RNA interference activity of single-stranded oligonucleotides linked between the passenger strand and the guide strand with an aryl phosphate linker

References

• Fire, A.; Xu, S.; Montgomery, M. K.; Kostas, S. A.; Driver, S. E.; Mello, C. C. Potent and Specific Genetic Interference by Double-Stranded RNA in Caenorhabditis elegans. Nature 1998, 391, 806–811. DOI: 10.1038/35888.
   PubMed Web of Science ®Google Scholar
• Elbashir, S. M.; Harborth, J.; Lendeckel, W.; Yalcin, A.; Weber, K.; Tuschl, T. Duplexes of 21-Nucleotide RNAs Mediate RNA Interference in Cultured Mammalian Cells. Nature 2001, 411, 494–498. DOI: 10.1038/35078107.
   PubMed Web of Science ®Google Scholar
• Chiu, Y. L.; Rana, T. M. siRNA Function in RNAi: A Chemical Modification Analysis. RNA 2003, 9, 1034–1048. DOI: 10.1261/rna.5103703.
   PubMed Web of Science ®Google Scholar
• Manoharan, M. RNA Interference and Chemically Modified Small Interfering RNAs. Curr. Opin. Chem. Biol. 2004, 8, 570–579. DOI: 10.1016/j.cbpa.2004.10.007.
   PubMed Web of Science ®Google Scholar
• Prakash, T. P.; Allerson, C. R.; Dande, P.; Vickers, T. A.; Sioufi, N.; Jarres, R.; Baker, B. F.; Swayze, E. E.; Griffey, R. H.; Bhat, B. Positional Effect of Chemical Modifications on Short Interference RNA Activity in Mammalian Cells. J. Med. Chem. 2005, 48, 4247–4253. DOI: 10.1021/jm050044o.
   PubMed Web of Science ®Google Scholar
• Schwarz, D. S.; Hutvágner, G.; Haley, B.; Zamore, P. D. Evidence That siRNAs Function as Guides, Not Primers, in the Drosophila and Human RNAi Pathways. Mol. Cell. 2002, 10, 537–548. DOI: 10.1016/S1097-2765(02)00651-2.
   PubMed Web of Science ®Google Scholar
• Czauderna, F.; Fechtner, M.; Dames, S.; Aygün, H.; Klippel, A.; Pronk, G. J.; Giese, K.; Kaufmann, J. Structural Variations and Stabilising Modifications of Synthetic siRNAs in Mammalian Cells. Nucleic Acids Res. 2003, 31, 2705–2716. DOI: 10.1093/nar/gkg393.
   PubMed Web of Science ®Google Scholar
• Chiu, Y. L.; Rana, T. M. RNAi in Human Cells: Basic Structural and Functional Features of Small Interfering RNA. Mol. Cell. 2002, 10, 549–561. DOI: 10.1016/S1097-2765(02)00652-4.
   PubMed Web of Science ®Google Scholar
• Shah, S.; Friedman, S. H. Tolerance of RNA Interference toward Modifications of the 5′ Antisense Phosphate of Small Interfering RNA. Oligonucleotides 2007, 17, 35–43. DOI: 10.1089/oli.2006.0067.
   PubMed Web of Science ®Google Scholar
• Nguyen, Q. N.; Chavli, R. V.; Marques, J. T.; Conrad, P. G. Jr.; Wang, D.; He, W.; Belisle, B. E.; Zhang, A.; Pastor, L. M.; Witney, F. R.; et al. Light Controllable siRNAs Regulate Gene Suppression and Phenotypes in Cells. Biochim. Biophys. Acta. 2006, 1758, 394–403. DOI: 10.1016/j.bbamem.2006.01.003.
   PubMed Web of Science ®Google Scholar
• Parmar, R.; Willoughby, J. L.; Liu, J.; Foster, D. J.; Brigham, B.; Theile, C. S.; Charisse, K.; Akinc, A.; Guidry, E.; Pei, Y.; et al. 5′-(E)-Vinylphosphonate: A Stable Phosphate Mimic Can Improve the RNAi Activity of siRNA–GalNAc Conjugates. Chembiochem 2016, 17, 985–989. DOI: 10.1002/cbic.201600130.
   PubMed Web of Science ®Google Scholar
• Prakash, T. P.; Kinberger, G. A.; Heather, M.; Murray, H. M.; Chappell, A.; Riney, A.; Graham, M. J.; Lima, W. F.; Swayze, E. E.; Seth, P. P. Synergistic Effect of Phosphorothioate, 5′-Vinylphosphonate and GalNAc Modifications for Enhancing Activity of Synthetic siRNA. Bioorg. Med. Chem. Lett. 2016, 26, 2817–2820. DOI: 10.1016/j.bmcl.2016.04.063.
   PubMed Web of Science ®Google Scholar
• Hardcastle, T.; Novosjolova, I.; Kotikam, V.; Cheruiyot, S. K.; Mutisya, D.; Kennedy, S. D.; Egli, M.; Kelley, M. L.; Smith, A. B.; Rozners, E. A Single Amide Linkage in the Passenger Strand Suppresses its Activity and Enhances Guide Strand Targeting of siRNAs. ACS Chem. Biol. 2018, 13, 533–536. DOI: 10.1021/acschembio.7b01012.
   PubMed Web of Science ®Google Scholar
• Kumar, P.; Parmar, P. G.; Brown, C. R.; Willoughby, J. L. S.; Foster, D. J.; Babu, I. R.; Schofield, S.; Jadhav, V.; Charisse, K.; Nair, J. K.; et al. 5′-Morpholino Modification of the Sense Strand of an siRNA Makes it a More Effective Passenger. Chem. Commun. (Camb). 2019, 55, 5139–5142. DOI: 10.1039/c9cc00977a.
   PubMed Web of Science ®Google Scholar
• Koizumi, M.; Hirota, Y.; Nakayama, M.; Tamura, M.; Obuchi, W.; Kurimoto, A.; Tsuchida, H.; Maeda, H. Design of 2′-O-Methyl RNA and DNA Double-Stranded Oligonucleotides: Naturally-Occurring Nucleotide Components with Strong RNA Interference Gene Expression Inhibitory Activity. Nucleosides Nucleotides Nucleic Acids. 2020, 39, 292–309. DOI: 10.1080/15257770.2019.1663384.
   PubMed Web of Science ®Google Scholar
• Harborth, J.; Elbashir, S. M.; Vandenburgh, K.; Manninga, H.; Scaringe, S. A.; Weber, K.; Tuschl, T. Sequence, Chemical, and Structural Variation of Small Interfering RNAs and Short Hairpin RNAs and the Effect on Mammalian Gene Silencing. Antisense. Nucleic Acid Drug Dev. 2003, 13, 83–105. DOI: 10.1089/108729003321629638.
   PubMedGoogle Scholar
• Hotoda, H.; Koizumi, M.; Koga, R.; Momota, K.; Ohmine, T.; Furukawa, H.; Nishigaki, T.; Kinoshita, T.; Kaneko, M.; Kimura, S.; et al. Biologically Active Oligodeoxyribonucleotides-IV: Anti-HIV-1 Activity of TGGGAG Having Hydrophobic Substituent at Its 5′-End via Phosphodiester Linkage. Nucleosides Nucleotides Nucleic Acids 1996, 15, 531–538. DOI: 10.1080/07328319608002403.
   Google Scholar
• Morita, K.; Kaneko, M.; Obika, S.; Imanishi, T.; Kitade, Y.; Koizumi, M. Biologically Stable 2-5A Analogues Containing 3′-O,4′-C-Bridged Adenosine as Potent RNase L Agonists. ChemMedChem. 2007, 2, 1703–1707. DOI: 10.1002/cmdc.200700150.
   PubMed Web of Science ®Google Scholar
• Adams, D.; Gonzalez-Duarte, A.; O’Riordan, W. D.; Yang, C. C.; Ueda, M.; Kristen, A. V.; Tournev, I.; Schmidt, H. H.; Coelho, T. Patisiran, an RNAi Therapeutic, for Hereditary Transthyretin Amyloidosis. N. Engl. J. Med. 2018, 379, 11–21.
   PubMed Web of Science ®Google Scholar
• Schirle, N. T.; MacRae, I. J. The Crystal Structure of Human Argonaute2. Science 2012, 336, 1037–1040.
   PubMed Web of Science ®Google Scholar
• Egli, M.; Manoharan, M. Re-Engineering RNA Molecules into Therapeutic Agents. Acc. Chem. Res. 2019, 52, 1036–1047. DOI: 10.1021/acs.accounts.8b00650.
   PubMed Web of Science ®Google Scholar
• Kotikam, V.; Rozners, E. Amide-Modified RNA: Using Protein Backbone to Modulate Function of Short Interfering RNAs. Acc. Chem. Res. 2020, 53, 1782–1790. DOI: 10.1021/acs.accounts.0c00249.
   PubMed Web of Science ®Google Scholar
• Villard, A. L.; Coussot, G.; Lefebvre, I.; Augustijns, P.; Aubertin, A. M.; Gosselin, G.; Peyrottes, S.; Périgaud, C. Phenyl Phosphotriester Derivatives of AZT: Variations upon the SATE Moiety. Bioorg. Med. Chem. 2008, 16, 7321–7329. DOI: 10.1016/j.bmc.2008.06.024.
   PubMed Web of Science ®Google Scholar
• Romanowska, J.; Szymańska-Michalak, A.; Boryski, J.; Stawiński, J.; Kraszewski, A.; Loddo, R.; Sanna, G.; Collu, G.; Secci, B.; La Colla, P. Aryl Nucleoside H-Phosphonates. Part 16: Synthesis and Anti-HIV-1 Activity of di-Aryl Nucleoside Phosphotriesters. Bioorg. Med. Chem. 2009, 17, 3489–3498. DOI: 10.1016/j.bmc.2009.02.033.
   PubMed Web of Science ®Google Scholar
• Koizumi, M.; Koga, R.; Hotoda, H.; Momota, K.; Ohmine, T.; Furukawa, H.; Agatsuma, T.; Nishigaki, T.; Abe, K.; Kosaka, T.; et al. Biologically Active Oligodeoxyribonucleotides-IX. Synthesis and anti-HIV-1 Activity of Hexadeoxyribonucleotides, TGGGAG, Bearing 3′- and 5′-End-Modification. Bioorg. Med. Chem. 1997, 5, 2235–2243. DOI: 10.1016/S0968-0896(97)00161-2.
   PubMed Web of Science ®Google Scholar
• Ueno, Y.; Watanabe, Y.; Shibata, A.; Yoshikawa, K.; Takano, T.; Kohara, M.; Kitade, Y. Synthesis of Nuclease-Resistant siRNAs Possessing Universal Overhangs. Bioorg. Med. Chem. 2009, 17, 1974–1981. DOI: 10.1016/j.bmc.2009.01.033.
   PubMed Web of Science ®Google Scholar
• Yu, J. Y.; DeRuiter, S. L.; Turner, D. L. RNA Interference by Expression of Short-Interfering RNAs and Hairpin RNAs in Mammalian Cells. Proc. Natl. Acad. Sci. USA. 2002, 99, 6047–6052. DOI: 10.1073/pnas.092143499.
   PubMed Web of Science ®Google Scholar
• Siolas, D.; Lerner, C.; Burchard, J.; Ge, W.; Linsley, P. S.; Paddison, P. J.; Hannon, G. J.; Cleary, M. A. Synthetic shRNAs as Potent RNAi Triggers. Nat. Biotechnol. 2005, 23, 227–231. DOI: 10.1038/nbt1052.
   PubMed Web of Science ®Google Scholar
• Kanda, A.; Ishizuka, E. T.; Shibata, A.; Matsumoto, T.; Toyofuku, H.; Noda, K.; Namba, K.; Ishida, S. A Novel Single-Strand RNAi Therapeutic Agent Targeting the (Pro)Renin Receptor Suppresses Ocular Inflammation. Mol. Ther. Nucleic Acids. 2017, 7, 116–126. DOI: 10.1016/j.omtn.2017.01.001.
   PubMedGoogle Scholar
• Kim, D.-H.; Behlke, M. A.; Rose, S. D.; Chang, M.-S.; Choi, S.; Rossi, J. J. Synthetic dsRNA Dicer Substrates Enhance RNAi Potency and Efficacy. Nat. Biotechnol. 2005, 23, 222–226. DOI: 10.1038/nbt1051.
   PubMed Web of Science ®Google Scholar