title: A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity.
abstract: 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.
authors.affiliation: Department of Molecular Biology, University of Aarhus, Arhus, Nucleic Acid Center, University of Southern Denmark, Odense, Denmark. jebb@mb.au.dk
authors.forename: Jesper B
authors.initials: JB
authors.lastname: Bramsen
authors.forename: Maria B
authors.initials: MB
authors.lastname: Laursen
authors.forename: Anne F
authors.initials: AF
authors.lastname: Nielsen
authors.forename: Thomas B
authors.initials: TB
authors.lastname: Hansen
authors.forename: Claus
authors.initials: C
authors.lastname: Bus
authors.forename: Niels
authors.initials: N
authors.lastname: Langkjaer
authors.forename: B Ravindra
authors.initials: BR
authors.lastname: Babu
authors.forename: Torben
authors.initials: T
authors.lastname: Højland
authors.forename: Mikhail
authors.initials: M
authors.lastname: Abramov
authors.forename: Arthur
authors.initials: A
authors.lastname: Van Aerschot
authors.forename: Dalibor
authors.initials: D
authors.lastname: Odadzic
authors.forename: Romualdas
authors.initials: R
authors.lastname: Smicius
authors.forename: Jens
authors.initials: J
authors.lastname: Haas
authors.forename: Cordula
authors.initials: C
authors.lastname: Andree
authors.forename: Jharna
authors.initials: J
authors.lastname: Barman
authors.forename: Malgorzata
authors.initials: M
authors.lastname: Wenska
authors.forename: Puneet
authors.initials: P
authors.lastname: Srivastava
authors.forename: Chuanzheng
authors.initials: C
authors.lastname: Zhou
authors.forename: Dmytro
authors.initials: D
authors.lastname: Honcharenko
authors.forename: Simone
authors.initials: S
authors.lastname: Hess
authors.forename: Elke
authors.initials: E
authors.lastname: Müller
authors.forename: Georgii V
authors.initials: GV
authors.lastname: Bobkov
authors.forename: Sergey N
authors.initials: SN
authors.lastname: Mikhailov
authors.forename: Eugenio
authors.initials: E
authors.lastname: Fava
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Meyer
authors.forename: Jyoti
authors.initials: J
authors.lastname: Chattopadhyaya
authors.forename: Marino
authors.initials: M
authors.lastname: Zerial
authors.forename: Joachim W
authors.initials: JW
authors.lastname: Engels
authors.forename: Piet
authors.initials: P
authors.lastname: Herdewijn
authors.forename: Jesper
authors.initials: J
authors.lastname: Wengel
authors.forename: Jørgen
authors.initials: J
authors.lastname: Kjems
mesh_terms: D045744:Cell Line, Tumor; D002470:Cell Survival; D006801:Humans; D034622:RNA Interference; D020871:RNA Stability; D034741:RNA, Small Interfering / Q000097:blood / Q000737:chemistry* / Q000633:toxicity; D034743:RNA-Induced Silencing Complex / Q000378:metabolism
chemical_list: D034741:RNA, Small Interfering; D034743:RNA-Induced Silencing Complex