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

Volumn 22, Issue 1, 2011, Pages 42-49

  Yoshikawa, Kayo ^a   Ogata, Aya ^a   Matsuda, Chiho ^b   Kohara, Michinori ^b   Iba, Hideo ^c   Kitade, Yukio ^a   Ueno, Yoshihito ^a  

^a GIFU UNIVERSITY   (Japan)

^b TOKYO METROPOLITAN INSTITUTE OF MEDICAL SCIENCE   (Japan)

^c THE UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

SYNTHESIS (CHEMICAL);

ANTISENSE; BIARYLS; DISEASE-CAUSING GENE; PROPERTY; RNA DUPLEXES; SMALL INTERFERING RNA; SYNTHESISED; THERAPEUTIC DRUGS;

RNA;

DOUBLE STRANDED RNA; NUCLEASE; SMALL INTERFERING RNA;

ANTIVIRAL ACTIVITY; ARTICLE; DRUG DESIGN; DRUG SELECTIVITY; ENZYMATIC DEGRADATION; HEPATITIS C VIRUS; NONHUMAN; RNA SEQUENCE; RNA SYNTHESIS; VIRUS REPLICATION;

EID: 78751618786     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc100301w     Document Type: Article

References (32)

1. Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., and Mello, C. C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Nature 391, 806-811
2. Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells Nature 411, 494-498
3. Elbashir, S. M., Lendeckel, W., and Tuschl, T. (2001) RNA interference is mediated by 21- and 22nucleotide RNAs Genes Dev. 15, 188-200
4. Bumcrot, D., Manoharan, M., Koteliansky, V., and Sah, D. W. Y. (2006) RNAi therapeutics: a potential new class of pharmaceutical drugs Nat. Chem. Biol. 2, 711-719
5. Behlke, M. A. (2006) Progress toward in vivo use of siRNAs Mol. Ther. 13, 644-670
6. Kim, D. A. and Rossi, J. J. (2007) Strategies for silencing human disease using RNA interference Nat. Rev. Genet. 8, 173-184
7. Schwarz, D. S., Hutvágner, G., Du, T., Xu, Z., Aronin, N., and Zamore, P. D. (2003) Asymmetry in the assembly of the RNAi enzyme complex Cell 115, 199-208
8. Khvorova, A., Reynolds, A., and Jayasena, S. D. (2003) Functional siRNAs and miRNAsexhibit strand bias Cell 115, 209-216
9. Tomari, Y., Matranga, C., Haley, B., Martinez, N., and Zamore, P. D. (2004) A protein sensor for siRNA asymmetry Science 306, 1377-1380
10. Steiner, F. A., Hoogstrate, S. W., Okihara, K. L., Thijssen, K. L., Ketting, R. F., Plasterk, R. H. A., and Sijen, T. (2007) Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans Nat. Struct. Mol. Biol. 14, 927-933
11. Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., Wu, L., Li, S., Zhou, H., Long, C., Chen, S., Hannon, G. J., and Qi, Y. (2008) Sorting of small RNAs into Arabidopsis Argonate complexes is directed by the 5′ terminal nucleotide Cell 133, 116-127
12. Kawamata, T., Seitz, H., and Tomari, Y. (2009) Structural determinants of miRNAs for RISC loading and slicer-independent unwinding Nat. Struct. Mol. Biol. 16, 953-960
13. Yoda, M., Kawamata, T., Paroo, Z., Ye, X., Iwasaki, S., Liu, Q., and Tomari, Y. (2010) ATP-dependent human RISC assembly pathways Nat. Struct. Mol. Biol. 16, 17-23
14. Ghildiyal, M., Xu, J., Seitz, H., Weng, Z., and Zamore, P. D. (2010) Sorting of Drosophila small silencing RNAs partitions microRNAstrands into the RNA interference pathway RNA 16, 43-56
15. Chen, P. Y., Weinmann, L., Gaidatzis, D., Pei, Y., Zavolan, M., Tuschl, T., and Meister, G. (2008) Strand-specific 5′-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity RNA 14, 263-274
16. Parker, J. S., Roe, S. M., and Barford, D. (2005) Structure insights into mRNA recognition from a PIWI domain-siRNA guide complex Nature 434, 663-666
17. Ma, J.-B., Yuan, Y.-R., Meister, G., Pei, Y., Tuschl, T., and Patel, D. J. (2005) Structure basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein Nature 434, 666-670
18. Wang, Y., Sheng, G., Juranek, S., Tuschl, T., and Patel, D. J. (2008) Structure of the guide-strand-containing argonaute silencing complex Nature 456, 209-213
19. Wang, Y., Juranek, S., Li, H., Sheng, G., Tuschl, T., and Patel, D. J. (2008) Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex Nature 456, 921-926
20. Wang, Y., Juranek, S., Li, H., Sheng, G., Wardle, G. S., Tuschl, T., and Patel, D. J. (2010) Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes Nature 461, 754-761
21. Ueno, Y., Komatsuzaki, S., Takasu, K., Kawai, S., Kitamura, Y., and Kitade, Y. (2009) Synthesis and properties of oligonucleotides containing novel fluorescent biaryl units Eur. J. Org. Chem. 28, 4763-4769
22. Ueno, Y., Watanabe, Y., Shibata, A., Yoshikawa, K., Takano, T., Kohara, M., and Kitade, Y. (2009) Synthesis of nuclease-resistant siRNAs possessing universal overhangs Bioorg. Med. Chem. 17, 1974-1981
23. Lingel, A., Simon, B., Izaurralde, E., and Sattler, M. (2003) Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain Nature 426, 465-469
24. Yan, K. S., Yan, S., Farooq, A., Han, A., Zeng, L., and Zhou, M.-M. (2003) Structure and conserved RNA binding of the PAZ domain Nature 426, 469-474
25. Song, J.-J., Liu, J., Tolia, N. H., Schneiderman, J., Smith, S. K., Martienssen, R. A., Hannon, G. J., and Joshua-Tor, L. (2003) The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes Nat. Struct. Biol. 12, 1026-1032
26. Ma, J.-B., Te, K., and Patel, D. J. (2004) Structure basis for overhang-specific small interfering RNA recognition by the PAZ domain Nature 429, 318-322
27. Somoza, Á., Terrazas, M., and Eritja, R. (2010) Modified siRNAs for the study of the PAZ domain Chem. Commun. 46, 4270-4272
28. Qiu, S., Adema, C. M., and Lane, T. (2005) A computational study of off-target effects of RNA interference Nucleic Acids. Res. 33, 1834-1847
29. Jackson, A. L., Burchard, J., Schelter, J., Chau, B. N., Cleary, M., Lim, L., and Linsley, P. S. (2006) Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity RNA 12, 1179-1187
30. Watanabe, T., Sudoh, M., Miyagishi, M., Akashi, H., Arai, M., Inoue, K., Taira, K., Yoshida, M., and Kohara, M. (2006) Intracellular-diced dsRNA has enhanced efficacy for silencing HCV RNA and overcomes variation in the viral genotype Gene Ther. 13, 883-892
31. Uhlmann, E., Vollmer, J., and Krieg, A. M. (2010) Nucleic acid-lipophilic conjugates. U.S. Patent Appl. US 20100183639A1.
32. Puglisi, J. D. and Tinoco, I., Jr. (1989) In Methods in Enzymology, Dahlberg, J. E. and Abelson, J. N., Eds.; pp 304 - 325, Vol 180, Academic Press, Inc., San Diego.