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Chowdhury M, Turner JA, Cappello D, Hajjami M, Hudson RHE. Chimeric GFP-uracil based molecular rotor fluorophores. Org Biomol Chem 2023; 21:9463-9470. [PMID: 37997774 DOI: 10.1039/d3ob01539d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Uracil has been modified at the 5-position to derive a small library of nucleobase-chromophores which were inspired by green fluorescent protein (GFP). The key steps in the syntheses were Erlenmeyer azlactone synthesis followed by amination by use of hexamethyl disilazane (HMDS) to produce the imidazolinone derivatives. The uracil analogues displayed emission in the green region of visible spectrum and exhibited microenvironmental sensitivity exemplified by polarity-based solvatochromism and viscosity-dependent emission enhancement. Solid-state quantum yields of approximately 0.2 and solvent dependent emission wavelengths beyond 500 nm were observed. Select analogues were incorporated into peptide nucleic acid (PNA) strands which upon duplex formation with DNA showed good response ranging from a turn-off of fluorescence in presence of an opposing mismatched residue to a greater than 3-fold turn-on of fluorescence upon binding to fully complementary DNA strand.
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Affiliation(s)
- Mria Chowdhury
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7. rhhudson@uwo
| | - Julia A Turner
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7. rhhudson@uwo
| | - Daniela Cappello
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7. rhhudson@uwo
| | - Maryam Hajjami
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7. rhhudson@uwo
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7. rhhudson@uwo
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DNA Oligonucleotides as Antivirals and Vaccine Constituents against SARS Coronaviruses: A Prospective Tool for Immune System Tuning. Int J Mol Sci 2023; 24:ijms24021553. [PMID: 36675069 PMCID: PMC9862924 DOI: 10.3390/ijms24021553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/26/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
The SARS-CoV-2 pandemic has demonstrated the need to create highly effective antivirals and vaccines against various RNA viruses, including SARS coronaviruses. This paper provides a short review of innovative strategies in the development of antivirals and vaccines against SARS coronaviruses, with a focus on antisense antivirals, oligonucleotide adjuvants in vaccines, and oligonucleotide vaccines. Well-developed viral genomic databases create new opportunities for the development of innovative vaccines and antivirals using a post-genomic platform. The most effective vaccines against SARS coronaviruses are those able to form highly effective memory cells for both humoral and cellular immunity. The most effective antivirals need to efficiently stop viral replication without side effects. Oligonucleotide antivirals and vaccines can resist the rapidly changing genomic sequences of SARS coronaviruses using conserved regions of their genomes to generate a long-term immune response. Oligonucleotides have been used as excellent adjuvants for decades, and increasing data show that oligonucleotides could serve as antisense antivirals and antigens in vaccine formulations, becoming a prospective tool for immune system tuning.
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Oberemok VV, Andreeva OA, Laikova KV, Novikov IA, Kubyshkin AV. Post-genomic platform for development of oligonucleotide vaccines against RNA viruses: diamond cuts diamond. Inflamm Res 2022; 71:729-739. [PMID: 35523969 PMCID: PMC9075145 DOI: 10.1007/s00011-022-01582-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/01/2022] [Indexed: 12/02/2022] Open
Abstract
The coronavirus pandemic has starkly demonstrated the need to create highly effective vaccines against various viral diseases. The emerging new platforms for vaccine creation (adenovirus vectors and mRNA vaccines) have shown their worth in the fight against the prevention of coronavirus infection. However, adenovirus vectors and mRNA vaccines have a serious disadvantage: as a rule, only the S protein of the coronavirus is presented as an antigen. This tactic for preventing infection allows the ever-mutating virus to escape quickly from the immunity protection provided by such vaccines. Today, viral genomic databases are well-developed, which makes it possible to create new vaccines on a fundamentally new post-genomic platform. In addition, the technology for the synthesis of nucleic acids is currently experiencing an upsurge in demand in various fields of molecular biology. The accumulated experience suggests that the unique genomic sequences of viruses can act as antigens that trigger powerful humoral and cellular immunity. To achieve this effect, the following conditions must be created: the structure of the nucleic acid must be single-stranded, have a permanent 3D nanostructure, and have a unique sequence absent in the vaccinated organism. Oligonucleotide vaccines are able to resist the rapidly changing genomic sequences of RNA viruses by using conserved regions of their genomes to generate a long-term immune response, acting according to the adage that a diamond cuts a diamond. In addition, oligonucleotide vaccines will not contribute to antibody-dependent enhanced infection, since the nucleic acid of the coronavirus is inside the viral particle. It is obvious that new epidemics and pandemics caused by RNA viruses will continue to arise periodically in the human population. The creation of new, safe, and effective platforms for the production of vaccines that can flexibly change and adapt to new subtypes of viruses is very urgent and at this moment should be considered as a strategically necessary task.
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Affiliation(s)
- V V Oberemok
- Department of Molecular Genetics and Biotechnologies, V.I. Vernadsky Crimean Federal University, Simferopol, Crimea. .,Engineering Center 'Genetic and Cell Biotechnologies', V.I. Vernadsky Crimean Federal University, Simferopol, Crimea.
| | - O A Andreeva
- Department of Molecular Genetics and Biotechnologies, V.I. Vernadsky Crimean Federal University, Simferopol, Crimea.,Engineering Center 'Genetic and Cell Biotechnologies', V.I. Vernadsky Crimean Federal University, Simferopol, Crimea
| | - K V Laikova
- Biochemistry Department, V.I. Vernadsky Crimean Federal University, Simferopol, Crimea
| | - I A Novikov
- Department of Molecular Genetics and Biotechnologies, V.I. Vernadsky Crimean Federal University, Simferopol, Crimea
| | - A V Kubyshkin
- Engineering Center 'Genetic and Cell Biotechnologies', V.I. Vernadsky Crimean Federal University, Simferopol, Crimea
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Saady A, Sudhakar P, Nassir M, Gedanken A. Ultrasonic assisted synthesis of styrylpyridinium dyes: Optical properties and DFT calculations. ULTRASONICS SONOCHEMISTRY 2020; 67:105182. [PMID: 32485662 DOI: 10.1016/j.ultsonch.2020.105182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/17/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
The ultrasonic technique has received considerable attention in several fields; in particular, it gained rapid momentum in organic synthesis due to the larger reaction rates, milder reaction conditions, and better yields. We report herein a facile synthesis of a series of styrylpyridinium based dyes under ultrasonic irradiation. Within short reaction time (15 min) under ultrasonic irradiation, compared to normal laboratory conditions, (4-16 h), we can achieve good to excellent yields. The reaction time is shortened because ultrasound can accelerate the generation of the nucleophile of the pyridinium salt and subsequently a nucleophilic addition of an aldehyde followed by dehydration affords the styrylpyridinium dye, (Knoevenagel condensation). The photophysical properties of all compounds are comprehensively investigated in different solvents. All the compounds exhibit negative solvatochromism both in absorption and fluorescence emission spectra. Such behavior is due to the higher dipole moment of these molecules at the ground state. DFT calculations were performed to understand the electronic structure of the molecules. Our results show the high efficacy of sonochemistry over other methods for preparation of styrylpyridinium dyes.
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Affiliation(s)
- Abed Saady
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Pagidi Sudhakar
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Molhm Nassir
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Aharon Gedanken
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel.
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Liu C, Tanaka K, Katsube T, Varès G, Maruyama K, Ninomiya Y, Fardous Z, Sun C, Fujimori A, Moreno SG, Nenoi M, Wang B. Altered Response to Total Body Irradiation of C57BL/6-Tg (CAG-EGFP) Mice. Dose Response 2020; 18:1559325820951332. [PMID: 32922229 PMCID: PMC7453463 DOI: 10.1177/1559325820951332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Application of green fluorescent protein (GFP) in a variety of biosystems as a unique bioindicator or biomarker has revolutionized biological research and made groundbreaking achievements, while increasing evidence has shown alterations in biological properties and physiological functions of the cells and animals overexpressing transgenic GFP. In this work, response to total body irradiation (TBI) was comparatively studied in GFP transgenic C57BL/6-Tg (CAG-EGFP) mice and C57BL/6 N wild type mice. It was demonstrated that GFP transgenic mice were more sensitive to radiation-induced bone marrow death, and no adaptive response could be induced. In the nucleated bone marrow cells of GFP transgenic mice exposed to a middle dose, there was a significant increase in both the percentage of cells expressing pro-apoptotic gene Bax and apoptotic cell death. While in wild type cells, lower expression of pro-apoptotic gene Bax and higher expression of anti-apoptotic gene Bcl-2, and significant lower induction of apoptosis were observed compared to GFP transgenic cells. Results suggest that presence of GFP could alter response to TBI at whole body, cellular and molecular levels in mice. These findings indicate that there could be a major influence on the interpretation of the results obtained in GFP transgenic mice.
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Affiliation(s)
- Cuihua Liu
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Kaoru Tanaka
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Takanori Katsube
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Guillaume Varès
- Cell Signal Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Kouichi Maruyama
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Yasuharu Ninomiya
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Zeenath Fardous
- Institute of Food and Radiation Biology, Atomic Energy Research Establishment, Bangladesh Atomic Energy Commission, People’s Republic of Bangladesh
| | - Chao Sun
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of China
| | - Akira Fujimori
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Stéphanie G. Moreno
- LRTS—François Jacob Institute of Biology, Fundamental Research Division, Atomic Energy and Alternative Energies Commission, Inserm, Fontenay-aux-Roses Cedex, France
| | - Mitsuru Nenoi
- Department of Safety Administration, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Bing Wang
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
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Saady A, Wojtyniak M, Varon E, Böttner V, Kinor N, Shav-Tal Y, Ducho C, Fischer B. Specific, Sensitive, and Quantitative Detection of HER-2 mRNA Breast Cancer Marker by Fluorescent Light-Up Hybridization Probes. Bioconjug Chem 2020; 31:1188-1198. [DOI: 10.1021/acs.bioconjchem.0c00130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Abed Saady
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Melissa Wojtyniak
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Eli Varon
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Verena Böttner
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Noa Kinor
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yaron Shav-Tal
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Bilha Fischer
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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Saady A, Steinman NY, Wojtyniak M, Ducho C, Fischer B. Synthesis of 2'-Deoxyuridine Modified with a 3,5-Difluoro-4-Methoxybenzylidene Imidazolinone Derivative for Incorporation into Oligonucleotide Probes for Detection of HER2 Breast Cancer Marker. ACTA ACUST UNITED AC 2020; 80:e104. [PMID: 32032480 DOI: 10.1002/cpnc.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nucleoside intercalator conjugates (NICs) describe an innovative methodology developed in our research group for preparation of fluorescence turn-on DNA hybridization probes targeting specific mRNA sequences (e.g., breast cancer markers). In this methodology, we conjugate a non-fluorescent intercalator to the base of a nucleic acid (e.g., uracil) via a flexible spacer. This modified monomer can be incorporated into oligonucleotides by solid-phase synthesis and a large fluorescence enhancement is observed when the modified oligonucleotide is hybridized with its complementary strand due to intercalation of the fluorophore between the two strands. 5-(6-p-Methoxybenzylidene imidazolinone-1-hexene)-2'-deoxyuridine (dUMBI ) is a synthetic monomer to which 4-methoxybenzylidene imidazolinone (MBI), the fluorescent chromophore of green fluorescent protein (GFP), has been conjugated via a flexible spacer. The detection of human epidermal growth factor receptor 2 (HER2) mRNA by this probe has already been established by our group. The fluorescent intensity of the single-strand DNA can be considered as negligible due to the free rotation of the fluorophore. Upon hybridization, however, the flexible spacer allows for the intercalation of the fluorophore between the hybridized strands, giving rise to enhanced fluorescence and indicating the presence of target mRNA. 3,5-Difluoro-4-methoxybenzylidene (DFMBI) has enhanced photophysical properties compared to MBI fluorophore. This protocol describes a simple, reliable, efficient, and general method for the synthesis of improved derivative dUDFMBI as a monomer of fluorescent turn-on DNA hybridization probe with application for detection of HER2 mRNA. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Synthesis of 5-[(6)-3,5-difluoro-4-methoxybenzylidene imidazolinone-1-hexene]-2'-deoxyuridine.
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Affiliation(s)
- Abed Saady
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel
| | - Noam Y Steinman
- Institute of Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Melissa Wojtyniak
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Bilha Fischer
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel
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