title: Modulation of thermal stability can enhance the potency of siRNA.
abstract: During RNA-induced silencing complex (RISC) assembly the guide (or antisense) strand has to separate from its complementary passenger (or sense) strand to generate the active RISC complex. Although this process was found to be facilitated through sense strand cleavage, there is evidence for an alternate mechanism, in which the strands are dissociated without prior cleavage. Here we show that the potency of siRNA can be improved by modulating the internal thermodynamic stability profile with chemical modifications. Using a model siRNA targeting the firefly luciferase gene with subnanomolar IC50, we found that placement of thermally destabilizing modifications, such as non-canonical bases like 2,4-difluorotoluene or single base pair mismatches in the central region of the sense strand (9-12 nt), significantly improve the potency. For this particular siRNA, the strongest correlation between the decrease in thermal stability and the increase in potency was found at position 10. Controls with stabilized sugar-phosphate backbone indicate that enzymatic cleavage of the sense strand prior to strand dissociation is not required for silencing activity. Similar potency-enhancing effects were observed as this approach was applied to other functional siRNAs targeting a different site on the firefly luciferase transcript or endogenously expressed PTEN.
authors.affiliation: Alnylam Pharmaceuticals Inc., 300 Third Street, Cambridge, MA 02142, USA.
authors.forename: Haripriya
authors.initials: H
authors.lastname: Addepalli
authors.lastname: Meena
authors.forename: Chang G
authors.initials: CG
authors.lastname: Peng
authors.forename: Gang
authors.initials: G
authors.lastname: Wang
authors.forename: Yupeng
authors.initials: Y
authors.lastname: Fan
authors.forename: Klaus
authors.initials: K
authors.lastname: Charisse
authors.forename: K Narayanannair
authors.initials: KN
authors.lastname: Jayaprakash
authors.forename: Kallanthottathil G
authors.initials: KG
authors.lastname: Rajeev
authors.forename: Rajendra K
authors.initials: RK
authors.lastname: Pandey
authors.forename: Gary
authors.initials: G
authors.lastname: Lavine
authors.forename: Ligang
authors.initials: L
authors.lastname: Zhang
authors.forename: Kerstin
authors.initials: K
authors.lastname: Jahn-Hofmann
authors.forename: Philipp
authors.initials: P
authors.lastname: Hadwiger
authors.forename: Muthiah
authors.initials: M
authors.lastname: Manoharan
authors.forename: Martin A
authors.initials: MA
authors.lastname: Maier
mesh_terms: D020137:Base Pair Mismatch; D006367:HeLa Cells; D006801:Humans; D034622:RNA Interference; D020871:RNA Stability; D034741:RNA, Small Interfering / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D034741:RNA, Small Interfering