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Banerjee A, Das A, Ghosh A, Gupta A, Sinha S. Synthesis and Biophysical Properties of Triazole-Incorporated PMOs (TzPMOs): A Convergent, Click Ligation Approach. J Org Chem 2024; 89:2895-2903. [PMID: 38344977 DOI: 10.1021/acs.joc.3c02242] [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: 03/02/2024]
Abstract
The synthesis of phosphorodiamidate morpholino oligonucleotides (PMOs) incorporating single or double triazole rings in the backbone has been achieved via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The synthetic approach implemented is fundamentally convergent, involving the ligation of a 5'-azide PMO fragment to a 3'-alkyne fragment both in solution and on solid support. To access the 3'-alkyne PMO fragment, we synthesized 3'-N-propargyl chlorophosphoramidate morpholino monomers for all four nucleobases. The resulting triazole-incorporated PMOs (TzPMOs) have exhibited comparable or improved binding affinity toward complementary deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) strands compared to its regular analogues. Finally, a full-length TzPMO was designed to target the Nanog gene, demonstrating almost identical hybridization properties when compared to its regular version. Circular dichroism studies revealed a B-type helical conformation for the duplexes formed by TzPMOs.
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Affiliation(s)
- Arpan Banerjee
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Abhishek Gupta
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
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2
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Baraniak D, Boryski J. Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry. Biomedicines 2021; 9:628. [PMID: 34073038 PMCID: PMC8229351 DOI: 10.3390/biomedicines9060628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.
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Affiliation(s)
- Dagmara Baraniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
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Abstract
This review offers a summary on the advances in the construction of 1,2,3-triazole-based sequence-defined oligomers and polymers through MAAC-based ISG or IEG strategies.
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Affiliation(s)
- Xiaojun Wang
- State Key Laboratory of Organic-Inorganic Composites
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Xueyan Zhang
- State Key Laboratory of Organic-Inorganic Composites
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Shengtao Ding
- State Key Laboratory of Organic-Inorganic Composites
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
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Fortuna A, Costa PJ, Piedade MFM, Conceição Oliveira M, Xavier NM. Synthesis of Triazole-Containing Furanosyl Nucleoside Analogues and Their Phosphate, Phosphoramidate or Phoshonate Derivatives as Potential Sugar Diphosphate or Nucleotide Mimetics. Chempluschem 2020; 85:1676-1691. [PMID: 32757384 DOI: 10.1002/cplu.202000424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/16/2020] [Indexed: 12/21/2022]
Abstract
The synthesis of stable and potentially bioactive xylofuranosyl nucleoside analogues and potential sugar diphosphate or nucleotide mimetics comprising a 1,2,3-triazole moiety is reported. 3'-O-Methyl-branched N-benzyltriazole isonucleosides were accessed in 5-7 steps and 42-54 % overall yields using a Cu(I)-catalyzed cycloaddition of 3-O-propargyl-1,2-O-isopropylidene-α-D-xylofuranose with benzyl azide as key step. Related isonucleotides were obtained by 5-O-phosphorylation of acetonide-protected 3-O-propargyl xylofuranose and further "click" cycloaddition or by Staudinger-phosphite reaction of a 5-azido N-benzyltriazole isonucleoside. Hydroxy-, amino- or bromomethyl triazole 5'-isonucleosides were synthesized by thermal cycloaddition of 5-azido 3-O-benzyl/dodecyl xylofuranoses with propargyl alcohol, propargylamine or propargyl bromide. Better yields (82-85 %) were obtained when using propargyl alcohol and a high 1,4-regioselectivity was attained with propargyl bromide. Further O/N-phosphorylation or Arbuzov reaction led to (triazolyl)methyl phosphates, phosphoramidates or phosphonates. The latter were converted into uracil nucleoside 5'-(triazolyl)methyl phosphonates as prospective nucleoside diphosphate mimetics.
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Affiliation(s)
- Andreia Fortuna
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Ed. C8, 5° Piso, Campo Grande, 1749-016, Lisboa, Portugal.,University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016, Lisboa, Portugal
| | - Paulo J Costa
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016, Lisboa, Portugal
| | - M Fátima M Piedade
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Ed. C8, 5° Piso, Campo Grande, 1749-016, Lisboa, Portugal.,Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - M Conceição Oliveira
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Nuno M Xavier
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Ed. C8, 5° Piso, Campo Grande, 1749-016, Lisboa, Portugal
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Fujino T, Suzuki T, Ooi T, Ikemoto K, Isobe H. Duplex-forming Oligonucleotide of Triazole-linked RNA. Chem Asian J 2019; 14:3380-3385. [PMID: 31478313 DOI: 10.1002/asia.201901112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 08/29/2019] [Indexed: 02/02/2023]
Abstract
An oligonucleotide of triazole-linked RNA (TL RNA) was synthesized by performing consecutive copper-catalyzed azide-alkyne cycloaddition reactions for elongation. The reaction conditions that had been optimized for the synthesis of 3-mer TL RNA were found to be inappropriate for longer oligonucleotides, and the conditions were reoptimized for the solid-phase synthesis of an 11-mer TL RNA oligonucleotide. Duplex formation of the 11-mer TL RNA oligonucleotide was examined with the complementary oligonucleotide of natural RNA to reveal the effects of the 2'-OH groups on the duplex stability.
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Affiliation(s)
- Tomoko Fujino
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
- Present address: Institute for Solid State Physics, The University of Tokyo, Kashiwanoha 5-1-5, Chiba, 277-8581, Japan
| | - Takeru Suzuki
- Department of Chemistry, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Tsugumi Ooi
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koki Ikemoto
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
- JST, ERATO Isobe Degenerate π-Integration Project, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroyuki Isobe
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
- JST, ERATO Isobe Degenerate π-Integration Project, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
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Fujino T, Suzuki T, Okada K, Kogashi K, Yasumoto KI, Sogawa K, Isobe H. Chimeric RNA Oligonucleotides Incorporating Triazole-Linked Trinucleotides: Synthesis and Function as mRNA in Cell-Free Translation Reactions. J Org Chem 2016; 81:8967-8976. [PMID: 27579606 DOI: 10.1021/acs.joc.6b01618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A method for the synthesis of chimeric oligonucleotides was developed to incorporate purine nucleobases and multiple triazole linkers in natural, phosphate-linked structures of RNA. A solution-phase synthesis method for triazole-linked RNA oligomers via copper-catalyzed azide-alkyne cycloaddition reaction was optimized and tolerated purine nucleobases and protecting groups for further transformations. Three TLRNA trinucleotides with 5'-protected hydroxy and 3'-phosphoramidite groups were prepared, and one congener with a representative sequence was subjected to automated, solid-phase phosphoramidite synthesis. The synthesis allowed the efficient preparation of 13-mer chimeric RNA oligonucleotides with two triazole linkers, ten phosphate linkers and purine/pyrimidine nucleobases. The chimeric oligonucleotide was found applicable to a cell-free translation system as mRNA and provided the genetic code for dipeptide production.
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Affiliation(s)
- Tomoko Fujino
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Takeru Suzuki
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Koudai Okada
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Kanako Kogashi
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Ken-Ichi Yasumoto
- Department of Biomolecular Sciences, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Kazuhiro Sogawa
- Department of Biomolecular Sciences, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Hiroyuki Isobe
- JST ERATO, Isobe Degenerate π-Integration Project and Advanced Institute for Materials Research, Tohoku University , Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Fujino T, Kogashi K, Okada K, Mattarella M, Suzuki T, Yasumoto K, Sogawa K, Isobe H. Chimeric RNA Oligonucleotides with Triazole and Phosphate Linkages: Synthesis and RNA Interference. Chem Asian J 2015; 10:2683-8. [PMID: 26248050 DOI: 10.1002/asia.201500765] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 11/12/2022]
Abstract
Chimeric RNA oligonucleotides with an artificial triazole linker were synthesized using solution-phase click chemistry and solid-phase automated synthesis. Scalable synthesis methods for jointing units for the chimeric structure have been developed, and after click-coupling of the jointing units with triazole linkers, a series of chimeric oligonucleotides was prepared by utilizing the well-established phosphoramidite method for the elongation. The series of chimeric 21-mer oligonucleotides that possessed the triazole linker at different strands and positions allowed for a screening study of the RNA interference to clarify the preference of the triazole modifications in small-interfering RNA molecules.
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Affiliation(s)
- Tomoko Fujino
- Department of Chemistry, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Kanako Kogashi
- Department of Chemistry, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Koudai Okada
- Department of Chemistry, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Martin Mattarella
- Department of Chemistry, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Takeru Suzuki
- Department of Chemistry, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Kenichi Yasumoto
- Department of Biomolecular Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Kazuhiro Sogawa
- Department of Biomolecular Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Hiroyuki Isobe
- Department of Chemistry, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan. .,JST, ERATO, Isobe Degenerate π-Integration Project and Advanced Institute for Materials Research, Tohoku University, Aoba-ku, Sendai, 980-8577, Japan.
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Peel BJ, Efthymiou TC, Desaulniers JP. Synthesis of triazole-nucleoside phosphoramidites and their use in solid-phase oligonucleotide synthesis. ACTA ACUST UNITED AC 2014; 55:4.57.1-38. [PMID: 25631534 DOI: 10.1002/0471142700.nc0457s55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Triazole-backbone oligonucleotides are macromolecules that have one or more triazole units that are acting as a backbone mimic. Triazoles within the backbone have been used within oligonucleotides for a variety of applications. This unit describes the preparation and synthesis of two triazole-nucleoside phosphoramidites [uracil-triazole-uracil (UtU) and cytosine-triazole-uracil (CtU)] based on a PNA-like scaffold, and their incorporation within oligonucleotides.
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Affiliation(s)
- Brandon J Peel
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
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Isobe H, Fujino T. Triazole-linked analogues of DNA and RNA ((TL)DNA and (TL)RNA): synthesis and functions. CHEM REC 2014; 14:41-51. [PMID: 24734308 DOI: 10.1002/tcr.201300023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Click chemistry has provided us with access to DNA and RNA analogues with non-natural triazole internucleoside linkages. The bond periodicity of the oligonucleotides was designed to enforce duplex formation with natural congeners, and the non-cleavable linkages protect the oligomers against nuclease digestion. This account reviews the progress of the triazole-linked analogues over the past five years. Reinforced by their synthetic robustness, these analogues may find various utilities as tools for exploratory research.
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Fujino T, Okada K, Isobe H. Conformational restriction of cyclic dinucleotides with triazole-linked cyclophane analogues. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.03.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Efthymiou T, Gong W, Desaulniers JP. Chemical architecture and applications of nucleic acid derivatives containing 1,2,3-triazole functionalities synthesized via click chemistry. Molecules 2012; 17:12665-703. [PMID: 23103533 PMCID: PMC6268694 DOI: 10.3390/molecules171112665] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/19/2012] [Accepted: 10/19/2012] [Indexed: 11/16/2022] Open
Abstract
There is considerable attention directed at chemically modifying nucleic acids with robust functional groups in order to alter their properties. Since the breakthrough of copper-assisted azide-alkyne cycloadditions (CuAAC), there have been several reports describing the synthesis and properties of novel triazole-modified nucleic acid derivatives for potential downstream DNA- and RNA-based applications. This review will focus on highlighting representative novel nucleic acid molecular structures that have been synthesized via the “click” azide-alkyne cycloaddition. Many of these derivatives show compatibility for various applications that involve enzymatic transformation, nucleic acid hybridization, molecular tagging and purification, and gene silencing. The details of these applications are discussed. In conclusion, the future of nucleic acid analogues functionalized with triazoles is promising.
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Affiliation(s)
| | | | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, ON L1H 7K4, Canada
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