s)
- Przemyslaw Wanat
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
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Warminski M, Sikorski PJ, Warminska Z, Lukaszewicz M, Kropiwnicka A, Zuberek J, Darzynkiewicz E, Kowalska J, Jemielity J. Amino-Functionalized 5' Cap Analogs as Tools for Site-Specific Sequence-Independent Labeling of mRNA. Bioconjug Chem 2017; 28:1978-1992. [PMID: 28613834 DOI: 10.1021/acs.bioconjchem.7b00291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mRNA is a template for protein biosynthesis, and consequently mRNA transport, translation, and turnover are key elements in the overall regulation of gene expression. Along with growing interest in the mechanisms regulating mRNA decay and localization, there is an increasing need for tools enabling convenient fluorescent labeling or affinity tagging of mRNA. We report new mRNA 5' cap analog-based tools that enable site-specific labeling of RNA within the cap using N-hydroxysuccinimide (NHS) chemistry. We explored two complementary methods: a co-transcriptional labeling method, in which the label is first attached to a cap analog and then incorporated into RNA by in vitro transcription, and a post-transcriptional labeling method, in which an amino-functionalized cap analog is incorporated into RNA followed by chemical labeling of the resulting transcript. After testing the biochemical properties of RNAs carrying the novel modified cap structures, we demonstrated the utility of fluorescently labeled RNAs in decapping assays, RNA decay assays, and RNA visualization in cells. Finally, we also demonstrated that mRNAs labeled by the reported method are translationally active. We envisage that the novel analogs will provide an alternative to radiolabeling of mRNA caps for in vitro studies and open possibilities for new applications related to the study of mRNA fates in vivo.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland
| | - Zofia Warminska
- Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland.,College of Interfaculty Individual Studies of Mathematics and Natural Sciences, University of Warsaw , 02-093, Warsaw, Poland
| | - Maciej Lukaszewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Anna Kropiwnicka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland.,Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland
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Warminski M, Kowalska J, Jemielity J. Synthesis of RNA 5'-Azides from 2'-O-Pivaloyloxymethyl-Protected RNAs and Their Reactivity in Azide-Alkyne Cycloaddition Reactions. Org Lett 2017. [PMID: 28636394 DOI: 10.1021/acs.orglett.7b01591] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Commercially available 2'-O-pivaloyloxymethyl (PivOM) phosphoramidites were employed in an SPS protocol for RNA 5' azides. The utility of the N3-RNAs in CuAAC and SPAAC was demonstrated by RNA 5' labeling, chemical ligation including fragment joining and cyclization, and bioconjugation. As a result, several new RNA conjugates that may be valuable tools for studies on biological events such as innate immune response (cyclic dinucleotides), post-transcriptional gene regulation (circular RNAs), or mRNA turnover (m7G capped RNAs) were obtained.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , Pasteura 5, 02-093 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland
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Kroczynska B, Blyth GT, Rafidi RL, Majchrzak-Kita B, Xu L, Saleiro D, Kosciuczuk EM, Jemielity J, Su B, Altman JK, Eklund EA, Fish EN, Platanias LC. Central Regulatory Role for SIN1 in Interferon γ (IFNγ) Signaling and Generation of Biological Responses. J Biol Chem 2017; 292:4743-4752. [PMID: 28174303 DOI: 10.1074/jbc.m116.757666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/30/2017] [Indexed: 12/25/2022] Open
Abstract
The precise signaling mechanisms by which type II IFN receptors control expression of unique genes to induce biological responses remain to be established. We provide evidence that Sin1, a known element of the mammalian target of rapamycin complex 2 (mTORC2), is required for IFNγ-induced phosphorylation and activation of AKT and that such activation mediates downstream regulation of mTORC1 and its effectors. These events play important roles in the assembly of the eukaryotic translation initiation factor 4F (eIF4F) and mRNA translation of IFN-stimulated genes. Interestingly, IFNγ-induced tyrosine phosphorylation of STAT1 is reduced in cells with targeted disruption of Sin1, leading to decreased transcription of several IFNγ-inducible genes in an mTORC2-independent manner. Additionally, our studies establish that Sin1 is essential for generation of type II IFN-dependent antiviral effects and antiproliferative responses in normal and malignant hematopoiesis. Together, our findings establish an important role for Sin1 in both transcription and translation of IFN-stimulated genes and type II IFN-mediated biological responses, involving both mTORC2-dependent and -independent functions.
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Affiliation(s)
- Barbara Kroczynska
- From the Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Feinberg School of Medicine, and.,the Department of Radiation Oncology, Northwestern University, Chicago, Illinois 60611
| | - Gavin T Blyth
- From the Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Feinberg School of Medicine, and
| | - Robert L Rafidi
- From the Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Feinberg School of Medicine, and
| | - Beata Majchrzak-Kita
- the Toronto General Research Institute, University Health Network, and Department of Immunology, University of Toronto, Toronto, Ontario M5G 2M1, Canada
| | - Lucy Xu
- From the Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Feinberg School of Medicine, and
| | - Diana Saleiro
- From the Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Feinberg School of Medicine, and
| | - Ewa M Kosciuczuk
- From the Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Feinberg School of Medicine, and.,the Division of Hematology-Oncology, Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
| | - Jacek Jemielity
- the Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Bing Su
- the Department of Immunobiology and the Vascular Biology and Therapeutics Program, Yale University, New Haven, Connecticut 06520, and.,the Shanghai Institute of Immunology and Department of Microbiology and Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200000, China
| | - Jessica K Altman
- From the Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Feinberg School of Medicine, and.,the Division of Hematology-Oncology, Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
| | - Elizabeth A Eklund
- From the Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Feinberg School of Medicine, and.,the Division of Hematology-Oncology, Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
| | - Eleanor N Fish
- the Toronto General Research Institute, University Health Network, and Department of Immunology, University of Toronto, Toronto, Ontario M5G 2M1, Canada
| | - Leonidas C Platanias
- From the Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Feinberg School of Medicine, and .,the Division of Hematology-Oncology, Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
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