Structure-guided design of immunomodulatory RNAs specifically targeting the cytoplasmic viral RNA sensor RIG-I

FEBS Lett. 2019 Nov;593(21):3003-3014. doi: 10.1002/1873-3468.13564. Epub 2019 Aug 19.


The cytoplasmic immune sensor RIG-I detects viral RNA and initiates an antiviral immune response upon activation. It has become a potential target for vaccination and immunotherapies. To develop the smallest but potent immunomodulatory RNA (immRNAs) species, we performed structure-guided RNA design and used biochemical, structural, and cell-based methods to select and characterize the immRNAs. We demonstrated that inserting guanosine at position 9 to the 10mer RNA hairpin (3p10LG9) activates RIG-I more robustly than the parental RNA. 3p10LG9 interacts strongly with the RIG-I helicase-CTD RNA sensing module and disrupts the auto-inhibitory interaction between the HEL2i and CARDs domains. We further showed that 3p10LA9 has a stronger cellular activity than 3p10LG9. Collectively, purine insertion at position 9 of the immRNA species triggered more robust activation of RIG-1.

Keywords: RIG-I; RNA ligands; immunomodulatory RNAs.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution
  • Cytosine / metabolism
  • DEAD Box Protein 58 / chemistry*
  • DEAD Box Protein 58 / metabolism*
  • HEK293 Cells
  • Humans
  • Immunity, Innate
  • Protein Binding
  • Protein Domains
  • RNA, Small Interfering / chemistry
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / pharmacology*
  • RNA, Viral / immunology*
  • Signal Transduction
  • Structure-Activity Relationship


  • RNA, Small Interfering
  • RNA, Viral
  • Cytosine
  • DDX58 protein, human
  • DEAD Box Protein 58