Enzymatically produced pools of canonical and Dicer-substrate siRNA molecules display comparable gene silencing and antiviral activities against herpes simplex virus

PLoS One. 2012;7(11):e51019. doi: 10.1371/journal.pone.0051019. Epub 2012 Nov 30.

Abstract

RNA interference (RNAi)-based sequence-specific gene silencing is applied to identify gene function and also possesses great potential for inhibiting virus replication both in animals and plants. Small interfering RNA (siRNA) molecules are the inducers of gene silencing in the RNAi pathway but may also display immunostimulatory activities and promote apoptosis. Canonical siRNAs are 21 nucleotides (nt) in length and are loaded to the RNA Induced Silencing Complex when introduced into the cells, while longer siRNA molecules are first processed by endogenous Dicer and thus termed Dicer-substrate siRNA (DsiRNA). We have applied RNA polymerases from bacteriophages T7 and phi6 to make high-quality double-stranded RNA molecules that are specific for the UL29 gene of herpes simplex virus (HSV). The 653 nt long double-stranded RNA molecules were converted to siRNA and DsiRNA pools using Dicer enzymes originating from human or Giardia intestinalis, producing siRNAs of approximately 21 and 27 nt in length, respectively. Chemically synthesised 21 and 27 nt single-site siRNA targeting the UL29 were used as references. The impact of these siRNAs on cell viability, inflammatory responses, gene silencing, and anti-HSV activity were assayed in cells derived from human nervous system and skin. Both pools and the canonical single-site siRNAs displayed substantial antiviral activity resulting in four orders of magnitude reduction in virus titer. Notably, the pool of DsiRNAs caused lower immunostimulation than the pool of canonical siRNAs, whereas the immunostimulation effect was in relation to the length with the single-site siRNAs. Our results also propose differences in the processivity of the two Dicers.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antiviral Agents / pharmacology*
  • Cell Line
  • Gene Silencing / drug effects*
  • Giardia / enzymology
  • Humans
  • Immunity, Innate / drug effects
  • Immunity, Innate / immunology
  • Interferons / pharmacology
  • RNA, Small Interfering / pharmacology*
  • Ribonuclease III / metabolism*
  • Simplexvirus / drug effects*
  • Simplexvirus / physiology
  • Species Specificity
  • Substrate Specificity / drug effects
  • Viral Proteins / metabolism
  • Virus Replication / drug effects

Substances

  • Antiviral Agents
  • RNA, Small Interfering
  • Viral Proteins
  • Interferons
  • Ribonuclease III

Grants and funding

This study was supported by grants from the Academy of Finland (grant number 250113 and 256069 to MMP, 256197, 255342 and 256518 to DHB and 128915 to VH; www.aka.fi) and Sigrid Juselius Foundation (to MMP and DHB; www.sigridjuselius.fi). AR has been a fellow of the Centre for International Mobility (CIMO, http://www.cimo.fi). HP has been funded by Alfred Kordelin foundation (http://www.kordelin.fi), Instrumentarium foundation (http://www.instrufoundation.fi) and FinPharma Doctoral program – Drug Discovery section (http://fpdp.fi). MN is a fellow in Turku Doctoral Programme of Biomedical Sciences (http://www.tubs.utu.fi). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.