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Pichon M, Levi-Acobas F, Kitoun C, Hollenstein M. 2',3'-Protected Nucleotides as Building Blocks for Enzymatic de novo RNA Synthesis. Chemistry 2024; 30:e202400137. [PMID: 38403849 DOI: 10.1002/chem.202400137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Besides being a key player in numerous fundamental biological processes, RNA also represents a versatile platform for the creation of therapeutic agents and efficient vaccines. The production of RNA oligonucleotides, especially those decorated with chemical modifications, cannot meet the exponential demand. Due to the inherent limits of solid-phase synthesis and in vitro transcription, alternative, biocatalytic approaches are in dire need to facilitate the production of RNA oligonucleotides. Here, we present a first step towards the controlled enzymatic synthesis of RNA oligonucleotides. We have explored the possibility of a simple protection step of the vicinal cis-diol moiety to temporarily block ribonucleotides. We demonstrate that pyrimidine nucleotides protected with acetals, particularly 2',3'-O-isopropylidene, are well-tolerated by the template-independent RNA polymerase PUP (polyU polymerase) and highly efficient coupling reactions can be achieved within minutes - an important feature for the development of enzymatic de novo synthesis protocols. Even though purines are not equally well-tolerated, these findings clearly demonstrate the possibility of using cis-diol-protected ribonucleotides combined with template-independent polymerases for the stepwise construction of RNA oligonucleotides.
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Affiliation(s)
- Maëva Pichon
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Camélia Kitoun
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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Boháčová S, Ludvíková L, Poštová Slavětínská L, Vaníková Z, Klán P, Hocek M. Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA. Org Biomol Chem 2019; 16:1527-1535. [PMID: 29431832 DOI: 10.1039/c8ob00160j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleosides, nucleotides and 2'-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleotides and DNA. Photodeprotection (photorelease) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined. Photocaged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR. DNA probes containing photocaged or free 5-hydroxymethylU in the recognition sequence of restriction endonucleases were prepared and used for the study of photorelease of caged DNA by UV or visible light at different wavelengths. The nitropiperonyl-protected nucleotide was found to be a superior building block because the corresponding dNTP is a good substrate for DNA polymerases, and the protecting group is efficiently cleavable by irradiation by UV or visible light (up to 425 nm).
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Affiliation(s)
- Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
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Salinas JC, Yu J, Østergaard M, Seth PP, Hanessian S. Conception and Synthesis of Oxabicyclic Nucleoside Phosphonates as Internucleotidic Phosphate Surrogates in Antisense Oligonucleotide Constructs. Org Lett 2018; 20:5296-5299. [PMID: 30146887 DOI: 10.1021/acs.orglett.8b02233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The stereocontrolled synthesis of a novel oxabicyclic nucleoside phosphonate comprising a perhydrofuropyran core unit was achieved. It was incorporated in an oligonucleotide sequence as a 5'-3' phosphonate-phosphate insert, and the stability properties of the resulting duplex were measured. The oxabicyclic nucleoside framework was designed so as to restrict rotation around angles γ, δ, and ε of a natural nucleoside.
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Affiliation(s)
- Juan C Salinas
- Department of Chemistry , Université de Montréal , P.O. Box 6128, Downtown Station , Montréal , QC H3C 3J7 , Canada
| | - Jeff Yu
- Department of Medicinal Chemistry , Ionis Pharmaceuticals , 2855 Gazelle Court , Carlsbad , California 92010 , United States
| | - Michael Østergaard
- Department of Medicinal Chemistry , Ionis Pharmaceuticals , 2855 Gazelle Court , Carlsbad , California 92010 , United States
| | - Punit P Seth
- Department of Medicinal Chemistry , Ionis Pharmaceuticals , 2855 Gazelle Court , Carlsbad , California 92010 , United States
| | - Stephen Hanessian
- Department of Chemistry , Université de Montréal , P.O. Box 6128, Downtown Station , Montréal , QC H3C 3J7 , Canada
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Barbeyron R, Vasseur JJ, Baraguey C, Smietana M. Synthesis of 3′-deoxy-3′-iminodiacetic acid and 3′-deoxy-3′-aminodiethanol thymidine analogues and NMR study of their complexation with boronic acids. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.03.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Riccardi C, Musumeci D, Irace C, Paduano L, Montesarchio D. RuIIIComplexes for Anticancer Therapy: The Importance of Being Nucleolipidic. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600943] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences; University of Napoli Federico II; Via Cintia 21 80126 Napoli Italy
| | - Domenica Musumeci
- Department of Chemical Sciences; University of Napoli Federico II; Via Cintia 21 80126 Napoli Italy
| | - Carlo Irace
- Department of Pharmacy; University of Napoli Federico II; Via D. Montesano 49 80131 Napoli Italy
| | - Luigi Paduano
- Department of Chemical Sciences; University of Napoli Federico II; Via Cintia 21 80126 Napoli Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences; University of Napoli Federico II; Via Cintia 21 80126 Napoli Italy
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D’Errico S, Oliviero G, Borbone N, Amato J, Piccialli V, Varra M, Mayol L, Piccialli G. Synthesis of new acadesine (AICA-riboside) analogues having acyclic D-ribityl or 4-hydroxybutyl chains in place of the ribose. Molecules 2013; 18:9420-31. [PMID: 23924994 PMCID: PMC6269997 DOI: 10.3390/molecules18089420] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/19/2013] [Accepted: 08/01/2013] [Indexed: 01/15/2023] Open
Abstract
The antiviral activity of certain acyclic nucleosides drew our attention to the fact that the replacement of the furanose ring by an alkyl group bearing hydroxyl(s) could be a useful structural modification to modulate the biological properties of those nucleosides. Herein, we report on the synthesis of some novel acadesine analogues, where the ribose moiety is mimicked by a D-ribityl or by a hydroxybutyl chain.
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Affiliation(s)
- Stefano D’Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy; E-Mails: (S.D.); (N.B.); (J.A.); (M.P.); (L.M.); (G.P.)
| | - Giorgia Oliviero
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy; E-Mails: (S.D.); (N.B.); (J.A.); (M.P.); (L.M.); (G.P.)
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy; E-Mails: (S.D.); (N.B.); (J.A.); (M.P.); (L.M.); (G.P.)
| | - Jussara Amato
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy; E-Mails: (S.D.); (N.B.); (J.A.); (M.P.); (L.M.); (G.P.)
| | - Vincenzo Piccialli
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Via Cintia 21, Napoli 80126, Italy; E-Mail:
| | - Michela Varra
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy; E-Mails: (S.D.); (N.B.); (J.A.); (M.P.); (L.M.); (G.P.)
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy; E-Mails: (S.D.); (N.B.); (J.A.); (M.P.); (L.M.); (G.P.)
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy; E-Mails: (S.D.); (N.B.); (J.A.); (M.P.); (L.M.); (G.P.)
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Montesarchio D, Mangiapia G, Vitiello G, Musumeci D, Irace C, Santamaria R, D'Errico G, Paduano L. A new design for nucleolipid-based Ru(iii) complexes as anticancer agents. Dalton Trans 2013; 42:16697-708. [DOI: 10.1039/c3dt52320a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Synthesis, self-aggregation and bioactivity properties of a cationic aminoacyl surfactant, based on a new class of highly functionalized nucleolipids. Eur J Med Chem 2012; 57:429-40. [DOI: 10.1016/j.ejmech.2012.06.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/20/2012] [Accepted: 06/21/2012] [Indexed: 01/13/2023]
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