title: Structure and sequence motifs of siRNA linked with in vitro down-regulation of morbillivirus gene expression.
abstract: The most challenging task in RNA interference is the design of active small interfering RNA (siRNA) sequences. Numerous strategies have been published to select siRNA. They have proved effective in some applications but have failed in many others. Nonetheless, all existing guidelines have been devised to select effective siRNAs targeting human or murine genes. They may not be appropriate to select functional sequences that target genes from other organisms like viruses. In this study, we have analyzed 62 siRNA duplexes of 19 bases targeting three genes of three morbilliviruses. In those duplexes, we have checked which features are associated with siRNA functionality. Our results suggest that the intramolecular secondary structure of the targeted mRNA contributes to siRNA efficiency. We also confirm that the presence of at least the sequence motifs U13, A or U19, as well as the absence of G13, cooperate to increase siRNA knockdown rates. Additionally, we observe that G11 is linked with siRNA efficacy. We believe that an algorithm based on these findings may help in the selection of functional siRNA sequences directed against viral genes.
authors.affiliation: CIRAD, UPR Contrôle des Maladies, Montpellier, France. renata.almeida@cirad.fr
authors.forename: Renata Servan
authors.initials: RS
authors.lastname: de Almeida
authors.forename: Djénéba
authors.initials: D
authors.lastname: Keita
authors.forename: Geneviève
authors.initials: G
authors.lastname: Libeau
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Albina
mesh_terms: D000818:Animals; D001483:Base Sequence; D002522:Chlorocebus aethiops; D015536:Down-Regulation; D015870:Gene Expression; D006801:Humans; D018103:Morbillivirus / Q000737:chemistry / Q000235:genetics*; D009690:Nucleic Acid Conformation; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics*; D014709:Vero Cells; D014764:Viral Proteins / Q000235:genetics
chemical_list: D034741:RNA, Small Interfering; D014764:Viral Proteins