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BioMed Research International
Volume 2014 (2014), Article ID 901617, 15 pages
Synthesis and Gene Silencing Properties of siRNAs Containing Terminal Amide Linkages
1Dipartimento Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
2Dipartimento di Chimica Farmaceutica e Tossicologica, Università “Federico II,” Via D. Montesano 49, 80131 Napoli, Italy
Received 10 December 2013; Accepted 23 January 2014; Published 26 March 2014
Academic Editor: Daniela De Stefano
Copyright © 2014 Maria Gaglione et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- A. Fire, S. Xu, M. K. Montgomery, S. A. Kostas, S. E. Driver, and C. C. Mello, “Potent and specific genetic interference by double-stranded RNA in caenorhabditis elegans,” Nature, vol. 391, no. 6669, pp. 806–811, 1998.
- S. M. Elbashir, J. Harborth, W. Lendeckel, A. Yalcin, K. Weber, and T. Tuschl, “Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells,” Nature, vol. 411, no. 6836, pp. 494–498, 2001.
- N. J. Caplen, S. Parrish, F. Imani, A. Fire, and R. A. Morgan, “Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 17, pp. 9742–9747, 2001.
- N. C. Lau, L. P. Lim, E. G. Weinstein, and D. P. Bartel, “An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans,” Science, vol. 294, no. 5543, pp. 858–862, 2001.
- S. Weitzer and J. Martinez, “The human RNA kinase hClp1 is active on 3′ transfer RNA exons and short interfering RNAs,” Nature, vol. 447, no. 7141, pp. 222–226, 2007.
- D. S. Schwarz, G. Hutvágner, T. Du, Z. Xu, N. Aronin, and P. D. Zamore, “Asymmetry in the assembly of the RNAi enzyme complex,” Cell, vol. 115, no. 2, pp. 199–208, 2003.
- P. J. F. Leuschner, S. L. Ameres, S. Kueng, and J. Martinez, “Cleavage of the siRNA passenger strand during RISC assembly in human cells,” EMBO Reports, vol. 7, no. 3, pp. 314–320, 2006.
- J.-B. Ma, K. Ye, and D. J. Patel, “Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain,” Nature, vol. 429, no. 6989, pp. 318–322, 2004.
- E. Elkayam, C. D. Kuhn, A. Tocilj et al., “The structure of human argonaute-2 in complex with miR-20a,” Cell, vol. 150, no. 1, pp. 100–110, 2012.
- V. Ambros, “The functions of animal microRNAs,” Nature, vol. 431, no. 7006, pp. 350–355, 2004.
- B. Berkhout and K.-T. Jeang, “MicroRNAs in viral gene regulation,” Biochimica et Biophysica Acta. Gene Regulatory Mechanisms, vol. 1809, no. 11-12, p. 587, 2011.
- A. Russo and N. Potenza, “Antiviral effects of human microRNAs and conservation of their target sites,” FEBS Letters, vol. 585, no. 16, pp. 2551–2555, 2011.
- D. R. Corey, “Chemical modification: the key to clinical application of RNA interference?” Journal of Clinical Investigation, vol. 117, no. 12, pp. 3615–3622, 2007.
- S. T. Crooke, “Progress in antisense technology,” Annual Review of Medicine, vol. 55, pp. 61–95, 2004.
- M. Gaglione and A. Messere, “Recent progress in chemically modified siRNAs,” Mini Reviews in Medicinal Chemistry, vol. 10, no. 7, pp. 578–595, 2010.
- A. Lingel, B. Simon, E. Izaurralde, and M. Sattler, “Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain,” Nature Structural and Molecular Biology, vol. 11, no. 6, pp. 576–577, 2004.
- S. Shah and S. H. Friedman, “Tolerance of RNA interference toward modifications of the 5′ antisense phosphate of small interfering RNA,” Oligonucleotides, vol. 17, no. 1, pp. 35–43, 2007.
- J.-B. Ma, Y.-R. Yuan, G. Meister, Y. Pei, T. Tuschl, and D. J. Patel, “Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein,” Nature, vol. 434, no. 7033, pp. 666–670, 2005.
- M. Egholm, P. E. Nielsen, O. Buchardt, and R. H. Berg, “Recognition of guanine and adenine in DNA by cytosine and thymine containing peptide nucleic acids (PNA),” Journal of the American Chemical Society, vol. 114, no. 24, pp. 9677–9678, 1992.
- B. Hyrup and P. E. Nielsen, “Peptide nucleic acids (PNA): synthesis, properties and potential applications,” Bioorganic and Medicinal Chemistry, vol. 4, no. 1, pp. 5–23, 1996.
- M. Komiyama, S. Ye, X. Liang et al., “PNA for one-base differentiating protection of DNA from nuclease and its use for SNPs detection,” Journal of the American Chemical Society, vol. 125, no. 13, pp. 3758–3762, 2003.
- E. Uhlmann, A. Peyman, G. Breipohl, and D. W. Will, “PNA: Synthetic polyamide nucleic acids with unusual binding properties,” Angewandte Chemie. International Edition, vol. 37, no. 20, pp. 2797–2823, 1998.
- E. Uhlmann, “Peptide nucleic acids (PNA) and PNA-DNA chimeras: from high binding affinity towards biological function,” Biological Chemistry, vol. 379, no. 8-9, pp. 1045–1052, 1998.
- D. Capasso, L. de Napoli, G. di Fabio et al., “Solid phase synthesis of DNA-3′-PNA chimeras by using Bhoc/Fmoc PNA monomers,” Tetrahedron, vol. 57, no. 46, pp. 9481–9486, 2001.
- V. Esposito, A. Randazzo, A. Messere et al., “Synthesis and structural characterization of PNA-DNA quadruplex-forming chimeras,” European Journal of Organic Chemistry, no. 17, pp. 3364–3371, 2003.
- L. Petraccone, E. Erra, A. Messere et al., “Targeting duplex DNA with DNA-PNA chimeras? Physico-chemical characterisation of a triplex DNA-PNA/DNA/DNA,” Biopolymers, vol. 73, no. 4, pp. 434–442, 2004.
- N. Potenza, L. Moggio, G. Milano et al., “RNA interference in mammalia cells by RNA-3′-PNA chimeras,” International Journal of Molecular Sciences, vol. 9, no. 3, pp. 299–315, 2008.
- A. Finotti, M. Borgatti, V. Bezzerri, et al., “Effects of decoy molecules targeting NFkappaB transcription factors in cystic fibrosis IB3-1 cells: recruitment of NFkappaB to the IL-8 gene promoter and transcription of the IL-8 gene,” Artificial DNA: PNA & XNA, vol. 2, no. 3, pp. 97–104, 2012.
- A. Zannetti, S. del Vecchio, A. Romanelli et al., “Inhibition of Sp1 activity by a decoy PNA-DNA chimera prevents urokinase receptor expression and migration of breast cancer cells,” Biochemical Pharmacology, vol. 70, no. 9, pp. 1277–1287, 2005.
- M. Borgatti, A. Romanelli, M. Saviano et al., “Resistance of decoy PNA-DNA chimeras to enzymatic degradation in cellular extracts and serum,” Oncology Research, vol. 13, no. 5, pp. 279–287, 2002.
- A. Romanelli, C. Pedone, M. Saviano et al., “Molecular interactions between nuclear factor κB (NF-κB) transcription factors and a PNA-DNA chimera mimicking NF-κB binding sites,” European Journal of Biochemistry, vol. 268, no. 23, pp. 6066–6075, 2001.
- Y.-L. Chiu, A. Ali, C.-Y. Chu, H. Cao, and T. M. Rana, “Visualizing a correlation between siRNA localization, cellular uptake, and RNAi in living cells,” Chemistry and Biology, vol. 11, no. 8, pp. 1165–1175, 2004.
- W. Gong and J. P. Desaulniers, “Gene-silencing properties of siRNAs that contain internal amide-bond linkages,” Bioorganic & Medicinal Chemistry Letters, vol. 22, no. 22, pp. 6934–6937, 2012.
- J. J. Turner, S. Jones, M. M. Fabani, G. Ivanova, A. A. Arzumanov, and M. J. Gait, “RNA targeting with peptide conjugates of oligonucleotides, siRNA and PNA,” Blood Cells, Molecules, and Diseases, vol. 38, no. 1, pp. 1–7, 2007.
- G. Breipohl, D. W. Will, A. Peyman, and E. Uhlmann, “Novel synthetic routes to PNA monomers and PNA-DNA linker molecules,” Tetrahedron, vol. 53, no. 43, pp. 14671–14686, 1997.
- A. Guzaev, H. Salo, A. Azhayev, and H. Lonnberg, “A new approach for chemical phosphorylation of oligonucleotides at the 5′-terminus,” Tetrahedron, vol. 51, no. 34, pp. 9375–9384, 1995.
- R. Huey, G. M. Morris, A. J. Olson, and D. S. Goodsell, “A semiempirical free energy force field with charge-based desolvation,” Journal of Computational Chemistry, vol. 28, no. 6, pp. 1145–1152, 2007.
- S. Cosconati, S. Forli, A. L. Perryman, R. Harris, D. S. Goodsell, and A. J. Olson, “Virtual screening with AutoDock: theory and practice,” Expert Opinion on Drug Discovery, vol. 5, no. 6, pp. 597–607, 2010.
- E. F. Pettersen, T. D. Goddard, C. C. Huang et al., “UCSF Chimera—a visualization system for exploratory research and analysis,” Journal of Computational Chemistry, vol. 25, no. 13, pp. 1605–1612, 2004.
- M. Sano, M. Sierant, M. Miyagishi, M. Nakanishi, Y. Takagi, and S. Sutou, “Effect of asymmetric terminal structures of short RNA duplexes on the RNA interference activity and strand selection,” Nucleic Acids Research, vol. 36, no. 18, pp. 5812–5821, 2008.
- Y. Ueno, Y. Watanabe, A. Shibata et al., “Synthesis of nuclease-resistant siRNAs possessing universal overhangs,” Bioorganic and Medicinal Chemistry, vol. 17, no. 5, pp. 1974–1981, 2009.
- Á. Somoza, M. Terrazas, and R. Eritja, “Modified siRNAs for the study of the PAZ domain,” Chemical Communications, vol. 46, no. 24, pp. 4270–4272, 2010.
- K. Yoshikawa, A. Ogata, C. Matsuda et al., “Incorporation of biaryl units into the 5′ and 3′ ends of sense and antisense strands of siRNA duplexes improves strand selectivity and nuclease resistance,” Bioconjugate Chemistry, vol. 22, no. 1, pp. 42–49, 2011.
- M. Gaglione, N. Potenza, G. di Fabio, et al., “Tuning RNA interference by enhancing siRNA/PAZ recognition,” ACS Medicinal Chemistry Letters, vol. 4, pp. 75–78, 2013.
- A. Boutla, C. Delidakis, I. Livadaras, M. Tsagris, and M. Tabler, “Short 5′-phosphorylated double-stranded RNAs induce RNA interference in Drosophila,” Current Biology, vol. 11, no. 22, pp. 1776–1780, 2001.
- D. S. Schwarz, G. Hutvágner, B. Haley, and P. D. Zamore, “Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways,” Molecular Cell, vol. 10, no. 3, pp. 537–548, 2002.
- A. Boland, F. Tritschler, S. Heimstädt, E. Izaurralde, and O. Weichenrieder, “Crystal structure and ligand binding of the MID domain of a eukaryotic Argonaute protein,” EMBO Reports, vol. 11, no. 7, pp. 522–527, 2010.
- A. Boland, E. Huntzinger, S. Schmidt, E. Izaurralde, and O. Weichenrieder, “Crystal structure of the MID-PIWI lobe of a eukaryotic argonaute protein,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 26, pp. 10466–10471, 2011.
- F. Frank, N. Sonenberg, and B. Nagar, “Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2,” Nature, vol. 465, no. 7299, pp. 818–822, 2010.
- J. S. Parker, S. M. Roe, and D. Barford, “Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex,” Nature, vol. 434, no. 7033, pp. 663–666, 2005.
- Y.-L. Chiu and T. M. Rana, “siRNA function in RNAi: a chemical modification analysis,” RNA, vol. 9, no. 9, pp. 1034–1048, 2003.
- T. P. Prakash, C. R. Allerson, P. Dande et al., “Positional effect of chemical modifications on short interference RNA activity in mammalian cells,” Journal of Medicinal Chemistry, vol. 48, no. 13, pp. 4247–4253, 2005.
- J. K. Watts, N. Choubdar, K. Sadalapure et al., “2′-Fluoro-4′-thioarabino-modified oligonucleotides: conformational switches linked to siRNA activity,” Nucleic Acids Research, vol. 35, no. 5, pp. 1441–1451, 2007.
- H. Peacock, A. Kannan, P. A. Beal, and C. J. Burrows, “Chemical modification of siRNA bases to probe and enhance RNA interference,” Journal of Organic Chemistry, vol. 76, no. 18, pp. 7295–7300, 2011.
- D. M. Kenski, A. J. Cooper, J. J. Li et al., “Analysis of acyclic nucleoside modifications in siRNAs finds sensitivity at position 1 that is restored by 5′-terminal phosphorylation both in vitro and in vivo,” Nucleic Acids Research, vol. 38, no. 2, pp. 660–671, 2009.
- Q. Xu, D. Katkevica, and E. Rozners, “Toward amide-modified RNA: synthesis of 3′-aminomethyl-5′- carboxy-3′,5′-dideoxy nucleosides,” Journal of Organic Chemistry, vol. 71, no. 16, pp. 5906–5913, 2006.
- D. R. Corey, “RNA learns from antisense,” Nature Chemical Biology, vol. 3, no. 1, pp. 8–11, 2007.
- W. Gong and J.-P. Desaulniers, “Synthesis and properties of rnas that contain a PNA-RNA dimer,” Nucleosides, Nucleotides and Nucleic Acids, vol. 31, no. 5, pp. 389–400, 2012.
- C. Selvam, S. Thomas, J. Abbott, S. D. Kennedy, and E. Rozners, “Amides as excellent mimics of phosphate linkages in RNA,” Angewandte Chemie. International Edition, vol. 50, no. 9, pp. 2068–2070, 2011.
- P. S. Pallan, P. von Matt, C. J. Wilds, K.-H. Altmann, and M. Egli, “RNA-binding affinities and crystal structure of oligonucleotides containing five-atom amide-based backbone structures,” Biochemistry, vol. 45, no. 26, pp. 8048–8057, 2006.
- T. K. Chakraborty, P. K. Gajula, and D. Koley, “Studies directed toward the development of amide-linked RNA mimics: synthesis of the monomeric building blocks,” Journal of Organic Chemistry, vol. 73, no. 17, pp. 6916–6919, 2008.