title: Minimal-length short hairpin RNAs: the relationship of structure and RNAi activity.
abstract: Small hairpin RNAs (shRNAs) are widely used in RNAi studies and typically consist of a stem of 19-29 base pairs (bp), a loop of at least 4 nucleotides (nt), and a dinucleotide overhang at the 3' end. Compared with shRNAs with 21-29 bp stems, we have found that shRNAs with 19-bp or shorter stems (sshRNAs) possess some unique structure-activity features that depend on whether the antisense strand is positioned 5' or 3' to the loop (L- or R-type sshRNAs, respectively). L sshRNAs can have IC(50)s in the very low picomolar range, and sshRNAs with nominal loop sizes of 1 or 4 nt were at least as active as those with longer loops. L sshRNAs remained highly potent even when the 3' end of the antisense strand was directly linked with the 5' end of the sense strand. In this case, the sense strand can be shorter than the antisense strand, and the loop can be formed entirely by the 3' end of the antisense strand. Monomer sshRNAs are not processed by recombinant Dicers in vitro. Although they can form dimers that are sometimes Dicer substrates, their RNAi activity is not dependent on the formation of such structures. Our findings have implications for the mechanism of action of sshRNAs, and the ability to design highly potent shRNAs with minimal length is encouraging for the prospects of the therapeutic use of direct-delivered shRNAs.
authors: SomaGenics, Inc., Santa Cruz, California 95060, USA. qge@somagenics.com
authors: Qing
authors: Q
authors: Ge
authors: Heini
authors: H
authors: Ilves
authors: Anne
authors: A
authors: Dallas
authors: Pavan
authors: P
authors: Kumar
authors: Joshua
authors: J
authors: Shorenstein
authors: Sergei A
authors: SA
authors: Kazakov
authors: Brian H
authors: BH
authors: Johnston
mesh_terms: D020137:Base Pair Mismatch / Q000502:physiology; D001483:Base Sequence / Q000502:physiology; D020134:Catalytic Domain; D002478:Cells, Cultured; D053487:DEAD-box RNA Helicases / Q000378:metabolism; D019281:Dimerization; D004526:Efficiency / Q000502:physiology; D006801:Humans; D007372:Interferons / Q000378:metabolism; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D034622:RNA Interference / Q000502:physiology; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism / Q000494:pharmacology*; D043244:Ribonuclease III / Q000378:metabolism; D013329:Structure-Activity Relationship; D013379:Substrate Specificity / Q000235:genetics
chemical_list: D034741:RNA, Small Interfering; D007372:Interferons; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases