title: Modification of the siRNA passenger strand by 5-nitroindole dramatically reduces its off-target effects.
abstract: During the formation of RNA-induced silencing complex (RISC), the passenger and guide strand of an siRNA duplex separate from each other to generate an active RISC complex. Accumulating evidence shows that an siRNA passenger strand can also assemble into a RISC complex and mediate RNA interference, thereby causing undesired off-target effects. To reduce this effect, the so-called "universal base" 5-nitroindole nucleotides were incorporated into an siRNA passenger strand. Melting temperature and circular dichroism spectrum measurements showed no significant changes compared to the unmodified duplex, thus indicating the formation of normal A-form conformation. Using a dual luciferase reporter assay, we have further shown that 5-nitroindole modification at position 15 of the siRNA passenger strand drastically decreased the RNAi (RNA interfering) potency of this strand, whereas the potency of the RNA guide strand was not much affected. These results could provide a practical approach for reducing off-target effects mediated by the siRNA passenger strand.
authors.affiliation: Department of Chemical Biology and State Key Laboratory of Elemento-organic Chemistry, Nankai University, Tianjin, China.
authors.forename: Junbin
authors.initials: J
authors.lastname: Zhang
authors.forename: Jie
authors.initials: J
authors.lastname: Zheng
authors.forename: Chang
authors.initials: C
authors.lastname: Lu
authors.forename: Quan
authors.initials: Q
authors.lastname: Du
authors.forename: Zicai
authors.initials: Z
authors.lastname: Liang
authors.forename: Zhen
authors.initials: Z
authors.lastname: Xi
mesh_terms: D057809:HEK293 Cells; D006801:Humans; D007211:Indoles / Q000138:chemical synthesis / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009943:Organophosphorus Compounds / Q000138:chemical synthesis / Q000737:chemistry; D034622:RNA Interference; D020871:RNA Stability; D034741:RNA, Small Interfering / Q000138:chemical synthesis / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D034743:RNA-Induced Silencing Complex / Q000378:metabolism; D012263:Ribonucleosides / Q000138:chemical synthesis / Q000737:chemistry; D014162:Transfection
chemical_list: D007211:Indoles; D009943:Organophosphorus Compounds; D034741:RNA, Small Interfering; D034743:RNA-Induced Silencing Complex; D012263:Ribonucleosides; C434331:phosphoramidite; C090067:5-nitroindole