Near-complementary off-target messenger RNA (Off-target mRNA)

Near-complementary off-target messenger RNAs (mRNAs) are transcripts that possess sequence similarity to the intended target of an oligonucleotide-based therapeutic, such as a small interfering RNA (siRNA) or an antisense oligonucleotide (ASO). These off-targets are unintentionally regulated or degraded because the drug's sequence can hybridize with them, even with less than perfect complementarity (Jackson et al., 2003, Nature Biotechnology). This phenomenon is a major hurdle in the development of RNA-targeted therapies, as it can lead to unintended gene silencing and subsequent cellular toxicity or adverse clinical effects (Fedorov et al., 2006, RNA). In the case of siRNAs, off-target effects often occur through "seed-region" complementarity in the 3' untranslated region (UTR) of mRNAs, mimicking the action of endogenous microRNAs (Birmingham et al., 2006, Nature Methods). For antisense oligonucleotides, off-targets may be cleaved by RNase H if the DNA-RNA heteroduplex formed is sufficiently stable to be recognized by the enzyme (Yoshida et al., 2019, Genes to Cells). Minimizing these interactions is critical for drug safety and involves sophisticated bioinformatic screening and chemical modifications, such as 2'-O-methyl or Locked Nucleic Acid (LNA) substitutions, to enhance specificity and reduce unintended binding (Kamola et al., 2015, Nucleic Acids Research).

Other names

Off-target transcriptsUnintended mRNA targetsSeed-matched off-targetsCross-hybridizing mRNAsOligonucleotide off-targets

Unintended binding of oligonucleotide drugs to mRNAs with partial sequence complementarity, leading to degradation via RNase H or RISC-mediated cleavage, or translational inhibition.