Amino-modified and lipid-conjugated dicer-substrate siRNA enhances RNAi efficacy

Bioconjugate Chemistry

Volumn 23, Issue 2, 2012, Pages 164-173

  Kubo, Takanori ^a   Takei, Yoshifumi ^b   Mihara, Keichiro ^c   Yanagihara, Kazuyoshi ^a   Seyama, Toshio ^a  

^a YASUDA WOMEN'S UNIVERSITY   (Japan)

^b NAGOYA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^c HIROSHIMA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME ACTIVITY; GENES; LANTHANUM COMPOUNDS; MOLECULAR BIOLOGY; RNA; SATURATED FATTY ACIDS;

AMINO-MODIFIED; ANTISENSE; BIOLOGICAL PROPERTIES; CELL TRANSFECTION; GENE SILENCING; GENE SUPPRESSION; LUCIFERASE ACTIVITIES; MEMBRANE PERMEABILITY; RENILLA LUCIFERASE; SMALL INTERFERING RNA;

PALMITIC ACID;

AMINE; COMPLEMENTARY RNA; DICER; DICER SUBSTRATE SMALL INTERFERING RNA; NUCLEASE; NUCLEOTIDE; PALMITIC ACID; RENILLA LUCIFERIN 2 MONOOXYGENASE; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; DRUG ACTIVITY; ENZYME DEGRADATION; GENE ACTIVITY; GENE REPRESSION; GENE SILENCING; GENE THERAPY; GENETIC TRANSFECTION; HELA CELL; HUMAN; HUMAN CELL; MEMBRANE PERMEABILITY; RNA CLEAVAGE; RNA INTERFERENCE;

RENILLA LUCIFERASE;

EID: 84856896229     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc200333w     Document Type: Article

References (57)

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 (Pubitemid 28099681)
2. John, M., Constien, R., Akinc, A., Goldberg, M., Moon, Y. A., Spranger, M., Hadwiger, P., Soutschek, J., Vornlocher, H. P., Manoharan, M., Stoffel, M., Langer, R., Anderson, D. G., Horton, J. D., Koteliansky, V., and Bumcrot, D. (2007) Effective RNAi-mediated gene silencing without interruption of the endogenous microRNA pathway Nature 449, 745-747 (Pubitemid 47552094)
3. Karagiannis, T. C. and El-Osta, A. (2005) RNA interference and potential therapeutic applications of short interfering RNAs Cancer Gene Ther. 12, 787-795 (Pubitemid 43086280)
4. Pan, X., Thompson, R., Meng, X., Wu, D., and Xu, L. (2011) Tumor-targeted RNA-interference: functional non-viral nanovectors Am. J. Cancer Res 1, 25-42
5. Geisbert, T. W., Lee, A. C., Robbins, M., Geisbert, J. B., Honko, A. N., Sood, V., Johnson, J. C., Jong, S., Tavakoli, I., Judge, A., Hensley, L. E., and MacLachlan, I. (2010) Postexposure protection of non-human primates against a lethal Ebola virus challenge with RNA interference: a proof-of-concept study The Lancet 375, 1896-1905
6. Myers, J. W., Jones, J. T., Meyer, T., and Ferrell, J. E. (2003) Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing Nat. Biotechnol. 21, 324-328 (Pubitemid 36314820)
7. Macrae, I. J., Zhou, K., Li, F., Repic, A., Brooks, A. N., Cande, W. Z., Adams, P. D., and Doudna, J. A. (2006) Structural basis for double-stranded RNA processing by Dicer Science 311, 195-198 (Pubitemid 43108178)
8. Silhavy, D., Molnar, A., Lucioli, A., Szittya, G., Hornyik, C., Tavazza, M., and Burgyan, J. (2002) A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs EMBO J. 21, 3070-3080 (Pubitemid 34670391)
9. Schütze, N. (2004) siRNA technology Mol. Cell. Endocrinol. 213, 115-119 (Pubitemid 38210044)
10. Leung, R. K. and Whittaker, P. A. (2005) RNA interference: from gene silencing to gene-specific therapeutics Pharmacol. Ther. 107, 222-239 (Pubitemid 40910042)
11. Amarzguioui, M., Holen, T., Babaie, E., and Prydz, H. (2003) Tolerance for mutations and chemical modifications in a siRNA Nucleic Acids Res. 31, 589-595 (Pubitemid 36175948)
12. Braasch, D. A., Jensen, S., Liu, T., Kaur, K., Arar, K., White, M. A., and Corey, D. R. (2003) RNA interference in mammalian cells by chemically-modified RNA Biochemistry 42, 7967-7975 (Pubitemid 36807714)
13. Sipa, K., Sochacka, E., Kazmierczak-Baranska, J., Maszewska, M., Janicka, M., Nowak, G., and Nawrot, B. (2007) Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA RNA 13, 1301-1316 (Pubitemid 47080475)
14. Choung, S., Kim, Y. J., Kim, S., Park, H. O., and Choi, Y. C. (2006) Chemical modification of siRNAs to improve serum stability without loss of efficacy Biochem. Biophys. Res. Commun. 342, 919-927 (Pubitemid 43320485)
15. Grunweller, A., Wyszko, E., Bieber, B., Jahnel, R., Erdmann, V. A., and Kurreck, J. A. (2003) Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2′-O-methyl RNA, phosphorothioates and small interfering RNA Nucleic Acids Res. 12, 3185-3193 (Pubitemid 37441778)
16. Hall, A. H., Wan, J., Spesock, A., Sergueeva, Z., Shaw, B. R., and Alexander, K. A. (2006) High potency silencing by single-stranded boranophosphate siRNA Nucleic Acids Res. 34, 2773-2781 (Pubitemid 43985638)
17. Chiu, Y. L. and Rana, T. M. (2003) siRNA function in RNAi: A chemical modification analysis RNA 9, 1034-1048 (Pubitemid 37093614)
18. Corey, D. R. (2007) Chemical modification: the key to clinical application of RNA interference? J. Clin. Invest. 117, 3615-3622 (Pubitemid 350224067)
19. Behlke, M. A. (2008) Chemical modification of siRNAs for in vivo use Oligonucleotides 18, 305-319 (Pubitemid 352791344)
20. Snøve, O., Jr. and Rossi, J. J. (2006) Chemical modifications rescue off-target effects of RNAi ACS Chem. Biol. 1, 274-276
21. Jung, S., Lee, S. H., Mok, H., Chung, H. J., and Park, T. G. (2010) Gene silencing efficiency of siRNA-PEG conjugates: Effect of PEGylation site and PEG molecular weight J. Controlled Release 144, 306-313
22. Oishi, M., Nagasaki, Y., Itaka, K., Nishiyama, N., and Kataoka, K. (2005) Lactosylated poly(ethylene glycol)-siRNA conjugate through acid-labile beta-thiopropionate linkage to construct pH-sensitive polyion complex micelles achieving enhanced gene silencing in hepatoma cells J. Am. Chem. Soc. 127, 1624-1625 (Pubitemid 40229133)
23. Moschos, S. A., Jones, S. W., Perry, M. N., Williams, A. E., Erjefalt, J. S., Turner, J. J., Barnes, P. J., Sproat, B. S., Gait, M. J., and Lindsay, M. A. (2007) Lung delivery studies using siRNA conjugated to TAT(48-60) and Penetratin reveal peptide induced reduction in gene expression and induction of innate immunity Bioconjugate Chem 18, 1450-1459 (Pubitemid 47464052)
24. Turner, J. J., Jones, S., Fabani, M. M., Ivanova, G., Arzumanov, A. A., and Gait, M. J. (2007) RNA targeting with peptide conjugates of oligonucleotides, siRNA and PNA Blood Cells Mol. Dis. 38, 1-7 (Pubitemid 44960863)
25. Detzer, A., Overhoff, M., Wunsche, W., Rompf, M., Turner, J. J., Ivanova, G. D., Gait, M. J., and Sczakiel, G. (2009) Increased RNAi is related to intracellular release of siRNA via a covalently attached signal peptide RNA 15, 627-636
26. Soutschek, J., Akinc, A., Bramlage, B., Charisse, K., Constien, R., Donoghue, M., Elbashir, S., Geick, A., Hadwiger, P., Harborth, J., John, M., Kesavan, V., Lavine, G., Pandey, P. K., Racie, T., Rajeev, K. G., Röhl, I., Toudjarska, I., Wang, G., Wuschko, S., Bumcrot, D., Koteliansky, V., Limmer, S., Manoharan, M., and Vornlocher, H. P. (2004) Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs Nature 432, 173-178 (Pubitemid 39545841)
27. Wolfrum, C., Shi, S., Jayaprakash, K. N., Jayaraman, M., Wang, G., Pandey, R. K., Rajeev, K. G., Nakayama, T., Charrise, K., Ndungo, E. M., Zimmermann, T., Koteliansky, V., Manoharan, M., and Stoffel, M. (2007) Mechanisms and optimization of in vivo delivery of lipophilic siRNAs Nat. Biotechnol. 25, 1149-1157 (Pubitemid 47538115)
28. Nishina, K., Unno, T., Uno, Y., Kubodera, T., Kanouchi, T., Mizusawa, H., and Yokota, T. (2008) Efficient in vivo delivery of siRNA to the liver by conjugation of alpha-tocopherol Mol. Ther. 16, 734-740 (Pubitemid 351426175)
29. Wong, N., Liu, Z., and Dai, H. (2005) Functionalization of carbon nanotubes via cleavable disulfide bonds for efficient intracellular delivery of siRNA and potent gene silencing J. Am. Chem. Soc. 127, 12492-12493 (Pubitemid 41292159)
30. Kim, D. H., Behlke, M. A., Rose, S. D., Chang, M. S., Choi, S., and Rossi, J. J. (2005) Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy Nat. Biotechnol. 23, 222-226 (Pubitemid 40255333)
31. Marques, J. T., Devosse, T., Wang, D., Zamanian-Daryoush, M., Serbinowski, P., Hartmann, R., Fujita, T., Behlke, M. A., and Williams, B. R. (2006) A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells Nat. Biotechnol. 24, 559-565
32. Rose, S. D., Kim, D. H., Amarzguioui, M., Heidel, J. D., Collingwood, M. A., Davis, M. E., Rossi, J. J., and Behlke, M. A. (2005) Functional polarity is introduced by Dicer processing of short substrate RNAs Nucleic Acids Res. 33, 4140-4156 (Pubitemid 41487274)
33. Amarzguioui, M., Lundberg, P., Cantin, E., Hagstrom, J., Behlke, M. A., and Rossi, J. J. (2006) Rational design and in vitro and in vivo delivery of Dicer substrate siRNA Nat. Protoc. 1, 508-517
34. Amarzguioui, M., Rossi, J. J., and Kim, D. (2005) Approaches for chemically synthesized siRNA and vector-mediated RNAi FEBS Lett. 579, 5974-5981 (Pubitemid 41484142)
35. Sano, M., Sierant, M., Miyagishi, M., Nakanishi, M., Takagi, Y., and Sutou, S. (2008) Effect of asymmetric terminal structures of short RNA duplexes on the RNA interference activity and strand selection Nucleic Acids Res. 36, 5812-5821
36. Sun, X., Rogoff, H. A., and Li, C. J. (2008) Asymmetric RNA duplexes mediate RNA interference in mammalian cells Nat. Biotechnol. 26, 1379-1382
37. Chu, C. Y. and Rana, T. M. (2008) Potent RNAi by short RNA triggers RNA 14, 1714-1719
38. Ding, H., Liao, G., Wang, H., and Zhou, Y. (2007) Asymmetrically designed siRNAs and shRNAs enhance the strand specificity and efficacy in RNAi J. RNAi Gene Silencing 4, 269-280
39. Turner, J. J., Jones, S. W., Moschos, S. A., Lindsay, M. A., and Gait, M. J. (2007) MALDI-TOF mass spectral analysis of siRNA degradation in serum confirms an RNase A-like activity Mol. Biosyst. 3, 43-50 (Pubitemid 44924958)
40. MacRae, I. J., Zhou, K., and Doudna, J. A. (2007) Structural determinants of RNA recognition and cleavage by Dicer Nat. Struct. Mol. Biol. 14, 934-940 (Pubitemid 47525174)
41. Vermeulen, A., Behlen, L., Reynolds, A., Wolfson, A., Marshall, W. S., Karpilow, J., and Khvorova, A. (2005) The contributions of dsRNA structure to Dicer specificity and efficiency RNA 11, 674-682 (Pubitemid 40594334)
42. Ameres, S. L., Martinez, J., and Schroeder, R. (2007) Molecular basis for target RNA recognition and cleavage by human RISC Cell 130, 101-112 (Pubitemid 47031315)
43. Salomon, W., Bulock, K., Lapierre, J., Pavco, P., Woolf, T., and Kamens, J. (2010) Modified dsRNAs that are not processed by Dicer maintain potency and are incorporated into the RISC Nucleic Acids Res. 38, 3771-3779
44. Eder, P. S., DeVine, R. J., Dagle, J. M., and Walder, J. A. (1991) Substrate specificity and kinetics of degradation of antisense oligonucleotides by a 3′ exonuclease in plasma Antisense Res. Dev. 1, 141-151
45. Kubo, T., Zhelev, Z., Ohba, H., and Bakalova, R. (2008) Chemically modified symmetric and asymmetric duplex RNAs: an enhanced stability to nuclease degradation and gene silencing effect Biochem. Biophys. Res. Commun. 365, 54-61 (Pubitemid 350103876)
46. Kubo, T., Zhelev, Z., Ohba, H., and Bakalova, R. (2007) Modified 27-nt dsRNAs with dramatically enhanced stability in serum and long-term RNAi activity Oligonucleotides 17, 445-464
47. Kubo, T., Zhelev, Z., Bakalova, R., and Ohba, H. (2007) Enhancement of gene silencing potency and nuclease stability by chemically modified duplex RNA Nucleic Acids Symp. Ser. 51, 407-408
48. Kubo, T., Zhelev, Z., Bakalova, R., and Ohba, H. (2008) Highly efficient gene suppression by chemically modified 27 nucleotide double-stranded RNAs Jpn. J. Appl. Phys. 47, 1346-1350
49. Collingwood, M. A., Rose, S. D., Huang, L., Hillier, C., Amarzguioui, M., Wiiger, M. T., Soifer, H. S., Rossi, J. J., and Behlke, M. A. (2008) Chemical modification patterns compatible with high potency dicer-substrate small interfering RNAs Oligonucleotides 18, 187-200 (Pubitemid 352019751)
50. Kubo, T., Ohba, H., Toyobuku, H., and Hayashi, H. (2009) Lipid-modified double-stranded RNA having potent RNA interference effect, PCT Int. Appl. WO/2009/054551.
51. Akinc, A., Zumbuehl, A., Goldberg, M., Leshchiner, E. S., Busini, V., Hossain, N., Bacallado, S. A., Nguyen, D. N., Fuller, J., Alvarez, R., Borodovsky, A., Borland, T., Constien, R., Fougerolles, A., Dorkin, J. R., Jayaprakash, K. N., Jayaraman, M., John, M., Koteliansky, V., Manoharan, M., Nechev, L., Qin, J., Racie, T., Raitcheva, D., Rajeev, K. G., Sah, D. WY., Soutschek, J., Toudjarska, I., Vornlocher, H. P., Zimmermann, T. S., Langer, R., and Anderson, D. G. (2008) A combinatorial library of lipid-like materials for delivery of RNAi therapeutics Nat. Biotechnol. 26, 561-569 (Pubitemid 351668042)
52. Kitamatsu, M., Kubo, T., Matsuzaki, R., Endoh, T., Ohtsuki, T., and Sisido, M. (2009) Carrier PNA for shRNA delivery into cells Bioorg. Med. Chem. Lett. 19, 3410-3413
53. Laufer, S. D. and Restle, T. (2008) Peptide-mediated cellular delivery of oligonucleotide-based therapeutics in vitro: quantitative evaluation of overall efficacy employing easy to handle reporter systems Curr. Pharm. Des. 14, 3637-3655
54. Eguchi, A., Meade, B. R., Chang, Y. C., Fredrickson, C. T., Willert, K., Puri, N., and Dowdy, S. F. (2009) Efficient siRNA delivery into primary cells by a peptide transduction domain-dsRNA binding domain fusion protein Nat. Biotechnol. 27, 567-571
55. Shim, M. S. and Kwon, Y. J. (2009) Acid-responsive linear polyethylenimine for efficient, specific, and biocompatible siRNA delivery Bioconjugate Chem. 20, 488-499
56. Alshamsan, A., Haddadi, A., Incani, V., Samuel, J., Lavasanifar, A., and Uludaǧ, H. (2009) Formulation and delivery of siRNA by oleic acid and stearic acid modified polyethylenimine Mol. Pharm. 6, 121-133
57. Yezhelyev, M. V., Qi, L., O'Regan, R. M., Nie, S., and Gao, X. (2008) Proton-sponge coated quantum dots for siRNA delivery and intracellular imaging J. Am. Chem. Soc. 130, 9006-9012 (Pubitemid 352000838)