large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity

The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA perfo...

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Bibliographic Details
Published in:Nucleic acids research 2009-05, Vol.37 (9), p.2867-2881
Main Authors: Bramsen, Jesper B, Laursen, Maria B, Nielsen, Anne F, Hansen, Thomas B, Bus, Claus, Langkjær, Niels, Babu, B. Ravindra, Højland, Torben, Abramov, Mikhail, Van Aerschot, Arthur, Odadzic, Dalibor, Smicius, Romualdas, Haas, Jens, Andree, Cordula, Barman, Jharna, Wenska, Malgorzata, Srivastava, Puneet, Zhou, Chuanzheng, Honcharenko, Dmytro, Hess, Simone, Müller, Elke, Bobkov, Georgii V, Mikhailov, Sergey N, Fava, Eugenio, Meyer, Thomas F, Chattopadhyaya, Jyoti, Zerial, Marino, Engels, Joachim W, Herdewijn, Piet, Wengel, Jesper, Kjems, Jørgen
Format: Article
Language:English
Subjects:
Cell Line, Tumor
Cell Survival
Chemistry
Humans
Kemi
NATURAL SCIENCES
NATURVETENSKAP
RNA
RNA Interference
RNA Stability
RNA, Small Interfering - blood
RNA, Small Interfering - chemistry
RNA, Small Interfering - toxicity
RNA-Induced Silencing Complex - metabolism
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Summary:The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3′-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkp106