Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets

Hanna Iribe; Kengo Miyamoto; Tomoko Takahashi; Yoshiaki Kobayashi; Jastina Leo; Misako Aida; Kumiko Ui-Tei

doi:10.1021/acsomega.7b00291

Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets

ACS Omega. 2017 May 31;2(5):2055-2064. doi: 10.1021/acsomega.7b00291. Epub 2017 May 12.

Authors

Hanna Iribe¹, Kengo Miyamoto², Tomoko Takahashi³, Yoshiaki Kobayashi³, Jastina Leo^{3

4}, Misako Aida², Kumiko Ui-Tei^{1

3}

Affiliations

¹ Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8581, Japan.
² Center for Quantum Life Sciences and Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
³ Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
⁴ Faculty of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, United States.

Abstract

Chemical modifications of 2'-O-methyl (2'-OMe) and locked nucleic acid (LNA) of the nucleotides in the seed region (positions 2-8) of the small interfering RNA (siRNA) guide strand significantly reduced seed-matched (SM) off-target effects. The siRNA with 2'-OMe modifications inhibited the expression of a completely-matched (CM) target gene, whereas that with LNA modifications did not inhibit the expression of the CM target. By computational predictions of conformational changes of siRNA by these modifications, we revealed that both modifications in the siRNA seed region reduce SM off-target effects by steric hindrance to base-pairing with target transcripts but LNA modifications also disturb the association of the siRNA guide strand with the Argonaute (AGO) protein by altering RNA conformation. Thus, chemical modifications of the siRNA guide strand, which alter steric conformation to disturb base-pairing with target transcripts but do not disturb the association with the AGO protein, may successfully suppress off-target effects without substantial loss of RNA silencing activity.