1
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Gormong EA, Sneddon DS, Reineke TM, Hoye TR. Neighboring Group Effects on the Rates of Cleavage of Si-O-Si-Containing Compounds. J Org Chem 2023; 88:1988-1995. [PMID: 36745769 PMCID: PMC11081635 DOI: 10.1021/acs.joc.2c02126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The presence of a nearby tethered functional group (G, G = tertiary amide or amine) can significantly impact the rate of cleavage of an Si-O bond. We report here an in situ 1H NMR spectroscopic investigation of the relative rates of cleavage of model substrates containing two different Si-O substructures, namely alkoxydisiloxanes [GRO-Si(Me2)-O-SiMe3] and carbodisiloxanes [GR-Si(Me2)-O-SiMe3]. The trends in the relative rates (which slowed with increasing chain length, with a notable exception) of alkoxydisiloxane hydrolyses were probed via computation. The results correlated well with the experimental data. In contrast to the hydrolysis of the alkoxydisiloxanes, the carbodisiloxanes were not fully hydrolyzed, but rather formed an equilibrium mixture of starting asymmetric disiloxane, two silanols, and a new symmetrical disiloxane. We also uncovered a facile siloxy-metathesis reaction of an incoming silanol with the carbodisiloxane substrate [e.g., Me2NR-Si(Me2)-O-SiMe3 + HOSiEt3 ⇋ Me2NR-Si(Me2)-O-SiEt3 + HOSiMe3] facilitated by the pendant dimethylamino group, a process that was also probed by computation.
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Affiliation(s)
- Ethan A Gormong
- Department of Chemistry, University of Minnesota, 207 Pleasant St, SE, Minneapolis, Minnesota 55455, United States
| | - Dorian S Sneddon
- Department of Chemistry, University of Minnesota, 207 Pleasant St, SE, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, 207 Pleasant St, SE, Minneapolis, Minnesota 55455, United States
| | - Thomas R Hoye
- Department of Chemistry, University of Minnesota, 207 Pleasant St, SE, Minneapolis, Minnesota 55455, United States
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2
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Synthesis of 2'-O-[3-(N-methylsulfamoyl)propan-1-yl]ribothymidine as a potentially applicable 2'-modified nucleoside for antisense oligonucleotides. Bioorg Med Chem 2022; 73:117002. [PMID: 36170759 DOI: 10.1016/j.bmc.2022.117002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 11/02/2022]
Abstract
A synthetic scheme was developed to derive a modified ribothymidine bearing a 3-(N-methylsulfamoyl)propyl group on 2'-oxygen (TMSP). For synthesis initiation, a nucleophilic attack of 1,2-ethanediol on 5'-protected 2,2'-anhydro-ribothymidine was performed to selectively modify the 2'-position. After protection of the 3'-hydroxy group, the hydroxyethyl group was oxidized to the aldehyde, which was coupled with isobutyl (diethoxyphosphinyl)methanesulfonate through the Horner-Wadsworth-Emmons reaction to yield the sulfonate intermediate. The intermediate was further converted to the desired TMSP. Using the phosphoramidite units derived from nucleosides, we synthesized oligonucleotides incorporating TMSP. Oligonucleotides modified with TMSP were found to have duplex stability, resistance toward 3'-exonuclease digestion, and antisense activity comparable to that of the oligonucleotide modified with a previously reported 2'-O-methylcarbamoylethyl group. Based on these results and the generality of the synthetic scheme, 2'-O-sulfamoylalkyl modification is expected to be used for the modulation of the properties of oligonucleotides by changing the substituents on the nitrogen, enabling the oligonucleotides to possess suitable properties for antisense oligonucleotides.
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3
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Zhang W, Li Y, Du S, Chai Z, He J. Activation of 8-17 DNAzyme with extra functional group at conserved residues is related to catalytic metal ion. Bioorg Med Chem Lett 2021; 48:128234. [PMID: 34214510 DOI: 10.1016/j.bmcl.2021.128234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/05/2021] [Accepted: 06/25/2021] [Indexed: 11/29/2022]
Abstract
In 8-17 DNAzyme, the end loop A6G7C8 is a highly conserved motif. Here we reported an activation approach by specific chemical modifications on A6 and C8 for more efficient Ca2+-mediated reaction. The importance of the end loop was further highlighted and its critical conservation broken for more powerful catalysts.
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Affiliation(s)
- Wenjie Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yang Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China
| | - Shanshan Du
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China
| | - Zhilong Chai
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China.
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4
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Ohkubo A, Muto K, Watanabe R, Ogata D. Chemical Synthesis of Modified Oligonucleotides Containing 5'-Amino-5'-Deoxy-5'-Hydroxymethylthymidine Residues. Curr Protoc 2021; 1:e70. [PMID: 33657278 DOI: 10.1002/cpz1.70] [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
Introduction of cationic modifications into an oligonucleotide can increase its nuclease resistance and duplex- or triplex-forming abilities. In a recent study, we found that the nuclease resistance and RNA binding selectivity of an oligonucleotide containing a 5'-(R)-amino-5'-deoxy-5'-(R)-hydroxymethylthymidine residue were greater than those of the unmodified oligonucleotide. In this article, we describe the synthesis of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine via dihydroxylation of the 5'-alkene derivative using either of two commercial AD (asymmetric dehydroxylation) mixes or via epoxidation and ring opening. We also provide detailed protocols for the syntheses of oligonucleotides containing 5'-amino-5'-deoxy-5'-hydroxymethylthymidine residues. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine phosphoramidites 9a and 9b Basic Protocol 2: Synthesis of oligonucleotides 1 and 2 containing 5'-amino-5'-deoxy-5'-hydoxymethylthymidine residues (R T and S T).
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Affiliation(s)
- Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kousuke Muto
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Rintaro Watanabe
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Daisuke Ogata
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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5
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Kishimura T, Tomori T, Masaki Y, Seio K. Synthesis of 2'-O-alkylcarbamoylethyl-modified oligonucleotides with enhanced nuclease resistance that form isostable duplexes with complementary RNA. Bioorg Med Chem Lett 2021; 35:127779. [PMID: 33434643 DOI: 10.1016/j.bmcl.2021.127779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/14/2020] [Accepted: 01/03/2021] [Indexed: 10/22/2022]
Abstract
To expand the variety of 2'-O-modified oligonucleotides, we synthesized 2'-O-carbamoylethyl-modified oligonucleotides bearing ethyl, n-propyl, n-butyl, n-pentyl, and n-octyl groups on their nitrogen atoms. The corresponding nucleosides were synthesized using 2'-O-benzyloxycarbonylethylthymidine, which was easily converted into the carboxylic acid through hydrogeneration; subsequent condensation with the appropriate amine gave the desired nucleoside. We evaluated the effect of the 2'-O-alkylcarbamoylethyl modifications on duplex stability by analyzing melting temperature, which revealed the formation of isostable duplexes. In addition, we also revealed that these modifications, especially octylcarbamoylethyl, endowed these oligonucleotides with resistance toward a 3'-exonuclease. These results highlight the usefulness of the 2'-O-alkylcarbamoylethyl modification for various biological applications.
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Affiliation(s)
- Tomohiro Kishimura
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Takahito Tomori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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6
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Ohkubo A, Muto K, Watanabe R, Nishizawa S, Hisamatsu S, Kanamori T. Chemical synthesis and properties of modified oligonucleotides containing 5'-amino-5'-deoxy-5'-hydroxymethylthymidine residues. Bioorg Med Chem 2020; 28:115407. [PMID: 32156498 DOI: 10.1016/j.bmc.2020.115407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022]
Abstract
In this study, we designed 5'-amino-5'-deoxy-5'-hydroxymethylthymidine as a new oligonucleotide modification with an amino group directly attached to the 5'-carbon atom. We successfully synthesized two isomers of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine via dihydroxylation of the 5'-vinyl group incorporated into 5'-deoxy-5'-C-methenylthymidine derivative. Moreover, it was found that the nuclease resistance, binding selectivity to single-stranded RNA, and triplex-forming ability of an oligonucleotide containing RT residues of the new compound were higher than those of the unmodified oligonucleotide.
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Affiliation(s)
- Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
| | - Kousuke Muto
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Rintaro Watanabe
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shuhei Nishizawa
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shugo Hisamatsu
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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7
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Masaki Y, Yamamoto K, Yoshida K, Maruyama A, Tomori T, Iriyama Y, Nakajima H, Kanaki T, Seio K. Modification of oligonucleotides with weak basic residues via the 2'-O-carbamoylethyl linker for improving nuclease resistance without loss of duplex stability and antisense activity. Org Biomol Chem 2020; 17:4835-4842. [PMID: 31033986 DOI: 10.1039/c9ob00668k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the improvement of nuclease resistance, four kinds of new modifications through a carbamoylethyl linker were designed. Among them, the 2'-O-[2-N-{2-(benzimidazol-1-yl)ethyl}carbamoylethyl] modification showed 20-fold longer half-life when treated with a 3' to 5' exonuclease compared to the 2'-O-methoxyethyl (MOE) modification, which is used in approved drugs. In addition, this large modification did not disturb the binding affinity or RNase H-dependent antisense activity. From these findings, it could be concluded that an adequate linker, such as carbamoylethyl in this study, could extend the utility of 2'-O-modification without loss of the properties of nucleic acids. This strategy would be useful for the development of nucleic acid therapeutics.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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8
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Masaki Y, Yamamoto K, Inde T, Yoshida K, Maruyama A, Nagata T, Tanihata J, Takeda S, Sekine M, Seio K. Synthesis of 2'-O-(N-methylcarbamoylethyl) 5-methyl-2-thiouridine and its application to splice-switching oligonucleotides. Bioorg Med Chem Lett 2018; 29:160-163. [PMID: 30551900 DOI: 10.1016/j.bmcl.2018.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 01/16/2023]
Abstract
The effect of 2'-O-(N-methylcarbamoyl)ethyl (MCE) modification on splice-switching oligonucleotides (SSO) was systematically evaluated. The incorporation of five MCE nucleotides at the 5'-termini of SSOs effectively improved the splice switching effect. In addition, the incorporation of 2'-O-(N-methylcarbamoylethyl)-5-methyl-2-thiouridine (s2TMCE), a duplex-stabilizing nucleotide with an MCE modification, into SSOs further improved splice switching. These SSOs may be useful for the treatment of genetic diseases associated with splicing errors.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Keishi Yamamoto
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Takeshi Inde
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Keita Yoshida
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Atsuya Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Jun Tanihata
- Department of Molecular Therapy, Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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9
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Masaki Y, Iriyama Y, Nakajima H, Kuroda Y, Kanaki T, Furukawa S, Sekine M, Seio K. Application of 2'-O-(2-N-Methylcarbamoylethyl) Nucleotides in RNase H-Dependent Antisense Oligonucleotides. Nucleic Acid Ther 2018; 28:307-311. [PMID: 30020852 PMCID: PMC6157346 DOI: 10.1089/nat.2018.0738] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An RNase H-dependent antisense oligonucleotide (ASO), having the 2'-O-(2-N-methylcarbamoylethyl) (MCE) modification, was evaluated in vitro and in vivo. The antisense activities of an ASO having the MCE modification were comparable with those of an ASO having the 2'-O-methoxyethyl (MOE) modification in both in vitro and in vivo experiments. In contrast, the hepatotoxic potential of the ASO having the MCE modification was lower than that of the ASO having the MOE modification. Thus, these findings suggested that the MCE modification could be used as an alternative to the MOE modification.
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Affiliation(s)
- Yoshiaki Masaki
- 1 Department of Life Science and Technology, Tokyo Institute of Technology , Yokohama, Japan
| | - Yusuke Iriyama
- 2 Nissan Chemical Corporation, Chemical Research Laboratories, Funabashi, Japan
| | - Hiroyuki Nakajima
- 3 Nissan Chemical Corporation, Biological Research Laboratories, Shiraoka, Japan
| | - Yusuke Kuroda
- 3 Nissan Chemical Corporation, Biological Research Laboratories, Shiraoka, Japan
| | - Tatsuro Kanaki
- 3 Nissan Chemical Corporation, Biological Research Laboratories, Shiraoka, Japan
| | - Satoshi Furukawa
- 3 Nissan Chemical Corporation, Biological Research Laboratories, Shiraoka, Japan
| | - Mitsuo Sekine
- 1 Department of Life Science and Technology, Tokyo Institute of Technology , Yokohama, Japan
| | - Kohji Seio
- 1 Department of Life Science and Technology, Tokyo Institute of Technology , Yokohama, Japan
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10
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Inde T, Nishizawa S, Hattori Y, Kanamori T, Yuasa H, Seio K, Sekine M, Ohkubo A. Synthesis of and triplex formation in oligonucleotides containing 2'-deoxy-6-thioxanthosine. Bioorg Med Chem 2018; 26:3785-3790. [PMID: 29914771 DOI: 10.1016/j.bmc.2018.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 12/18/2022]
Abstract
This study aimed to synthesize triplex-forming oligonucleotides (TFOs) containing 2'-deoxy-6-thioxanthosine (s6X) and 2'-deoxy-6-thioguanosine (s6Gs) residues and examined their triplex-forming ability. Consecutive arrangement of s6X and s6Gs residues increased the triplex-forming ability of the oligonucleotides more than 50 times, compared with the unmodified TFOs. Moreover, the stability of triplex containing a mismatched pair was much lower than that of the full-matched triplex, though s6X could form a s6X-GC mismatched pair via tautomerization of s6X. The present results reveal excellent properties of modified TFOs containing s6Xs and s6Gs residues, which may be harnessed in gene therapy and DNA nanotechnology.
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Affiliation(s)
- Takeshi Inde
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shuhei Nishizawa
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Yuusaku Hattori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Hideya Yuasa
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
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11
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Nguyen JC, Dzowo YK, Wolfbrandt C, Townsend J, Kukatin S, Wang H, Resendiz MJE. Synthesis, Thermal Stability, Biophysical Properties, and Molecular Modeling of Oligonucleotides of RNA Containing 2'-O-2-Thiophenylmethyl Groups. J Org Chem 2016; 81:8947-8958. [PMID: 27584708 DOI: 10.1021/acs.joc.6b01615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Dodecamers of RNA [CUACGGAAUCAU] were functionalized with C2'-O-2-thiophenylmethyl groups to obtain oligonucleotides 10-14 and 17. The modified nucleotides were incorporated into RNA strands via solid-phase synthesis. The biophysical properties of these ONs were used to quantify the effects of this modification on RNA:RNA and RNA:DNA duplexes. A combination of UV-vis and circular dichroism were used to determine thermal stabilities of all strands, which hybridized into A-form geometries. Destabilization of the double stranded RNA was measured as a function of number of consecutive modifications, reflected in decreased thermal denaturation values (ΔTm, ca. 2.5-11.5 °C). Van't Hoff plots on a duplex containing one modification (10:15) displayed a ca. ΔΔG° of +4 kcal/mol with respect to its canonical analogue. Interestingly, hybridization of two modified strands (13:17, containing a total of eight modifications) resulted in increased stability and a distinct secondary structure, reflected in its CD spectrum. Molecular modeling based on DFT calculations shed light on the nature of this stability, with induced changes in the torsional angle δ (C5'-C4'-C3'-O3) and phosphate-phosphate distances that are in agreement with a compacted structure. The described synthetic methodology and structural information will be useful in the design of thermodynamically stable structures containing chemically reactive modifications.
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Affiliation(s)
- Joseph C Nguyen
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Yannick Kokouvi Dzowo
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Carly Wolfbrandt
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Justin Townsend
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Stanislav Kukatin
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Haobin Wang
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Marino J E Resendiz
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
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12
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Nakatake D, Yazaki R, Ohshima T. Chemoselective Transesterification of Acrylate Derivatives for Functionalized Monomer Synthesis Using a Hard Zinc Alkoxide Generation Strategy. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600737] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Daiki Nakatake
- Graduate school of Pharmaceutical Sciences; Kyushu University; Maidashi Higashi-ku 812-8582 Fukuoka Japan
| | - Ryo Yazaki
- Graduate school of Pharmaceutical Sciences; Kyushu University; Maidashi Higashi-ku 812-8582 Fukuoka Japan
| | - Takashi Ohshima
- Graduate school of Pharmaceutical Sciences; Kyushu University; Maidashi Higashi-ku 812-8582 Fukuoka Japan
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13
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Wrigstedt P, Kavakka J, Heikkinen S, Nieger M, Räisänen M, Repo T. The Reactivity of Thymine and Thymidine 5,6-Epoxides with Organometallic Reagents - A Route to Thymidine (6-4) Photoproduct Analogues. J Org Chem 2016; 81:3848-59. [PMID: 27080560 DOI: 10.1021/acs.joc.6b00495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This report describes an efficient procedure for the generation and isolation of various thymine and thymidine 5,6-epoxides from the corresponding trans-5,6-bromohydrins by reaction with triethylamine. The quantitative isolation of the epoxides, accomplished by solvent precipitation of triethylamine hydrobromide, enabled their regiospecific ring-opening at C6 position by organometallic nucleophiles. The reaction was amenable to a broad range of alkyl, aryl, alkenyl, and alkynyl organomagnesium, -zinc, -aluminum, or -boron reagents, although the reactivity was strongly affected by the electronic effects of N3 protecting group. Additionally, the reaction featured excellent cis-diastereoselectivity providing access to C6-carbon-functionalized dihydrothymidine cis-alcohols, which are synthetic derivatives of UV-induced DNA lesions, namely, thymidine (6-4) photoproducts.
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Affiliation(s)
- Pauli Wrigstedt
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Jari Kavakka
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Sami Heikkinen
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Martin Nieger
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Minna Räisänen
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Timo Repo
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
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14
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Gräfe D, Zschoche S, Appelhans D, Voit B. Tetra-sensitive graft copolymer gels with high volume changes. RSC Adv 2016. [DOI: 10.1039/c6ra01857b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
For the preparation of multi-responsive graft copolymer gels for hydrogel-based microsystem technologies, a poly(4-vinylbenzoic acid) macromonomer was prepared in a three-step synthesis.
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Affiliation(s)
- D. Gräfe
- Leibniz-Institut für Polymerforschung Dresden e. V
- 01069 Dresden
- Germany
- Technische Universität Dresden
- Chair of Organic Chemistry of Polymers
| | - S. Zschoche
- Leibniz-Institut für Polymerforschung Dresden e. V
- 01069 Dresden
- Germany
| | - D. Appelhans
- Leibniz-Institut für Polymerforschung Dresden e. V
- 01069 Dresden
- Germany
| | - B. Voit
- Leibniz-Institut für Polymerforschung Dresden e. V
- 01069 Dresden
- Germany
- Technische Universität Dresden
- Chair of Organic Chemistry of Polymers
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15
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Milton S, Honcharenko D, Rocha CSJ, Moreno PMD, Smith CIE, Strömberg R. Nuclease resistant oligonucleotides with cell penetrating properties. Chem Commun (Camb) 2015; 51:4044-7. [PMID: 25664358 DOI: 10.1039/c4cc08837a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
2'-O-AECM modified oligonucleotides provide an unusual combination of remarkable properties. This includes the combination of high resistance towards enzymatic degradation and the spontaneous cellular uptake of AECM oligonucleotides.
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Affiliation(s)
- Stefan Milton
- Karolinska Institutet, Department of Biosciences and Nutrition, Novum, Hälsovägen 7, SE-14183, Huddinge, Sweden.
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16
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Yamada T, Masaki Y, Okaniwa N, Kanamori T, Ohkubo A, Tsunoda H, Seio K, Sekine M. Synthesis and properties of oligonucleotides modified with 2'-O-(2-carboxyethyl)nucleotides and their carbamoyl derivatives. Org Biomol Chem 2015; 12:6457-64. [PMID: 25019462 DOI: 10.1039/c4ob01260g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
2'-O-Methyl oligoribonucleotides with four kinds of 2'-O-modified uridine derivatives were synthesised. Their duplex stability, hydration behavior and exonuclease resistance were studied by spectroscopic analyses and molecular dynamics simulations. Consequently, 2'-O-modification of the uridine residue with 2-carbamoylethyl or 2-(N-methylcarbamoyl)ethyl groups resulted in a significant improvement of the exonuclease resistance without the loss of duplex stability.
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Affiliation(s)
- Takeshi Yamada
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta-cho, Midoriku, Yokohama, Japan.
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17
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Masaki Y, Inde T, Nagata T, Tanihata J, Kanamori T, Seio K, Takeda S, Sekine M. Enhancement of exon skipping in mdx52 mice by 2′-O-methyl-2-thioribothymidine incorporation into phosphorothioate oligonucleotides. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00468j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Incorporation of 2′-O-methyl-2-thioribothymidine (s2Tm) into antisense oligoribonucleotides significantly enhanced the exon skipping activity in Duchenne muscular dystrophy model mice.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Takeshi Inde
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Tetsuya Nagata
- Department of Molecular Therapy
- Institute of Neuroscience
- National Center of Neurology and Psychiatry
- Kodaira
- Japan
| | - Jun Tanihata
- Department of Molecular Therapy
- Institute of Neuroscience
- National Center of Neurology and Psychiatry
- Kodaira
- Japan
| | - Takashi Kanamori
- Education Academy of Computational Life Sciences
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Kohji Seio
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy
- Institute of Neuroscience
- National Center of Neurology and Psychiatry
- Kodaira
- Japan
| | - Mitsuo Sekine
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama
- Japan
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18
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Rodriguez AA, Cedillo I, Mowery BP, Gaus HJ, Krishnamoorthy SS, McPherson AK. Formation of the N(2)-acetyl-2,6-diaminopurine oligonucleotide impurity caused by acetyl capping. Bioorg Med Chem Lett 2014; 24:3243-6. [PMID: 24980055 DOI: 10.1016/j.bmcl.2014.06.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 11/25/2022]
Abstract
The acetyl 'capping' reaction routinely employed during phosphorothioate oligonucleotide synthesis has been implicated in the formation of an impurity species with a mass 41 amu greater than the expected oligonucleotide molecule. The impurity has been found to arise by conversion of a protected guanine nucleobase to N(2)-acetyl-2,6-diaminopurine. A two-part mechanism is proposed consisting of transamidation of the protecting group on guanine and substitution of guanine's O(6) atom.
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Affiliation(s)
- Andrew A Rodriguez
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States.
| | - Isaiah Cedillo
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Brendan P Mowery
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Hans J Gaus
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | | | - Andrew K McPherson
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
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19
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Sharma VK, Rungta P, Prasad AK. Nucleic acid therapeutics: basic concepts and recent developments. RSC Adv 2014. [DOI: 10.1039/c3ra47841f] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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20
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Järver P, O'Donovan L, Gait MJ. A chemical view of oligonucleotides for exon skipping and related drug applications. Nucleic Acid Ther 2013; 24:37-47. [PMID: 24171481 DOI: 10.1089/nat.2013.0454] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Peter Järver
- Medical Research Council , Laboratory of Molecular Biology, Cambridge, United Kingdom
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21
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Milton S, Ander C, Honcharenko D, Honcharenko M, Yeheskiely E, Strömberg R. Synthesis and Stability of a 2′-O-[N-(Aminoethyl)carbamoyl]methyladenosine-Containing Dinucleotide. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300699] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Baraguey C, Lescrinier E, Lavergne T, Debart F, Herdewijn P, Vasseur JJ. The biolabile 2′-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure. Org Biomol Chem 2013; 11:2638-47. [DOI: 10.1039/c3ob27005j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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23
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Seio K, Tokugawa M, Kanamori T, Tsunoda H, Ohkubo A, Sekine M. Synthesis and properties of cationic 2'-O-[N-(4-aminobutyl)carbamoyl] modified oligonucleotides. Bioorg Med Chem Lett 2012; 22:2470-3. [PMID: 22406150 DOI: 10.1016/j.bmcl.2012.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/21/2012] [Accepted: 02/03/2012] [Indexed: 01/11/2023]
Abstract
2'-O-[N-(4-Aminobutylcarbamoyl)]uridine (U(abcm)) was synthesized and incorporated into oligonucleotides. The oligonucleotides incorporating U(abcm) formed more stable duplexes with their complementary and mismatched RNAs than those containing 2'-O-carbamoyluridine (U(cm)). The stability of duplex with a U(abcm)-rG base pair showed higher thermostability than the duplex having unmodified U-rG base pair. The U(abcm) residue showed enhanced resistance to snake venome phosphodiesterase.
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Affiliation(s)
- Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
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24
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Baszczyňski O, Jansa P, Dračínský M, Kaiser MM, Špaček P, Janeba Z. An efficient oxa-Michael addition to diethyl vinylphosphonate under mild reaction conditions. RSC Adv 2012. [DOI: 10.1039/c2ra00938b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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25
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Harakawa T, Tsunoda H, Ohkubo A, Seio K, Sekine M. Development of an efficient method for phosphorodiamidate bond formation by using inorganic salts. Bioorg Med Chem Lett 2011; 22:1445-7. [PMID: 22225640 DOI: 10.1016/j.bmcl.2011.12.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 11/29/2011] [Accepted: 12/03/2011] [Indexed: 02/01/2023]
Abstract
Phosphorodiamidate morpholino oligonucleotides (PMOs) have been extensively applied in antisense strategies for gene regulation because of their high stability in serum and low toxicity. However, chain elongation of PMOs requires long reaction time because few efficient methods have been developed for the formation of phosphorodiamidate bonds. In this Letter, we examined the effect of various additives to improve the reaction efficiency for formation of the phosphorodiamidate bond in the synthesis of PMOs. The addition of certain inorganic salts to the reaction media was found to be more effective. Particularly, lithium bromide was the most effective reagent and led to considerable acceleration (ca. 10-fold improvement).
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Affiliation(s)
- Taro Harakawa
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsutacho, Midoriku, Yokohama 226-8501, Japan
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26
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Milton S, Ander C, Yeheskiely E, Strömberg R. Stability of a 2′-O-(Carbamoylmethyl)adenosine-Containing Dinucleotide. European J Org Chem 2011. [DOI: 10.1002/ejoc.201101264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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