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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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Kawai H, Doi T, Ito Y, Kameyama T, Torimoto T, Kashida H, Asanuma H. Perylene-Cy3 FRET System to Analyze Photoactive DNA Structures. Chemistry 2021; 27:12845-12850. [PMID: 34269491 DOI: 10.1002/chem.202101738] [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: 05/26/2021] [Indexed: 11/10/2022]
Abstract
We report a new Förster resonance energy transfer (FRET) system for structural analyses of DNA duplexes using perylene and Cy3 as donor and acceptor, respectively, linked at the termini of a DNA duplex via D-threoninol. Experimentally obtained FRET efficiencies were in good agreement with theoretical values calculated based on canonical B-form DNA. Due to the relatively long Förster radius, this system can be used to analyze large DNA structures, and duplexes containing photo-reactive molecules can be analyzed since perylene can be excited with visible light. The system was used to analyze a DNA duplex containing stilbene, demonstrating that in the region of the stilbene cluster the duplex adopts a ladder-like structure rather than helical one. Upon photodimerization between stilbene residues, FRET efficiencies indicated the reaction does not disturb DNA duplex. This FRET system will be useful for analysis of photoreactions of nucleobases as well as a wide range of nucleic acid structures.
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Affiliation(s)
- Hayato Kawai
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Tetsuya Doi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Yuka Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Tatsuya Kameyama
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Tsukasa Torimoto
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
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Matsumoto K, Saito-Tarashima N, Wada T, Yonaha O, Minakawa N. Synthesis and properties of oligonucleotides containing a 2,6-diamino-3-deazapurine:furanopyrimidine base pair. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 41:943-960. [PMID: 31994434 DOI: 10.1080/15257770.2019.1694687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Furanopyrimidine (FPy) and 2,6-diamino-3-deazapurine (DC3Pu) nucleosides with the ability to interact in DDD and AAA H-bonding patterns, respectively, were prepared. The N-1 pKa value of the DC3Pu nucleoside was estimated to be 6.4, which is due to the lack of a nitrogen atom at the 3-position, suggesting that DC3Pu acts as a base interacting in a DDD H-bonding pattern under near physiological conditions. As DC3Pu and FPy are expected to form a thermally stable DDD:AAA type of base pair in an oligodeoxynucleotide (ODN) duplex, they were incorporated into ODNs, and the Tm value of the ODN duplex was determined. However, the ODN duplex containing a DC3Pu:FPy pair has a lower thermal stability than that containing a G:C pair does, although its thermal stability is equal to that of an ODN duplex with an A:T pair even under acidic conditions.
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Affiliation(s)
- Koki Matsumoto
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | | | - Tomoya Wada
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | - Orie Yonaha
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima, Japan
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Abstract
In this review, we have summarized the research effort into the development of unnatural base pairs beyond standard Watson-Crick (WC) base pairs for synthetic biology. Prior to introducing our research results, we present investigations by four outstanding groups in the field. Their research results demonstrate the importance of shape complementarity and stacking ability as well as hydrogen-bonding (H-bonding) patterns for unnatural base pairs. On the basis of this research background, we developed unnatural base pairs consisting of imidazo[5',4':4.5]pyrido[2,3-d]pyrimidines and 1,8-naphthyridines, i.e., Im : Na pairs. Since Im bases are recognized as ring-expanded purines and Na bases are recognized as ring-expanded pyrimidines, Im : Na pairs are expected to satisfy the criteria of shape complementarity and enhanced stacking ability. In addition, these pairs have four non-canonical H-bonds. Because of these preferable properties, ImNN : NaOO, one of the Im : Na pairs, is recognized as a complementary base pair in not only single nucleotide insertion, but also the PCR.
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Lee DS, O'Keefe RA, Ha PK, Grandis JR, Johnson DE. Biochemical Properties of a Decoy Oligodeoxynucleotide Inhibitor of STAT3 Transcription Factor. Int J Mol Sci 2018; 19:ijms19061608. [PMID: 29848966 PMCID: PMC6032396 DOI: 10.3390/ijms19061608] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/29/2018] [Indexed: 12/13/2022] Open
Abstract
Cyclic STAT3 decoy (CS3D) is a second-generation, double-stranded oligodeoxynucleotide (ODN) that mimics a genomic response element for signal transducer and activator of transcription 3 (STAT3), an oncogenic transcription factor. CS3D competitively inhibits STAT3 binding to target gene promoters, resulting in decreased expression of proteins that promote cellular proliferation and survival. Previous studies have demonstrated antitumor activity of CS3D in preclinical models of solid tumors. However, prior to entering human clinical trials, the efficiency of generating the CS3D molecule and its stability in biological fluids should be determined. CS3D is synthesized as a single-stranded ODN and must have its free ends ligated to generate the final cyclic form. In this study, we report a ligation efficiency of nearly 95 percent. The ligated CS3D demonstrated a half-life of 7.9 h in human serum, indicating adequate stability for intravenous delivery. These results provide requisite biochemical characterization of CS3D that will inform upcoming clinical trials.
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Affiliation(s)
- David S Lee
- School of Medicine, University of California at San Francisco, San Francisco, CA 94115, USA.
| | - Rachel A O'Keefe
- Department of Otolaryngology-Head and Neck Surgery, University of California at San Francisco, San Francisco, CA 94115, USA.
| | - Patrick K Ha
- Department of Otolaryngology-Head and Neck Surgery, University of California at San Francisco, San Francisco, CA 94115, USA.
| | - Jennifer R Grandis
- Department of Otolaryngology-Head and Neck Surgery, University of California at San Francisco, San Francisco, CA 94115, USA.
| | - Daniel E Johnson
- Department of Otolaryngology-Head and Neck Surgery, University of California at San Francisco, San Francisco, CA 94115, USA.
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Design and synthesis of some new piritrexim analogs as potential anticancer agents. RESEARCH ON CHEMICAL INTERMEDIATES 2018. [DOI: 10.1007/s11164-017-3132-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Meyer A, Vasseur JJ, Dumy P, Morvan F. Phthalimide-Oxy Derivatives for 3′- or 5′-Conjugation of Oligonucleotides by Oxime Ligation and Circularization of DNA by “Bis- or Tris-Click” Oxime Ligation. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Albert Meyer
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
| | - François Morvan
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
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9
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Yang H, Seela F. Circular DNA by "Bis-Click" Ligation: Template-Independent Intramolecular Circularization of Oligonucleotides with Terminal Alkynyl Groups Utilizing Bifunctional Azides. Chemistry 2015; 22:1435-44. [PMID: 26685101 DOI: 10.1002/chem.201503615] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 12/19/2022]
Abstract
A highly effective and convenient "bis-click" strategy was developed for the template-independent circularization of single-stranded oligonucleotides by employing copper(I)-assisted azide-alkyne cycloaddition. Terminal triple bonds were incorporated at both ends of linear oligonucleotides. Alkynylated 7-deaza-2'-deoxyadenosine and 2'-deoxyuridine residues with different side chains were used in solid-phase synthesis with phosphoramidite chemistry. The bis-click ligation of linear 9- to 36-mer oligonucleotides with 1,4-bis(azidomethyl)benzene afforded circular DNA in a simple and selective way; azido modification of the oligonucleotide was not necessary. Short ethynyl side chains were compatible with the circularization of longer oligonucleotides, whereas octadiynyl residues were used for short 9-mers. Compared with linear duplexes, circular bis-click constructs exhibit a significantly increased duplex stability over their linear counterparts. The intramolecular bis-click ligation protocol is not limited to DNA, but may also be suitable for the construction of other macrocycles, such as circular RNAs, peptides, or polysaccharides.
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Affiliation(s)
- Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany), Fax: (+49) 251-53406857
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany. .,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany), Fax: (+49) 251-53406857.
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Xiao X, Gang Y, Wang H, Wang J, Zhao L, Xu L, Liu Z. Double-stranded RNA transcribed from vector-based oligodeoxynucleotide acts as transcription factor decoy. Biochem Biophys Res Commun 2014; 457:221-6. [PMID: 25550185 DOI: 10.1016/j.bbrc.2014.12.091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/20/2014] [Indexed: 12/24/2022]
Abstract
In this study, we designed a short hairpin RNA vector-based oligodeoxynucleotide (VB-ODN) carrying transcription factor (TF) consensus sequence which could function as a decoy to block TF activity. Specifically, VB-ODN for Nuclear factor-κB (NF-κB) could inhibit cell viability and decrease downstream gene expression in HEK293 cells without affecting expression of NF-κB itself. The specific binding between VB-ODN produced double-stranded RNA and NF-κB was evidenced by electrophoretic mobility shift assay. Moreover, similar VB-ODNs designed for three other TFs also inhibit their downstream gene expression but not that of themselves. Our study provides a new design of decoy for blocking TF activity.
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Affiliation(s)
- Xiao Xiao
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China
| | - Yi Gang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China; Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, Shaanxi Province, PR China
| | - Honghong Wang
- No. 518 Hospital of Chinese People's Liberation Army, Xi'an 710043, Shaanxi Province, PR China
| | - Jiayin Wang
- The Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Lina Zhao
- Department of Radiation Oncology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China
| | - Li Xu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China.
| | - Zhiguo Liu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China.
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Pujari SS, Ingale SA, Seela F. High-density functionalization and cross-linking of DNA: "click" and "bis-click" cycloadditions performed on alkynylated oligonucleotides with fluorogenic anthracene azides. Bioconjug Chem 2014; 25:1855-70. [PMID: 25154019 DOI: 10.1021/bc5003532] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High density functionalization of DNA with ethynyl and octadiynyl side chains followed by CuAAC "click labeling" with 9-azidomethylanthracene was performed. Alkynyl DNA was also cross-linked with fluorogenic 9,10-bis-azidomethylanthracene employing the "bis-click" reaction. By this means the fluorescence of the anthracene moiety was imparted to the virtually nonfluorescent DNA. Phosphoramidites of 8-aza-7-deaza-2'-deoxyadenosine with short and long linker arms in a steric nondemanding 7-position were utilized in solid phase oligodeoxynucleotide synthesis. High density alkynylated DNA-without anthracene residues-was found to be of comparable stability with both long and short linker arms. High density anthracene functionalized DNA became less stable with the short linker compared to that with the long linker connectivity. Interstrand cross-linked homodimers constructed from alkynylated oligonucleotides with fluorogenic 9,10-bis-azidomethylanthracene were hybridized with complementary strands to form double helices. They are more stable when the linker was located at a terminus than in a central position. Short linker anthracene adducts were destabilizing compared to long linker adducts. The fluorogenic anthracene residues not only have a significant effect on the duplex stability, but also impart fluorescence to the species. Fluorescence of cross-linked double helices with long linker connectivity was quenched when the cross-link was in a terminal position and was dequenched when the linker was connecting the two double helices at the center of the molecule. The fluorescence of the anthracene cross-linked double helices was strongly increased (dequenched) when the correct base pair was formed, while no change occurred upon mismatch formation.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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