title: Effective inhibition of HIV-1 production by short hairpin RNAs and small interfering RNAs targeting a highly conserved site in HIV-1 Gag RNA is optimized by evaluating alternative length formats.
abstract: We have previously identified a target site in HIV-1 RNA that was particularly accessible to a ribozyme and a short hairpin RNA (shRNA). To design small interfering RNAs (siRNAs) targeting this site, we evaluated the effects of siRNAs with different lengths on HIV-1 production. The potency and efficacy of these siRNAs were dependent on the length of their intended sense strand with trends for symmetrical and asymmetrical formats that were similar. Although a typical canonical format with a 21-nucleotide (nt) sense strand was effective at inhibiting HIV-1 production, Dicer substrate siRNAs (dsiRNAs) with the longest lengths (27 to 29 nucleotides) were the most effective. Induction of double-stranded RNA immune responses and effects on cell viability were not detected in cells transfected with different siRNAs, suggesting that the differences observed were not related to indirect effects on HIV-1 production. For the corresponding shRNA designs, a different trend in potency and efficacy against HIV-1 production was observed, with the most effective shRNAs having stem lengths from 20 to 27 bp. Our results highlight the importance of evaluating different designs to identify the best siRNA and shRNA formats for any particular target site and provide a set of highly effective molecules for further development as drug and gene therapies for HIV-1 infection.
authors.affiliation: Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montreal, Quebec, Canada Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Scarborough
authors.affiliation: Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montreal, Quebec, Canada Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.
authors.forename: Kelsey L
authors.initials: KL
authors.lastname: Adams
authors.affiliation: Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montreal, Quebec, Canada.
authors.forename: Aïcha
authors.initials: A
authors.lastname: Daher
authors.affiliation: Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montreal, Quebec, Canada Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada Department of Medicine, McGill University, Montreal, Quebec, Canada anne.gatignol@mcgill.ca.
authors.forename: Anne
authors.initials: A
authors.lastname: Gatignol
mesh_terms: D000998:Antiviral Agents / Q000009:adverse effects / Q000494:pharmacology*; D002470:Cell Survival / Q000187:drug effects; D057809:HEK293 Cells; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics; D006801:Humans; D061986:MCF-7 Cells; D034622:RNA Interference; D012330:RNA, Double-Stranded / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D014779:Virus Replication / Q000187:drug effects / Q000235:genetics
chemical_list: D000998:Antiviral Agents; D012330:RNA, Double-Stranded; D034741:RNA, Small Interfering; D012367:RNA, Viral