Off-target messenger RNAs with seed-region complementarity

Off-target messenger RNAs with seed-region complementarity represent a major class of unintended targets for RNA interference (RNAi) therapeutics, such as small interfering RNAs (siRNAs). This phenomenon occurs when the seed region of an siRNA guide strand—typically nucleotides 2 through 8—binds to complementary sequences in the 3' untranslated regions (UTRs) of non-target mRNAs (Jackson et al., 2003; Birmingham et al., 2006). This interaction mimics the natural regulatory mechanism of microRNAs (miRNAs), leading to the unintended downregulation of numerous genes across the transcriptome. Such off-target effects are a significant concern in drug development as they can lead to cellular toxicity, altered biological pathways, and adverse clinical outcomes. Modern siRNA design strategies, including chemical modifications like 2'-O-methyl substitutions at position 2 of the guide strand, are employed to destabilize these off-target interactions while maintaining on-target potency (Jackson et al., 2006; Janas et al., 2018).

Other names

Seed-mediated off-targetsmiRNA-like off-target effectssiRNA off-target mRNAsOff-target transcripts

Unintended binding of the siRNA guide strand seed region (nucleotides 2-8) to partially complementary sequences in the 3' UTR of non-target mRNAs, leading to RISC-mediated silencing (Jackson et al., 2003).