title: Modified siRNA structure with a single nucleotide bulge overcomes conventional siRNA-mediated off-target silencing.
abstract: Off-target gene silencing is a major concern when using RNA interference. Imperfect pairing of the antisense strand with unintended mRNA targets is one of the main causes of small interfering RNA (siRNA) off-target silencing. To overcome this, we have developed "bulge-siRNA," a modified siRNA backbone structure with a single nucleotide (nt) bulge placed in the antisense strand. We found that siRNAs with a bulge at position 2 of the antisense strand were able to discriminate better between perfectly matched and mismatched targets, with no loss in silencing of the intended target. Genome-wide analysis also revealed that the bulge-siRNAs significantly reduced off-target silencing of transcripts with complementarity to the seed region of the siRNA antisense strand. When compared to 2'-methoxy ribosyl (2'-OMe) modified siRNAs previously developed to alleviate antisense off-target silencing; the bulge modification could better discriminate between on- versus off-targets. Our results suggest that the bulge-siRNA structure is a simple, yet superior alternative to chemical modifications for minimizing off-target silencing triggered by conventional siRNA structures.
authors.affiliation: Department of Chemistry, Global Research Laboratory for RNAi Medicine, Sungkyunkwan University, Suwon, Korea.
authors.forename: Pooja
authors.initials: P
authors.lastname: Dua
authors.forename: Jae Wook
authors.initials: JW
authors.lastname: Yoo
authors.forename: Soyoun
authors.initials: S
authors.lastname: Kim
authors.forename: Dong-ki
authors.initials: DK
authors.lastname: Lee
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D002470:Cell Survival; D020869:Gene Expression Profiling; D006367:HeLa Cells; D006801:Humans; D046228:Microarray Analysis; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics*; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics
chemical_list: D009711:Nucleotides; D012333:RNA, Messenger; D034741:RNA, Small Interfering