Off-target messenger RNA (Off-target mRNA) (Off-target mRNA)

Off-target messenger RNA (mRNA) with partial sequence complementarity refers to unintended transcripts that are inadvertently regulated by RNA-targeted therapeutics such as small interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs). This phenomenon occurs when the therapeutic oligonucleotide binds to an mRNA sequence that is not the intended target but possesses sufficient complementarity, particularly in the seed region (nucleotides 2-8 of the guide strand) [Jackson et al., 2006, Nature Methods]. Such binding can lead to the degradation of the off-target mRNA via the RNA-induced silencing complex (RISC) or RNase H, or it may cause translational repression [Birmingham et al., 2006, Nature Methods]. These off-target effects are a primary source of toxicity and non-specific activity in RNAi-based drug development, potentially leading to the downregulation of essential genes and subsequent cellular dysfunction [Wittrup and Lieberman, 2015, Nature Reviews Genetics]. To mitigate these risks, researchers employ chemical modifications, such as 2-O-methyl or locked nucleic acids (LNAs), and utilize sophisticated bioinformatic tools to ensure high specificity for the intended target [Setten et al., 2019, Nature Reviews Drug Discovery]. Understanding and monitoring these off-target interactions is crucial for the safety assessment and regulatory approval of oligonucleotide-based medicines [Bennett et al., 2017, Annual Review of Pharmacology and Toxicology].

Other names

Off-target transcriptsSeed-mediated off-targetsUnintended mRNA targetsPartial complementarity off-targets

Unintended hybridization of therapeutic oligonucleotides (siRNAs, ASOs) to transcripts with partial sequence complementarity, leading to RISC-mediated degradation, RNase H cleavage, or translational repression [Jackson et al., 2006, Nature Methods; Bennett et al., 2017, Annual Review of Pharmacology and Toxicology].