Nucleic Acids Research, 2003, Vol. 31, No. 2 589-595
© 2003 Oxford University Press
Tolerance for mutations and chemical modifications in a siRNA
The Biotechnology Centre of Oslo, University of Oslo, Gaustadalleen 21, N-0349, Oslo, Norway
*To whom correspondence should be addressed. Tel: +47 22840532; Fax: +47 22840501; Email: hans.prydz{at}biotek.uio.no
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Short interfering RNA (siRNA), the active agent of RNA interference, shows promise of becoming a valuable tool in both basic and clinical research. We explore the tolerance to mutations and chemical modifications in various parts of the two 21-nt strands of a siRNA targeting the blood clotting initiator Tissue Factor. The mutations were G/C transversions. The chemical modifications were 2'-O-methylation, 2'-O-allylation and phosphorothioates. We found that siRNA generally tolerated mutations in the 5' end, while the 3' end exhibited low tolerance. This observation may facilitate the design of siRNA for specific targeting of transcripts containing single nucleotide polymorphisms. We further demonstrate that in our system the single antisense strand of the wild-type siRNA is almost as effective as the siRNA duplex, while the corresponding methylated M2+4 version of the antisense had reduced activity. Most of the chemically modified versions tested had near-wild-type initial activity, while the long-term activity was increased for certain siRNA species. Our results may improve the design of siRNAs for in vivo experiments.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. Vigne, S. Duraffour, G. Andrei, R. Snoeck, D. Garin, and J.-M. Crance Inhibition of Vaccinia Virus Replication by Two Small Interfering RNAs Targeting B1R and G7L Genes and Their Synergistic Combination with Cidofovir Antimicrob. Agents Chemother., June 1, 2009; 53(6): 2579 - 2588. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. S.P. Yuen, E. Akkaya, Y. Wang, M. Takiguchi, S. Peak, M. Sullivan, A. S. Protheroe, and V. M. Macaulay Validation of the type 1 insulin-like growth factor receptor as a therapeutic target in renal cancer Mol. Cancer Ther., June 1, 2009; 8(6): 1448 - 1459. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Shah, P. K. Jain, A. Kala, D. Karunakaran, and S. H. Friedman Light-activated RNA interference using double-stranded siRNA precursors modified using a remarkable regiospecificity of diazo-based photolabile groups Nucleic Acids Res., May 28, 2009; (2009) gkp415v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. B. Bramsen, M. B. Laursen, A. F. Nielsen, T. B. Hansen, C. Bus, N. Langkjaer, B. R. Babu, T. Hojland, M. Abramov, A. Van Aerschot, et al. A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity Nucleic Acids Res., May 1, 2009; 37(9): 2867 - 2881. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Terrazas and E. T. Kool RNA major groove modifications improve siRNA stability and biological activity Nucleic Acids Res., February 1, 2009; 37(2): 346 - 353. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P.N. Pushparaj, J.J. Aarthi, J. Manikandan, and S.D. Kumar siRNA, miRNA, and shRNA: in vivo Applications Journal of Dental Research, November 1, 2008; 87(11): 992 - 1003. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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 Res., October 1, 2008; 36(18): 5812 - 5821. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. S. Fjeldbo, K. Misund, C.-C. Gunther, M. Langaas, T. S. Steigedal, L. Thommesen, A. Laegreid, and T. Bruland Functional studies on transfected cell microarray analysed by linear regression modelling Nucleic Acids Res., September 1, 2008; 36(15): e97 - e97. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Dahlgren, H.-Y. Zhang, Q. Du, M. Grahn, G. Norstedt, C. Wahlestedt, and Z. Liang Analysis of siRNA specificity on targets with double-nucleotide mismatches Nucleic Acids Res., May 1, 2008; 36(9): e53 - e53. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Ohkubo, R. Kasuya, K. Sakamoto, K. Miyata, H. Taguchi, H. Nagasawa, T. Tsukahara, T. Watanobe, Y. Maki, K. Seio, et al. 'Protected DNA Probes' capable of strong hybridization without removal of base protecting groups Nucleic Acids Res., April 1, 2008; 36(6): 1952 - 1964. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Eberle, K. Giessler, C. Deck, K. Heeg, M. Peter, C. Richert, and A. H. Dalpke Modifications in Small Interfering RNA That Separate Immunostimulation from RNA Interference J. Immunol., March 1, 2008; 180(5): 3229 - 3237. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Mikat and A. Heckel Light-dependent RNA interference with nucleobase-caged siRNAs RNA, December 1, 2007; 13(12): 2341 - 2347. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Sipa, E. Sochacka, J. Kazmierczak-Baranska, M. Maszewska, M. Janicka, G. Nowak, and B. Nawrot Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA RNA, August 1, 2007; 13(8): 1301 - 1316. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Jagannath and M. Wood RNA interference based gene therapy for neurological disease Brief Funct Genomic Proteomic, May 3, 2007; (2007) elm005v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. De Paula, M. V. L.B. Bentley, and R. I. Mahato Hydrophobization and bioconjugation for enhanced siRNA delivery and targeting RNA, April 1, 2007; 13(4): 431 - 456. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. R. Mook, F. Baas, M. B. de Wissel, and K. Fluiter Evaluation of locked nucleic acid-modified small interfering RNA in vitro and in vivo Mol. Cancer Ther., March 1, 2007; 6(3): 833 - 843. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Xu, Y. Zhang, L. Kang, M. J. Roossinck, and K. S. Mysore Computational Estimation and Experimental Verification of Off-Target Silencing during Posttranscriptional Gene Silencing in Plants Plant Physiology, October 1, 2006; 142(2): 429 - 440. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Koller, S. Propp, H. Murray, W. Lima, B. Bhat, T. P. Prakash, C. R. Allerson, E. E. Swayze, E. G. Marcusson, and N. M. Dean Competition for RISC binding predicts in vitro potency of siRNA Nucleic Acids Res., September 11, 2006; 34(16): 4467 - 4476. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. L. Jackson, J. Burchard, D. Leake, A. Reynolds, J. Schelter, J. Guo, J. M. Johnson, L. Lim, J. Karpilow, K. Nichols, et al. Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing RNA, July 1, 2006; 12(7): 1197 - 1205. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Amarzguioui, Q. Peng, M. T. Wiiger, V. Vasovic, E. Babaie, T. Holen, J. M. Nesland, and H. Prydz Ex vivo and In vivo Delivery of Anti-Tissue Factor Short Interfering RNA Inhibits Mouse Pulmonary Metastasis of B16 Melanoma Cells. Clin. Cancer Res., July 1, 2006; 12(13): 4055 - 4061. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Dowler, D. Bergeron, A.-L. Tedeschi, L. Paquet, N. Ferrari, and M. J. Damha Improvements in siRNA properties mediated by 2'-deoxy-2'-fluoro-{beta}-D-arabinonucleic acid (FANA) Nucleic Acids Res., March 22, 2006; 34(6): 1669 - 1675. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Sabariegos, M. Gimenez-Barcons, N. Tapia, B. Clotet, and M. A. Martinez Sequence Homology Required by Human Immunodeficiency Virus Type 1 To Escape from Short Interfering RNAs J. Virol., January 15, 2006; 80(2): 571 - 577. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. A. KRAYNACK and B. F. BAKER Small interfering RNAs containing full 2'-O-methylribonucleotide-modified sense strands display Argonaute2/eIF2C2-dependent activity RNA, January 1, 2006; 12(1): 163 - 176. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. J. Atkinson, K. W. Young, S. J. Ennion, J. N. C. Kew, S. R. Nahorski, and R. A. J. Challiss Altered Expression of Gq/11{alpha} Protein Shapes mGlu1 and mGlu5 Receptor-Mediated Single Cell Inositol 1,4,5-Trisphosphate and Ca2+ Signaling Mol. Pharmacol., January 1, 2006; 69(1): 174 - 184. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. W. Pham and E. J. Sontheimer Molecular Requirements for RNA-induced Silencing Complex Assembly in the Drosophila RNA Interference Pathway J. Biol. Chem., November 25, 2005; 280(47): 39278 - 39283. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. B. Sanchez, M. Perez, T. Cornu, and J. C. de la Torre RNA Interference-Mediated Virus Clearance from Cells both Acutely and Chronically Infected with the Prototypic Arenavirus Lymphocytic Choriomeningitis Virus J. Virol., September 1, 2005; 79(17): 11071 - 11081. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Holen, S. E. Moe, J. G. Sorbo, T. J. Meza, O. P. Ottersen, and A. Klungland Tolerated wobble mutations in siRNAs decrease specificity, but can enhance activity in vivo Nucleic Acids Res., August 19, 2005; 33(15): 4704 - 4710. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S.-K. Lee, D. M. Dykxhoorn, P. Kumar, S. Ranjbar, E. Song, L. E. Maliszewski, V. Francois-Bongarcon, A. Goldfeld, N. M. Swamy, J. Lieberman, et al. Lentiviral delivery of short hairpin RNAs protects CD4 T cells from multiple clades and primary isolates of HIV Blood, August 1, 2005; 106(3): 818 - 826. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Du, H. Thonberg, J. Wang, C. Wahlestedt, and Z. Liang A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites Nucleic Acids Res., March 21, 2005; 33(5): 1671 - 1677. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. S. E. Heale, H. S. Soifer, C. Bowers, and J. J. Rossi siRNA target site secondary structure predictions using local stable substructures Nucleic Acids Res., February 18, 2005; 33(3): e30 - e30. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Chen, L. Zhang, H.-Y. Zhang, X. Xiong, B. Wang, Q. Du, B. Lu, C. Wahlestedt, and Z. Liang A universal plasmid library encoding all permutations of small interfering RNA PNAS, February 15, 2005; 102(7): 2356 - 2361. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. M. Westerhout, M. Ooms, M. Vink, A. T. Das, and B. Berkhout HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome Nucleic Acids Res., February 1, 2005; 33(2): 796 - 804. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Gitlin, J. K. Stone, and R. Andino Poliovirus Escape from RNA Interference: Short Interfering RNA-Target Recognition and Implications for Therapeutic Approaches J. Virol., January 15, 2005; 79(2): 1027 - 1035. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Elmén, Håk. Thonberg, K. Ljungberg, M. Frieden, M. Westergaard, Y. Xu, B. Wahren, Z. Liang, H. Ørum, T. Koch, et al. Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality Nucleic Acids Res., January 14, 2005; 33(1): 439 - 447. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. H. S. Hall, J. Wan, E. E. Shaughnessy, B. Ramsay Shaw, and K. A. Alexander RNA interference using boranophosphate siRNAs: structure-activity relationships Nucleic Acids Res., November 15, 2004; 32(20): 5991 - 6000. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Hu, S. Hipolito, R. Lynn, V. Abraham, S. Ramos, and F. Wong-Staal Relative gene-silencing efficiencies of small interfering RNAs targeting sense and antisense transcripts from the same genetic locus Nucleic Acids Res., August 27, 2004; 32(15): 4609 - 4617. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Kiriakidou, P. T. Nelson, A. Kouranov, P. Fitziev, C. Bouyioukos, Z. Mourelatos, and A. Hatzigeorgiou A combined computational-experimental approach predicts human microRNA targets Genes & Dev., May 15, 2004; 18(10): 1165 - 1178. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Martinez and T. Tuschl RISC is a 5' phosphomonoester-producing RNA endonuclease Genes & Dev., May 1, 2004; 18(9): 975 - 980. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Kronke, R. Kittler, F. Buchholz, M. P. Windisch, T. Pietschmann, R. Bartenschlager, and M. Frese Alternative Approaches for Efficient Inhibition of Hepatitis C Virus RNA Replication by Small Interfering RNAs J. Virol., April 1, 2004; 78(7): 3436 - 3446. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Pancoska, Z. Moravek, and U. M. Moll Efficient RNA interference depends on global context of the target sequence: quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA Nucleic Acids Res., March 1, 2004; 32(4): 1469 - 1479. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Pusch, D. Boden, R. Silbermann, F. Lee, L. Tucker, and B. Ramratnam Nucleotide sequence homology requirements of HIV-1-specific short hairpin RNA Nucleic Acids Res., November 15, 2003; 31(22): 6444 - 6449. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Saxena, Z. O. Jonsson, and A. Dutta Small RNAs with Imperfect Match to Endogenous mRNA Repress Translation: IMPLICATIONS FOR OFF-TARGET ACTIVITY OF SMALL INHIBITORY RNA IN MAMMALIAN CELLS J. Biol. Chem., November 7, 2003; 278(45): 44312 - 44319. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Boden, O. Pusch, F. Lee, L. Tucker, and B. Ramratnam Human Immunodeficiency Virus Type 1 Escape from RNA Interference J. Virol., November 1, 2003; 77(21): 11531 - 11535. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-L. CHIU and T. M. RANA siRNA function in RNAi: A chemical modification analysis RNA, September 1, 2003; 9(9): 1034 - 1048. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Grunweller, E. Wyszko, B. Bieber, R. Jahnel, V. A. Erdmann, and J. Kurreck Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2'-O-methyl RNA, phosphorothioates and small interfering RNA Nucleic Acids Res., June 15, 2003; 31(12): 3185 - 3193. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Czauderna, M. Fechtner, S. Dames, H. Aygun, A. Klippel, G. J. Pronk, K. Giese, and J. Kaufmann Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells Nucleic Acids Res., June 1, 2003; 31(11): 2705 - 2716. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Holen, M. Amarzguioui, E. Babaie, and H. Prydz Similar behaviour of single-strand and double-strand siRNAs suggests they act through a common RNAi pathway Nucleic Acids Res., May 1, 2003; 31(9): 2401 - 2407. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Sohail, G. Doran, J. Riedemann, V. Macaulay, and E. M. Southern A simple and cost-effective method for producing small interfering RNAs with high efficacy Nucleic Acids Res., April 1, 2003; 31(7): e38 - e38. [Abstract] [Full Text] [PDF]
|
|