title: Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency.
abstract: In RNA interference (RNAi), guide RNAs direct RNA-induced silencing complexes (RISC) to their mRNA targets, thus enabling the cleavage that leads to gene silencing. We describe a strong inverse correlation between the degree of guide-RNA secondary structure formation and gene silencing by small interfering (si)RNA. Unstructured guide strands mediate the strongest silencing whereas structures with base-paired ends are inactive. Thus, the availability of terminal nucleotides within guide structures determines the strength of silencing. A to G and C to U base exchanges, which involve wobble base-pairing with the target but preserve complementarity, turned inactive into active guide structures, thereby expanding the space of functional siRNAs. Previously observed base degenerations among mature micro (mi)RNAs together with the data presented here suggest a crucial role of the guide-RNA structures in miRNA action. The analysis of the effect of the secondary structures of guide-RNA sequences on RNAi efficiency provides a basis for better understanding RNA silencing pathways and improving the design of siRNAs.
authors.affiliation: Max-Planck-Institute for Infection Biology, Dept. of Immunology, Berlin, Germany. patzel@mpiib-berlin.mpg.de
authors.forename: Volker
authors.initials: V
authors.lastname: Patzel
authors.forename: Sascha
authors.initials: S
authors.lastname: Rutz
authors.forename: Isabell
authors.initials: I
authors.lastname: Dietrich
authors.forename: Christian
authors.initials: C
authors.lastname: Köberle
authors.forename: Alexander
authors.initials: A
authors.lastname: Scheffold
authors.forename: Stefan H E
authors.initials: SH
authors.lastname: Kaufmann
mesh_terms: D000465:Algorithms; D001709:Biotechnology / Q000379:methods; D002460:Cell Line; D017931:DNA Primers / Q000737:chemistry; D020868:Gene Silencing; D049452:Green Fluorescent Proteins / Q000378:metabolism; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense / Q000737:chemistry; D010957:Plasmids / Q000378:metabolism; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000378:metabolism*; D013816:Thermodynamics; D058727:RNA, Small Untranslated
chemical_list: D017931:DNA Primers; D035683:MicroRNAs; D016376:Oligonucleotides, Antisense; D034741:RNA, Small Interfering; D049452:Green Fluorescent Proteins; D012313:RNA; D058727:RNA, Small Untranslated