Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (498K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (180)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Czauderna, F.
Right arrow Articles by Kaufmann, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Czauderna, F.
Right arrow Articles by Kaufmann, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 11 2705-2716
© 2003 Oxford University Press

Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells

Frank Czauderna, Melanie Fechtner, Sibylle Dames, Hüseyin Aygün1, Anke Klippel, Gijsbertus J. Pronk, Klaus Giese and Jörg Kaufmann

Atugen AG, Otto Warburg Haus (No. 80), Robert-Roessle-Strasse 10, 13125 Berlin, Germany and 1 BioSpring, Hanauer Landstrasse 526, 60386 Frankfurt, Germany

*To whom correspondence should be addressed. Tel: +49 30 9489 2833; Fax: +49 30 9489 2801; Email: kaufmann{at}atugen.com

Double-stranded short interfering RNAs (siRNA) induce post-transcriptional silencing in a variety of biological systems. In the present study we have investigated the structural requirements of chemically synthesised siRNAs to mediate efficient gene silencing in mammalian cells. In contrast to studies with Drosophila extracts, we found that synthetic, double-stranded siRNAs without specific nucleotide overhangs are highly efficient in gene silencing. Blocking of the 5'-hydroxyl terminus of the antisense strand leads to a dramatic loss of RNA interference activity, whereas blocking of the 3' terminus or blocking of the termini of the sense strand had no negative effect. We further demonstrate that synthetic siRNA molecules with internal 2'-O-methyl modification, but not molecules with terminal modifications, are protected against serum-derived nucleases. Finally, we analysed different sets of siRNA molecules with various 2'-O-methyl modifications for stability and activity. We demonstrate that 2'-O-methyl modifications at specific positions in the molecule improve stability of siRNAs in serum and are tolerated without significant loss of RNA interference activity. These second generation siRNAs will be better suited for potential therapeutic application of synthetic siRNAs in vivo.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Immunol.Home page
Y. Darcan-Nicolaisen, H. Meinicke, G. Fels, O. Hegend, A. Haberland, A. Kuhl, C. Loddenkemper, M. Witzenrath, S. Kube, W. Henke, et al.
Small Interfering RNA against Transcription Factor STAT6 Inhibits Allergic Airway Inflammation and Hyperreactivity in Mice
J. Immunol., June 15, 2009; 182(12): 7501 - 7508.
[Abstract] [Full Text] [PDF]

Home page
 Molecular Cancer TherapeuticsHome page
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]

Home page
 Nucleic Acids ResHome page
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]

Home page
 Nucleic Acids ResHome page
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]

Home page
 Cancer Res.Home page
M. Aleku, P. Schulz, O. Keil, A. Santel, U. Schaeper, B. Dieckhoff, O. Janke, J. Endruschat, B. Durieux, N. Roder, et al.
Atu027, a Liposomal Small Interfering RNA Formulation Targeting Protein Kinase N3, Inhibits Cancer Progression
Cancer Res., December 1, 2008; 68(23): 9788 - 9798.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
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]

Home page
 Am. J. Physiol. Renal Physiol.Home page
H. Yuan, L. Lanting, Z.-G. Xu, S.-L. Li, P. Swiderski, S. Putta, M. Jonnalagadda, M. Kato, and R. Natarajan
Effects of cholesterol-tagged small interfering RNAs targeting 12/15-lipoxygenase on parameters of diabetic nephropathy in a mouse model of type 1 diabetes
Am J Physiol Renal Physiol, August 1, 2008; 295(2): F605 - F617.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
G. M. Birdsey, N. H. Dryden, V. Amsellem, F. Gebhardt, K. Sahnan, D. O. Haskard, E. Dejana, J. C. Mason, and A. M. Randi
Transcription factor Erg regulates angiogenesis and endothelial apoptosis through VE-cadherin
Blood, April 1, 2008; 111(7): 3498 - 3506.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
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]

Home page
 RNAHome page
J. A.H. Hoerter and N. G. Walter
Chemical modification resolves the asymmetry of siRNA strand degradation in human blood serum
RNA, November 1, 2007; 13(11): 1887 - 1893.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Li, P. S. Pallan, M. A. Maier, K. G. Rajeev, S. L. Mathieu, C. Kreutz, Y. Fan, J. Sanghvi, R. Micura, E. Rozners, et al.
Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme
Nucleic Acids Res., October 8, 2007; 35(19): 6424 - 6438.
[Abstract] [Full Text] [PDF]

Home page
 J. Pharmacol. Exp. Ther.Home page
S. M. Garraway, Q. Xu, and C. E. Inturrisi
Design and Evaluation of Small Interfering RNAs That Target Expression of the N-Methyl-D-aspartate Receptor NR1 Subunit Gene in the Spinal Cord Dorsal Horn
J. Pharmacol. Exp. Ther., September 1, 2007; 322(3): 982 - 988.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
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]

Home page
 Brief Funct Genomic ProteomicHome page
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]

Home page
 Toxicol PatholHome page
H. M. Martineau and I. T. Pyrah
Review of the Application of RNA Interference Technology in the Pharmaceutical Industry
Toxicol Pathol, April 1, 2007; 35(3): 327 - 336.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
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]

Home page
 Molecular Cancer TherapeuticsHome page
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]

Home page
 Nucleic Acids ResHome page
M. Fisher, M. Abramov, A. Van Aerschot, D. Xu, R. L. Juliano, and P. Herdewijn
Inhibition of MDR1 expression with altritol-modified siRNAs
Nucleic Acids Res., February 28, 2007; 35(4): 1064 - 1074.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Puthenveetil, L. Whitby, J. Ren, K. Kelnar, J. F. Krebs, and P. A. Beal
Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification
Nucleic Acids Res., October 18, 2006; 34(17): 4900 - 4911.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
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]

Home page
 RNAHome page
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]

Home page
 Nucleic Acids ResHome page
T. Ohrt, D. Merkle, K. Birkenfeld, C. J. Echeverri, and P. Schwille
In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by Exportin 5
Nucleic Acids Res., March 6, 2006; 34(5): 1369 - 1380.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
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]

Home page
 J. Gen. Virol.Home page
J. Peng, Y. Zhao, J. Mai, W. K. Pang, X. Wei, P. Zhang, and Y. Xu
Inhibition of hepatitis B virus replication by various RNAi constructs and their pharmacodynamic properties
J. Gen. Virol., December 1, 2005; 86(12): 3227 - 3234.
[Abstract] [Full Text] [PDF]

Home page
 GutHome page
M Ocker, D Neureiter, M Lueders, S Zopf, M Ganslmayer, E G Hahn, C Herold, and D Schuppan
Variants of bcl-2 specific siRNA for silencing antiapoptotic bcl-2 in pancreatic cancer
Gut, September 1, 2005; 54(9): 1298 - 1308.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Endocrinol.Home page
W. Liu, S. L. Asa, and S. Ezzat
1{alpha},25-Dihydroxyvitamin D3 Targets PTEN-Dependent Fibronectin Expression to Restore Thyroid Cancer Cell Adhesiveness
Mol. Endocrinol., September 1, 2005; 19(9): 2349 - 2357.
[Abstract] [Full Text] [PDF]

Home page
 JCBHome page
R. L. Juliano, V. R. Dixit, H. Kang, T. Y. Kim, Y. Miyamoto, and D. Xu
Epigenetic manipulation of gene expression: a toolkit for cell biologists
J. Cell Biol., June 20, 2005; 169(6): 847 - 857.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
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]

Home page
 Nucleic Acids ResHome page
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]

Home page
 Nucleic Acids ResHome page
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]

Home page
 RNAHome page
J. M. LAYZER, A. P. MCCAFFREY, A. K. TANNER, Z. HUANG, M. A. KAY, and B. A. SULLENGER
In vivo activity of nuclease-resistant siRNAs
RNA, May 1, 2004; 10(5): 766 - 771.
[Abstract] [Full Text] [PDF]

Home page
 Genes Dev.Home page
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]

Home page
 Nucleic Acids ResHome page
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]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.