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Komine H, Mori S, Morihiro K, Ishida K, Okuda T, Kasahara Y, Aoyama H, Yamaguchi T, Obika S. Synthesis and Evaluation of Artificial Nucleic Acid Bearing an Oxanorbornane Scaffold. Molecules 2020; 25:E1732. [PMID: 32283778 PMCID: PMC7180610 DOI: 10.3390/molecules25071732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 01/07/2023] Open
Abstract
Natural oligonucleotides have many rotatable single bonds, and thus their structures are inherently flexible. Structural flexibility leads to an entropic loss when unwound oligonucleotides form a duplex with single-stranded DNA or RNA. An effective approach to reduce such entropic loss in the duplex-formation is the conformational restriction of the flexible phosphodiester linkage and/or sugar moiety. We here report the synthesis and biophysical properties of a novel artificial nucleic acid bearing an oxanorbornane scaffold (OxNorNA), where the adamant oxanorbornane was expected to rigidify the structures of both the linkage and sugar parts of nucleic acid. OxNorNA phosphoramidite with a uracil (U) nucleobase was successfully synthesized over 15 steps from a known sugar-derived cyclopentene. Thereafter, the given phosphoramidite was incorporated into the designed oligonucleotides. Thermal denaturation experiments revealed that oligonucleotides modified with the conformationally restricted OxNorNA-U properly form a duplex with the complementally DNA or RNA strands, although the Tm values of OxNorNA-U-modified oligonucleotides were lower than those of the corresponding natural oligonucleotides. As we had designed, entropic loss during the duplex-formation was reduced by the OxNorNA modification. Moreover, the OxNorNA-U-modified oligonucleotide was confirmed to have extremely high stability against 3'-exonuclease activity, and its stability was even higher than those of the phosphorothioate-modified counterparts (Sp and Rp). With the overall biophysical properties of OxNorNA-U, we expect that OxNorNA could be used for specialized applications, such as conformational fixation and/or bio-stability enhancement of therapeutic oligonucleotides (e.g., aptamers).
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Affiliation(s)
- Hibiki Komine
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Shohei Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kenta Ishida
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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Abstract
DNA oligomers containing dimethylene and trimethylene intrastrand crosslinks (IaCLs) between the O4 and O6 atoms of neighboring thymidine (T) and 2'-deoxyguanosine (dG) residues were prepared by solid-phase synthesis. UV thermal denaturation (Tm ) experiments revealed that these IaCLs had a destabilizing effect on the DNA duplex relative to the control. Circular dichroism spectroscopy suggested these IaCLs induced minimal structural distortions. Susceptibility to dealkylation by reaction with various O6 -alkylguanine DNA alkyltransferases (AGTs) from human and Escherichia coli was evaluated. It was revealed that only human AGT displayed activity towards the IaCL DNA, with reduced efficiency as the IaCL shortened (from four to two methylene linkages). Changing the site of attachment of the ethylene linkage at the 5'-end of the IaCL to the N3 atom of T had minimal influence on duplex stability and structure, and was refractory to AGT activity.
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Affiliation(s)
- Derek K O'Flaherty
- Department of Chemistry and Biochemistry, Concordia University Montreal, 7141 Sherbrooke Street W., Montreal, Quebec, H4B 1R6, Canada.,Present address: Howard Hughes Medical Institute, Department of Molecular Biology and, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University Montreal, 7141 Sherbrooke Street W., Montreal, Quebec, H4B 1R6, Canada
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Kostov O, Páv O, Rosenberg I. Nucleoside-O-Methyl-(H)-Phosphinates: Novel Monomers for the Synthesis of Methylphosphonate Oligonucleotides Using H-Phosphonate Chemistry. ACTA ACUST UNITED AC 2017; 70:4.76.1-4.76.22. [PMID: 28921496 DOI: 10.1002/cpnc.35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This unit comprises the straightforward synthesis of protected 2'-deoxyribonucleoside-O-methyl-(H)-phosphinates in both 3'- and 5'-series. These compounds represent a new class of monomers compatible with the solid-phase synthesis of oligonucleotides using H-phosphonate chemistry and are suitable for the preparation of both 3'- and 5'-O-methylphosphonate oligonucleotides. The synthesis of 4-toluenesulfonyloxymethyl-(H)-phosphinic acid as a new reagent for the preparation of O-methyl-(H)-phosphinic acid derivatives is described. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ondřej Kostov
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic
| | - Ondřej Páv
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic
| | - Ivan Rosenberg
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic
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Menzi M, Wild B, Pradère U, Malinowska AL, Brunschweiger A, Lightfoot HL, Hall J. Towards Improved Oligonucleotide Therapeutics Through Faster Target Binding Kinetics. Chemistry 2017; 23:14221-14230. [PMID: 28746731 DOI: 10.1002/chem.201701670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 01/19/2023]
Abstract
When used as inhibitors of gene expression in vivo, oligonucleotides require modification of their structures to boost their binding affinity for complementary target RNAs. To date, hundreds of modifications have been designed and tested but few have proven to be useful. Among those investigated are mono- and polyamino-groups. These are positively charged at physiological pH and have been appended to oligonucleotides in an effort to reduce electrostatic repulsion during hybridization to RNAs, but have generally shown relatively minor benefits to binding. We conjugated spermine to uracils in oligonucleotides via a triazole linker so that the polyamine fits in the major groove of a subsequently formed RNA-duplex. The modifications produced large increases in target-binding affinity of the oligonucleotides. Using surface plasmon resonance-based assays, we showed that the increases derived mainly from faster annealing (kon ). We propose that the spermine fragments play a similar role to that of natural polyamines during oligonucleotide-target interactions in cells, and may be advantageous for oligonucleotides that operate catalytic mechanisms.
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Affiliation(s)
- Mirjam Menzi
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Bettina Wild
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Ugo Pradère
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Anna L Malinowska
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Andreas Brunschweiger
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Helen L Lightfoot
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
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Ochi Y, Nakagawa O, Hayashi J, Wada SI, Urata H. A New Nucleic Acid Prodrug Responsive to High Thiol Concentration: Synthesis of 2'-O-Methyldithiomethyl- Modified Oligonucleotides by Post-Synthetic Modification. ACTA ACUST UNITED AC 2015; 62:4.63.1-4.63.20. [PMID: 26380903 DOI: 10.1002/0471142700.nc0463s62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This unit describes the synthesis of 2'-O-methyldithiomethyluridine-containing oligonucleotides, which can be deprotected to yield the parental oligoribonucleotides under high concentrations of glutathione similar in cytoplasm. The 2'-O-methyldithiomethyl group is sensitive to reductive conditions, so that it is incompatible to 3'-O-phosphoramidite modification in nucleosides. Thus, a novel post-synthetic approach to obtain 2'-O-methyldithiomethyluridine-containing oligonucleotides was developed, in which 2'-O-(2,4,6-trimethoxybenzylthiomethyl)uridine-modified oligonucleotides are readily converted by treatment with dimethyl(methylthio)sulfonium tetrafluoroborate to the 2'-O-methyldithiomethyluridine-modified oligonucleotides. The 2'-O-methyldithiomethyluridine-modified oligonucleotides are readily and cleanly converted to the parental oligonucleotides under high thiol conditions, such as 10 mM glutathione and dithiothreitol.
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Affiliation(s)
- Yosuke Ochi
- Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Osamu Nakagawa
- Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan.,Present address: Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Junsuke Hayashi
- Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Shun-Ichi Wada
- Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Hidehito Urata
- Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
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Kupryushkin MS, Pyshnyi DV, Stetsenko DA. Phosphoryl guanidines: a new type of nucleic Acid analogues. Acta Naturae 2014; 6:116-8. [PMID: 25558402 PMCID: PMC4273099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A new type of nucleic acid analogues with a phosphoryl guanidine group is described. Oxidation of polymer-supported dinucleoside 2-cyanoethyl phosphite by iodine in the presence of 1,1,3,3-tetramethyl guanidine yields a dinucleotide with an internucleoside tetramethyl phosphoryl guanidine (Tmg) group as the main product. The Tmg group is stable under conditions of solid-phase DNA synthesis and subsequent cleavage and deprotection with ammonia. Oligonucleotides with one or more Tmg groups bind their complementary DNA or RNA with affinity similar to that of natural oligodeoxyribonucleotides.
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Affiliation(s)
- M. S. Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk 630090, Russia
| | - D. V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk 630090, Russia
| | - D. A. Stetsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk 630090, Russia
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