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Pal C, Velusamy A, Sunkari YK, Chakraborty TK. Studies on sugar puckering and glycosidic stabilities of 3'-amino-5'-carboxymethyl-3',5'-dideoxy nucleoside mimics. Org Biomol Chem 2019; 16:6735-6740. [PMID: 30187064 DOI: 10.1039/c8ob01788c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of nucleoside amino acid monomers and dimers has been carried out to evaluate and characterize the impact of the neutral amide backbone on key attributes like puckering of the sugar rings and glycosidic bond strengths of these analogs. The conformational analysis suggests that amide-linked nucleotides have a high predilection towards N-type conformers. The glycosidic bond strength was found to be slightly weaker compared to ribonucleosides under acidic conditions at high temperatures. The results will be helpful to explore in future the development of fully amide-linked oligonucleotides for therapeutic purposes.
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Affiliation(s)
- Chandan Pal
- Department of Organic Chemistry, Indian Institute of Science, Bengaluru 560 012, India.
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2
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Morihiro K, Kasahara Y, Obika S. Biological applications of xeno nucleic acids. MOLECULAR BIOSYSTEMS 2017; 13:235-245. [PMID: 27827481 DOI: 10.1039/c6mb00538a] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Xeno nucleic acids (XNAs) are a group of chemically modified nucleic acid analogues that have been applied to various biological technologies such as antisense oligonucleotides, siRNAs and aptamers.
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Affiliation(s)
- Kunihiko Morihiro
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Gene silencing by 2′- O -methyldithiomethyl-modified siRNA, a prodrug-type siRNA responsive to reducing environment. Bioorg Med Chem Lett 2016; 26:845-848. [DOI: 10.1016/j.bmcl.2015.12.074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 12/12/2015] [Accepted: 12/22/2015] [Indexed: 11/19/2022]
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Kamiya Y, Iishiba K, Doi T, Tsuda K, Kashida H, Asanuma H. Terminus-free siRNA prepared by photo-crosslinking activated via slicing by Ago2. Biomater Sci 2015; 3:1534-8. [PMID: 26526389 DOI: 10.1039/c5bm00231a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the development of photo-crosslinked siRNA strands modified at each terminus with p-cyanostilbene. The siRNA was nuclease resistant and retained RNAi activity. We further studied the activation mechanism of the covalently-crosslinked siRNA. Interestingly Dicer, which is known to generate siRNA with overhanging 3' ends from the precursor siRNA, did not cleave the crosslinked siRNA at all. Our results suggest that the activation of the crosslinked siRNAs required cleavage by Argonaute2.
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Affiliation(s)
- Yukiko Kamiya
- Department of Molecular Design and Engineering, Graduate school of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
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5
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Braun FCM, van den Brandt J, Thomas S, Lange S, Schrank J, Gand C, Przybylski GK, Schmoeckel K, Bröker BM, Schmidt CA, Grabarczyk P. In Vivo Silencing of A20 via TLR9-Mediated Targeted SiRNA Delivery Potentiates Antitumor Immune Response. PLoS One 2015; 10:e0135444. [PMID: 26327508 PMCID: PMC4556692 DOI: 10.1371/journal.pone.0135444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 07/23/2015] [Indexed: 11/23/2022] Open
Abstract
A20 is an ubiquitin-editing enzyme that ensures the transient nature of inflammatory signaling pathways induced by cytokines like TNF-α and IL-1 or pathogens via Toll-like receptor (TLR) pathways. It has been identified as a negative regulator of dendritic cell (DC) maturation and attenuator of their immunostimulatory properties. Ex vivo A20-depleted dendritic cells showed enhanced expression of pro-inflammatory cytokines and costimulatory molecules, which resulted in hyperactivation of tumor-infiltrating T lymphocytes and inhibition of regulatory T cells. In the present study, we demonstrate that a synthetic molecule consisting of a CpG oligonucleotide TLR9 agonist linked to A20-specific siRNAs silences its expression in TLR9+ mouse dendritic cells in vitro and in vivo. In the B16 mouse melanoma tumor model, silencing of A20 enhances the CpG-triggered induction of NFκB activity followed by elevated expression of IL-6, TNF-α and IL-12. This leads to potentiated antitumor immune responses manifested by increased numbers of tumor-specific cytotoxic T cells, high levels of tumor cell apoptosis and delayed tumor growth. Our findings confirm the central role of A20 in controlling the immunostimulatory potency of DCs and provide a strategy for simultaneous A20 silencing and TLR activation in vivo.
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Affiliation(s)
- Floriane C. M. Braun
- Clinic of Internal Medicine C, Department of Molecular Hematology, University Medicine Greifswald, Greifswald, Germany
| | - Jens van den Brandt
- Central Core & Research Facility of Laboratory Animals, University of Greifswald, Greifswald, Germany
| | - Sören Thomas
- Clinic of Internal Medicine C, Department of Molecular Hematology, University Medicine Greifswald, Greifswald, Germany
| | - Sandra Lange
- Clinic of Internal Medicine C, Department of Molecular Hematology, University Medicine Greifswald, Greifswald, Germany
| | - Juliane Schrank
- Clinic of Internal Medicine C, Department of Molecular Hematology, University Medicine Greifswald, Greifswald, Germany
| | - Claudia Gand
- Clinic of Internal Medicine C, Department of Molecular Hematology, University Medicine Greifswald, Greifswald, Germany
| | - Grzegorz K. Przybylski
- Clinic of Internal Medicine C, Department of Molecular Hematology, University Medicine Greifswald, Greifswald, Germany
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Katrin Schmoeckel
- Institute of Immunology and Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Barbara M. Bröker
- Institute of Immunology and Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Christian A. Schmidt
- Clinic of Internal Medicine C, Department of Molecular Hematology, University Medicine Greifswald, Greifswald, Germany
| | - Piotr Grabarczyk
- Clinic of Internal Medicine C, Department of Molecular Hematology, University Medicine Greifswald, Greifswald, Germany
- * E-mail:
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6
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Kamiya Y, Takai J, Ito H, Murayama K, Kashida H, Asanuma H. Enhancement of stability and activity of siRNA by terminal substitution with serinol nucleic acid (SNA). Chembiochem 2014; 15:2549-55. [PMID: 25233814 DOI: 10.1002/cbic.201402369] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Indexed: 12/21/2022]
Abstract
RNA interference (RNAi ), sequence-specific gene silencing triggered by double-stranded, small interfering RNA (siRNA), has become a facile and effective tool for biological research and holds potential for therapeutic applications. However, the application of siRNA is hindered by susceptibility to nucleases and off-target effects. In this study, we introduced artificial nucleotides, serinol nucleic acid (SNA), with an acyclic scaffold, at the termini of siRNA strands. Our aim was appropriately to accommodate the antisense strand in an RNA-induced silencing complex (RISC) by inhibiting sense-strand incorporation and thus improve resistance to nuclease-mediated degradation. Substitution of SNA into siRNA at both termini of the sense strand and at the 3' terminus of the antisense strand improved antisense strand selectivity remarkably in the formation of RISC, RNAi activity, and nuclease resistance.
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Affiliation(s)
- Yukiko Kamiya
- EcoTopia Science Institute and Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
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Wada S, Obika S, Shibata MA, Yamamoto T, Nakatani M, Yamaoka T, Torigoe H, Harada-Shiba M. Development of a 2',4'-BNA/LNA-based siRNA for Dyslipidemia and Assessment of the Effects of Its Chemical Modifications In Vivo. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e45. [PMID: 23344237 PMCID: PMC3464879 DOI: 10.1038/mtna.2012.32] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recent advances in RNA interference (RNAi)-based drug development have partially allowed systemic administration of these agents in vivo with promising therapeutic effects. However, before chemically modified small-interfering RNAs (siRNAs) can be applied clinically, their in vivo effects should be thoroughly assessed. And while many studies have assessed the effects of chemically modified siRNAs in vitro, there has been no comprehensive assessment of their effects in vivo. Here, we aimed to elucidate the effects of administering chemically modified siRNAs in vivo and to propose a 2′,4′-bridged nucleic acid (BNA)/locked nucleic acid (LNA)-based siRNA candidate for dyslipidemia. A potentially therapeutic siRNA, siL2PT-1M, was modified with phosphorothioate (PS) and 2′,4′-BNA/LNA in its sense strand and with 2′-methoxy (2′-OMe) nucleotides in its immunostimulatory motif; administration of siL2PT-1M resulted in sustained reductions in serum total cholesterol (TC) (24 days) and a concomitant apolipoprotein B (apoB) mRNA reduction in liver without adverse effects. The 2′,4′-BNA/LNA modification in the sense strand was greatly augmented the duration of the RNAi effect, whereas cholesterol conjugation shortened the duration. Cholesterol-conjugated immunostimulatory siRNA (isRNA) induced higher serum interferon-α (IFN-α) levels than did nonmodified isRNA, indicating that the immune reaction was facilitated by cholesterol conjugation. Our results indicated that modification of the adenosine residues complementary to the immunostimulatory motif and of central 5′-UG-3′ in the sense strand would ameliorate the negative immune response.
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Affiliation(s)
- Shunsuke Wada
- 1] Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan [2] Graduate School of Chemical Sciences and Technology, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Synthesis, gene-silencing activity and nuclease resistance of 3′–3′-linked double short hairpin RNA. Bioorg Med Chem 2010; 18:8277-83. [DOI: 10.1016/j.bmc.2010.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 09/30/2010] [Accepted: 10/01/2010] [Indexed: 02/04/2023]
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