Off-target messenger RNAs with partial complementarity to the siRNA seed region (siRNA off-targets)

Off-target messenger RNAs with partial complementarity to the siRNA seed region represent a major class of unintended interactions in RNA interference (RNAi) therapeutics. This phenomenon occurs when the seed region of an siRNA—typically nucleotides 2 through 8 of the antisense strand—binds to the 3' untranslated region (UTR) of transcripts other than the intended target (Birmingham et al., 2006). This binding mimics the natural mechanism of microRNAs (miRNAs), leading to the downregulation of hundreds of unintended genes across the transcriptome (Jackson et al., 2003). Such off-target effects can result in cellular toxicity or altered physiological states, posing a significant challenge for drug safety and specificity in clinical development (Setten et al., 2019). To mitigate these risks, researchers employ chemical modifications, such as 2'-O-methyl substitutions at position 2 of the antisense strand, and advanced bioinformatic screening to minimize seed-mediated complementarity (Janas et al., 2018). Understanding and controlling these interactions is critical for the development of safe siRNA-based drugs like Patisiran and Inclisiran, as unintended silencing of essential genes can lead to adverse clinical outcomes.

Other names

Seed-mediated off-targetsmiRNA-like off-target effectssiRNA-mediated off-target silencingUnintended mRNA targets

Unintended binding of the siRNA antisense strand seed region (nucleotides 2-8) to the 3' untranslated regions (UTRs) of non-target mRNAs, leading to their degradation or translational inhibition via the RNA-induced silencing complex (RISC) (Birmingham et al., 2006; Jackson et al., 2003).