Base modification strategies to modulate immune stimulation by an siRNA

Rachel Anne P Valenzuela, Scott R. Suter, Alexi A. Ball-Jones, José M. Ibarra-Soza, Yuxuan Zheng, Peter A. Beal

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Immune stimulation triggered by siRNAs is one of the major challenges in the development of safe RNAi-based therapeutics. Within an immunostimulatory siRNA sequence, this hurdle is commonly addressed by using ribose modifications (e.g., 2′-OMe or 2′-F), which results in decreased cytokine production. However, as immune stimulation by siRNAs is a sequence-dependent phenomenon, recognition of the nucleobases by the trigger receptor(s) is also likely. Here, we use the recently published crystal structures of Toll-like receptor 8 (TLR8) bound to small-molecule agonists to generate computational models for ribonucleotide binding by this immune receptor. Our modeling suggested that modification of either the Watson-Crick or Hoogsteen face of adenosine would disrupt nucleotide/TLR8 interactions. We employed chemical synthesis to alter either the Watson-Crick or Hoogsteen face of adenosine and evaluated the effect of these modifications in an siRNA guide strand by measuring the immunostimulatory and RNA interference properties. For the siRNA guide strand tested, we found that modifying the Watson-Crick face is generally more effective at blocking TNFα production in human peripheral blood mononuclear cells (PBMCs) than modification at the Hoogsteen edge. We also observed that modifications near the 5′-end were more effective at blocking cytokine production than those placed at the 3′-end. This work advances our understanding of how chemical modifications can be used to optimize siRNA performance.

Original languageEnglish (US)
Pages (from-to)262-267
Number of pages6
JournalChemBioChem
Volume16
Issue number2
DOIs
StatePublished - Dec 8 2014
Externally publishedYes

Fingerprint

Small Interfering RNA
Toll-Like Receptor 8
Adenosine
Cytokines
Ribonucleotides
Ribose
Chemical modification
RNA Interference
Blood Cells
Blood
Nucleotides
Crystal structure
RNA
Molecules

Keywords

  • Immune stimulation
  • Nucleobase modification
  • SiRNA
  • TLR8
  • Toll-like receptors

ASJC Scopus subject areas

  • Biochemistry
  • Organic Chemistry
  • Molecular Medicine
  • Molecular Biology

Cite this

Valenzuela, R. A. P., Suter, S. R., Ball-Jones, A. A., Ibarra-Soza, J. M., Zheng, Y., & Beal, P. A. (2014). Base modification strategies to modulate immune stimulation by an siRNA. ChemBioChem, 16(2), 262-267. https://doi.org/10.1002/cbic.201402551

Base modification strategies to modulate immune stimulation by an siRNA. / Valenzuela, Rachel Anne P; Suter, Scott R.; Ball-Jones, Alexi A.; Ibarra-Soza, José M.; Zheng, Yuxuan; Beal, Peter A.

In: ChemBioChem, Vol. 16, No. 2, 08.12.2014, p. 262-267.

Research output: Contribution to journalArticle

Valenzuela, RAP, Suter, SR, Ball-Jones, AA, Ibarra-Soza, JM, Zheng, Y & Beal, PA 2014, 'Base modification strategies to modulate immune stimulation by an siRNA', ChemBioChem, vol. 16, no. 2, pp. 262-267. https://doi.org/10.1002/cbic.201402551
Valenzuela RAP, Suter SR, Ball-Jones AA, Ibarra-Soza JM, Zheng Y, Beal PA. Base modification strategies to modulate immune stimulation by an siRNA. ChemBioChem. 2014 Dec 8;16(2):262-267. https://doi.org/10.1002/cbic.201402551
Valenzuela, Rachel Anne P ; Suter, Scott R. ; Ball-Jones, Alexi A. ; Ibarra-Soza, José M. ; Zheng, Yuxuan ; Beal, Peter A. / Base modification strategies to modulate immune stimulation by an siRNA. In: ChemBioChem. 2014 ; Vol. 16, No. 2. pp. 262-267.
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